BRAINS License Yes Karen Pease, karen-pease@uiowa.edu NITRC Karen Pease BRAINSImageEval is a Qt-based GUI application designed for radiologists and trained raters to quickly evaluate MRI and other 3D medical images. BRAINSImageEval BRAINS License http://www.nitrc.org/projects/brainsimageeval/ karen-pease@uiowa.edu BSD License Yes Yannick Schwartz, yannick.schwartz@gmail.com NITRC Yannick Schwartz pyxnat is a simple python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data. pyxnat BSD License http://www.nitrc.org/projects/pyxnat/ yannick.schwartz@gmail.com Free For Non-Commercial Use Only Yes Jeffrey Hawley, jeffrey-hawley@uiowa.edu NITRC Jeffrey Hawley We have started the Non-rigid Image Registration Evaluation Project NIREP to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations using richly annotated image databases using computer simulated data and increasing the number and types of evaluation criteria. The goal of this project is to establish maintain and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms. NIREP Free For Non-Commercial Use Only http://www.nitrc.org/projects/nirep/ jeffrey-hawley@uiowa.edu HFH hippocampus segmentation Yes Kourosh Jafari-Khouzani, kjafari@rad.hfh.edu NITRC Kourosh Jafari-Khouzani This dataset contains T1-weighted MR images of 50 subjects 40 of whom are patients with temporal lobe epilepsy and 10 are nonepileptic subjects. Hippocampus labels are provided for 25 subjects for training. The users may submit their segmentation outcomes for the remaining 25 testing images to get a table of segmentation metrics. More information about the dataset may be found from the following reference K. Jafari-Khouzani K. Elisevich S. Patel and H. Soltanian-Zadeh “Dataset of magnetic resonance images of nonepileptic subjects and temporal lobe epilepsy patients for validation of hippocampal segmentation techniques” Neuroinformatics 2011. 2011-2-23 HippSegDataset MRI Dataset for Hippocampus Segmentation HFH hippocampus segmentation http://www.nitrc.org/projects/hippseg_2011/ kjafari@rad.hfh.edu BSD License Yes Daniel Marcus, dmarcus@wustl.edu NITRC Other OS,MacOS,Linux,SunOSSolaris,Microsoft Yes Java Daniel Marcus The Functional Image Viewer also known as FIV is a tool for visualizing functional and anatomic MRI data. 2006-12-31 Beta 1.0 FIV English, Web Environment, Win32 MS Windows, End Users, Beta, BSD License, X11 Applications, ANALYZE, Other Environment, Microsoft, Other OS, SunOSSolaris, MacOS, Linux, Image Display, DICOM, MINC, NIfTI-1, Java http://www.nitrc.org/projects/fiv/ dmarcus@wustl.edu Penn Hippocampus Atlas Yes John Pluta, jpluta26@gmail.com NITRC John Pluta The Penn Hippocampus Atlas is a resource consisting of segmented and normalized high-resolution postmortem MRI of the human hippocampus. The atlas is described in Yushkevich et al. A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T Neuroimage 442385-398 2009. Data can be accessed using the Download link on this page. Additional data raw images is available through the SCM link. It requires knowing how to use CVS. 2011-2-07 Alpha 1.0.0 Penn Hippocampus Atlas Data, Alpha, End Users, Penn Hippocampus Atlas, Web Environment, NIfTI-1 http://www.nitrc.org/projects/pennhippoatlas/ jpluta26@gmail.com BSD License Yes Charles Gasparovic, chuck@unm.edu NITRC MacOS,POSIXUNIX-like,Windows C Charles Gasparovic BrainCSI is a tool for analysis of Magnetic Resonance Spectroscopy MRS data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images. 2011-3-02 Planning alpha-0.1.2-Linux 2011-3-02 Planning alpha-0.1.2-Mac 2011-3-02 Planning alpha-0.1.2-WindowsInstaller 2011-3-01 Planning alpha-0.1.2-Windows BrainCSI Win32 MS Windows, X11 Applications, Console Text Based, Application, DICOM, NIfTI-1, MacOS, Windows, POSIXUNIX-like, C, English, Planning, End Users, BSD License http://www.nitrc.org/projects/braincsi/ chuck@unm.edu FSL License,GNU General Public License GPL Yes Jung Suh, bezalel72@gmail.com NITRC Linux,Cygwin Yes C,shbash Jung Suh Automatic Hippocampal Estimator using Atlas-based Delineation AHEAD is an open-source turnkey software for automatic hippocampus segmentation. Its primary use is for delineating hippocampus in T1-weighted MRI images. AHEAD is developed by Jung W. Suh Hongzhi Wang Sandhitsu Das Brian Avants Philip Cook John Pluta and Paul Yushkevich and colleagues at the Penn Image Computing and Science Laboratory PICSL at the University of Pennsylvania. 2011-8-15 Alpha Ver1.0 2011-7-20 Alpha ver0.93 2011-6-22 Alpha AHEAD ver 0.9 2011-1-25 Alpha First version AHEAD Console Text Based, English, Alpha, NIfTI-1, C, shbash, GNU General Public License GPL, FSL License, Volume Measurement, Anatomic, End Users, Developers, Linux, Cygwin http://www.nitrc.org/projects/ahead/ bezalel72@gmail.com Freeware Yes Qian Wang, qianwang@email.unc.edu NITRC Yes Qian Wang The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping cerebellum removal tissue segmentation and HAMMER registration. 2012-1-15 Patch for Symmetric HAMMER 2011-2-25 Link 2011-2-12 HAMMER Suite Windowns x64 2011-2-12 HAMMER Suite Windowns x86 2011-2-12 HAMMER Suite Linix 64bit HAMMER Suite Freeware http://www.nitrc.org/projects/hammer_suite/ qianwang@email.unc.edu Yes Leon French, leonfrench@gmail.com NITRC Leon French WhiteText is a corpus of manually annotated brain region mentions. It was created to facilitate text mining of neuroscience literature. The corpus contains 1377 abstracts with 17585 brain region annotations. Interannotator agreement was evaluated for a subset of the documents and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6000 unique brain region terms and 17000 words. The corpus can be found at httpwww.chibi.ubc.caWhiteText Previous evaluation of automated recognition of the mentions is described in amp;quot;Automated Recognition of Brain Region Mentions in Neuroscience Literatureamp;quot; by French Lane Xu and Pavlidis. httpwww.ncbi.nlm.nih.govpmcarticlesPMC2741206 WhiteText - annotated neuroscience text http://www.nitrc.org/projects/whitetext/ leonfrench@gmail.com Academic Free License amp;quot;AFLamp;quot; Yes Linglong Kong, llkong@bios.unc.edu NITRC Yes Linglong Kong A functional analysis of diffusion tensor tract statistics FADTTS pipeline was developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest such as age diagnostic status and gender and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development the neural bases of neuropsychiatric disorders and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability testing the joint effects and constructing their simultaneous confidence bands. 2012-1-26 fadtts and lprspdm V1.13 2012-1-25 fadtts and lprspdm V1.12 2012-1-25 fadtts and lprspdm V1.11 release 2012-1-24 fadtts and lprspdm V1.10 2011-2-21 FADTTS V1.02 2011-1-24 FADTTS V1.01 2011-1-24 FADTTS V1.0 Functional Analysis of Diffusion Tensor Academic Free License amp;quot;AFLamp;quot; http://www.nitrc.org/projects/fadtts/ llkong@bios.unc.edu Academic Free License amp;quot;AFLamp;quot; Yes Linglong Kong, llkong@bios.unc.edu NITRC Yes Linglong Kong Functional Regression Analysis of DTI Tract Statistics FRATS for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest such as age diagnostic status and gender in real applications. The resulting analysis pipeline can be used for understanding normal brain development the neural bases of neuropsychiatric disorders and the joint effects of environmental and genetic factors on white matter fiber bundles. 2011-1-24 FRATS V1.0 Functional Regression Analysis of DTI Academic Free License amp;quot;AFLamp;quot; http://www.nitrc.org/projects/frats/ llkong@bios.unc.edu Yes Karl Helmer, helmer@nmr.mgh.harvard.edu NITRC Yes Karl Helmer The Morphometry Testbed MBIRN of the Biomedical Informatics Research Network BIRN focuses on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions such as Alzheimer’s disease. With the completion of the initial BIRN testbed phase each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains. The new BIRN incarnation can be found at httpwww.birncommunity.org 2008-3-20 ProductionStable V1.0 Morphometry BIRN Segmentation, Visualization, Data, Knowledge Environment, Quantification, Workflow, ProductionStable, MR, End Users, Developers, English, DICOM, NIfTI-1 http://www.nitrc.org/projects/mbirn/ helmer@nmr.mgh.harvard.edu MITX Consortium License Yes Elizabeth Jurrus, liz@sci.utah.edu NITRC MacOS,Linux,Windows Yes C Elizabeth Jurrus The ShapeWorks software is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning and is applicable to a wide range of shape analysis problems including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model compactness with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data computing point-based shape models and visualizing the results. 2011-9-07 Beta ShapeWorksv1.0_Linux64 ShapeWorks MITX Consortium License, Workflow, Shape Analysis, Surface Rendering, Other Format, Console Text Based, Win32 MS Windows, X11 Applications, English, Beta, C, Developers, End Users, MacOS, Windows, Linux http://www.nitrc.org/projects/shapeworks/ liz@sci.utah.edu GNU General Public License GPL Yes Jose Luis Manners, jose.manners@tcg.com NITRC Jose Luis Manners This project contains custom extensions to the GForge collaborative environment used to create NITRC. These features include MediaWiki integration ratings and reviews Nutch Web crawling integration improved project searching BBCode extensions and front and project summary page re-design. See our Release Notes page for specifics httpwww.nitrc.orgpluginsmwikiindex.phpnitrcNITRC_Release_Notes 2011-8-04 v2.1.1 NITRC GForge Extensions Domain Independent, GNU General Public License GPL http://www.nitrc.org/projects/nitrcext/ jose.manners@tcg.com GNU General Public License GPL Yes Jonathan Clayden, jon.clayden@gmail.com NITRC MacOS,Linux,Other UNIX-like Yes C,shbash,R Jonathan Clayden The TractoR Tractography with R project includes R packages for reading writing and visualising magnetic resonance images stored in Analyze NIfTI and DICOM file formats DICOM support is read only. It also contains functions specifically designed for working with diffusion MRI and tractography including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R. Please note that package files and source code can be downloaded from TractoRs Google Code home page via links on the left. 2010-6-16 ProductionStable Latest release TractoR Tractography with R Console Text Based, English, ProductionStable, DICOM, NIfTI-1, ANALYZE, R, shbash, C, GNU General Public License GPL, Tractography, Atlas Application, Quantification, Segmentation, Statistical Operation, MacOS, Linux, Other UNIX-like, Visualization, Modeling, Developers, End Users http://www.nitrc.org/projects/tractor/ jon.clayden@gmail.com GNU Lesser General Public License LGPL Yes Xue Yang, xue.yang@Vanderbilt.Edu NITRC Yes Xue Yang Biological parametric mapping has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities both for regressors and regressands along with scalar valued observations. This approach offers great promise for direct voxelwise assessment of structural and functional relationships with multiple imaging modalities. However as presented the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences e.g. artifactual low p-values due to slight mis-registration or variation in anatomy between subjects. To enable widespread application of this approach we introduce robust regression and non-parametric regression in the neuroimaging context of application of the general linear model. 2011-6-08 rbpm version 2.1 2011-4-07 bnpm version 2.0 2011-4-07 rbpm version 2.0 2011-1-04 bnpm version 1.0 2011-1-03 rbpm version 1.0 Robust Biological Parametric Mapping GNU Lesser General Public License LGPL http://www.nitrc.org/projects/rbpm/ xue.yang@Vanderbilt.Edu GNU General Public License GPL Yes Keiji Harada, kharada@atr.jp NITRC MacOS,Linux,Windows Yes MATLAB Keiji Harada This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file. 2011-8-05 Mature 1.2 2011-8-05 Mature 1.1.3 2011-6-07 Mature 1.3.1 NeuroshareLibrary Console Text Based, Japanese, English, Mature, MATLAB, Developers, End Users, Other Audience, MacOS, Windows, Linux, Format Conversion, Other Format, GNU General Public License GPL http://www.nitrc.org/projects/nslib_v1_3_1/ kharada@atr.jp BSD License Yes Mark Scully, mark-scully@uiowa.edu NITRC MacOS,POSIXUNIX-like,Windows C Mark Scully NOTE All new development is being managed in a github repository. Please visit httpsgithub.comBRAINSiaBRAINSStandAlone GTRACT is a Diffusion Tensor fiber tracking suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. 2008-3-28 Beta GTRACT Version 3.0Beta GTRACT NIfTI-1, Other Format, MacOS, Windows, POSIXUNIX-like, C, English, Beta, End Users, Developers, BSD License, Console Text Based, Other Environment, Morphology, Tensor Metric, Tractography, DICOM http://www.nitrc.org/projects/vmagnotta/ mark-scully@uiowa.edu Yes Mark Scully, mark-scully@uiowa.edu NITRC Mark Scully The BRAINS suite of tools BRAINSFit GTRACT BRAINS BRAINSTracer... and others use a common set of anonymized data for nightly regression testing. This data is about 1.2GB of anonymized imaging data of many different file formats used to ensure t BRAINSTestData http://www.nitrc.org/projects/brainstestdata/ mark-scully@uiowa.edu GNU General Public License GPL Yes R Bakker, erpuntbakker@gmail.com NITRC OS Independent PHP,JavaScript R Bakker The INCF Scalable Brain Atlas scalablebrainatlas.incf.org is a web-based interactive brain atlas viewer containing a growing number of atlas templates for various species including mouse macaque and human. Standard features include fast brain region lookup point and click to select a region and view its full 3D extent mark a stereotaxic coordinate and view all regions in a hierarchy. Built-in extensions are the CoCoMac plugin which provides a spatial display of Macaque connectivity and a service to transform stereotaxic coordinates to and from the INCF Waxholm space for the mouse. Three dimensional renderings of brain regions are available through a Matlab interface local installation of Matlab required. The SBA is designed to be customizable. External users can create plugins hosted on their own servers to interactively attach images or data to spatial atlas locations. Scalable Brain Atlas English, ProductionStable, Beta, JavaScript, PHP, GNU General Public License GPL, Tractography, Three Dimensional Display, Atlas Data, Atlas Application, Web Environment, End Users, Developers, OS Independent http://www.nitrc.org/projects/sba/ erpuntbakker@gmail.com GNU Lesser General Public License LGPL Yes Karl Krissian, karl.krissian@gmail.com NITRC MacOS,Linux,Windows Yes C,Python Karl Krissian AMILab is an opensource software for image analysis processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level AMILab includes a 2D3D image viewer a 3D polygon viewer based on OpenGL a 2D Curve viewer to visualize 2D curves histograms and coloropacity transfer functions and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK. 2011-12-07 Beta 3.2 AMILab Active Contour, Intensity Contour, Format Conversion, Fourier Transform, Quality Metrics, Spline Interpolation, Animation, Two Dimensional Display, Ray Tracing, Surface Rendering, Medial Axis, Motion Analysis, Volume Rendering, Filtering, Artifact Removal, Beta, Domain Independent, Win32 MS Windows, KDE, Gnome, Developers, End Users, GNU Lesser General Public License LGPL, English, MacOS, Windows, Linux, C, Python, ANALYZE, DICOM, MINC, Nrrd, bshortbfloat, Other Format http://www.nitrc.org/projects/amilab/ karl.krissian@gmail.com Yes Frédéric Girs, frederic.girs@tudor.lu NITRC OS Independent Frédéric Girs This project assists the community in the support of information about upcoming Conferences Workshops and Meetings. Such support may be documents news files etc. To see a listing of upcoming Events please use the NITRC Community Events Page at httpwww.nitrc.orgincfevent_list.php and tab at right. To announce an Event please use the amp;quot;Submit an Eventamp;quot; at the NITRC Community Events Page httpwww.incf.orgEventseventscreateObjecttype_name=Event and tab at right. Note INCF account is currently required. All users are encouraged to check this site for upcoming meetings and promote future meetings here. Conferences Workshops and Meetings Knowledge Environment, Beta, Domain Independent, Web Environment, Developers, End Users, English, OS Independent http://www.nitrc.org/projects/meetings/ frederic.girs@tudor.lu GNU General Public License GPL Yes Clementine Ouziel, clementine.ouziel@gmail.com NITRC Clementine Ouziel This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can movezoom on all the images at the same time. Very useful for quality control image comparison. 2012-1-25 Mriwatcher 1.1 MacOS 10.7 MriWatcher GNU General Public License GPL http://www.nitrc.org/projects/mriwatcher/ clementine.ouziel@gmail.com GNU General Public License GPL Yes Andrew Noske, andrew_noske@yahoo.com NITRC Yes Andrew Noske IMOD is a free cross - platform set of image processing modeling and display programs used for tomographic reconstruction reconstruction and segmentation of 3D volumes. IMOD has tools for assembling and aligning data within multiple types and sizes of image stacks viewing 3D data from any orientation and modeling and displaying the image files. IMOD - 3D Reconstruction and Analysis GNU General Public License GPL http://www.nitrc.org/projects/imod/ andrew_noske@yahoo.com Non-Commercial Software License Agreement Yes Jon Freeman, jon.freeman@tufts.edu NITRC Jon Freeman MouseTracker is a free user-friendly software package that allows researchers to record and analyze real-time hand movements en route to responses on the screen via the coordinates of an MR-safe mouse trackball or sensor. By looking at how the hand settles into a response alternative--and how it may be partially pulled toward other alternatives--researchers glean information about real-time mental processing. Its like opening up a single reaction time into a continuous stream of rich cognitive output. Experiments can incorporate images letter strings and sounds. Once recorded participants mouse trajectories can be visualized averaged and explored and measures of curvature complexity velocity acceleration and angle can be computed. Precise characterizations of mouse trajectories temporal and spatial dynamics are available and these can shed light on a variety of important empirical questions across psychology neuroscience and beyond. 2010-12-07 2.22 MouseTracker Non-Commercial Software License Agreement http://www.nitrc.org/projects/mousetracker/ jon.freeman@tufts.edu Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes James Anderson, james.r.anderson@utah.edu NITRC Yes James Anderson Viking is a multi-user modular viewing and annotation system which functions with any type of stacked 2D imagery. Originally designed for transmission electron microscopy connectome data Viking has been used for confocal bright field and OCT images. Available from httpconnectomes.utah.edu A paper describing Viking is here httponlinelibrary.wiley.comdoi10.1111j.1365-2818.2010.03402.xabstract Viking requires images be available over HTTP and follow a standard URL naming convention with basic meta-data in an accompanying XML file. Consult the website or author about making imagesvolumes compatible with Viking. Viking is capable of texture mapping images in real-time on to meshes using the GPU if needed. Viking runs on Windows. An optional annotation module allows concurrent markup of data sets via a WSDL web service and requires a separate server installation. Server installation is non-trivial and until it improves we are open to hosting databases on the our annotation server. Viking Viewer for Connectomics Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported http://www.nitrc.org/projects/viking_viewer/ james.r.anderson@utah.edu Freeware Yes Michael Martinez, martinezmj@uthscsa.edu NITRC OS Independent,Windows Vista,MacOS,Linux,SunOSSolaris,Windows XP Yes Java Michael Martinez Mango is a viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango each geared for a different platform Mango – Desktop – Mac OS X Windows and Linux webMango – Browser – Safari Firefox Chrome and Internet Explorer iMango – Mobile – Apple iPad Key Features - Built-in support for DICOM NIFTI Analyze and NEMA-DES formats - Customizable Create plugins custom filters color tables file formats and atlases - ROI Editing Threshold and component-based tools for painting and tracing ROIs - Surface Rendering Interactive surface models supporting cut planes and overlays - Image Registration Semi-automatic image coregistration and manual transform editing - Image Stacking Threshold and transparency-based image overlay stacking - Analysis Histogram cross-section time-series analysis image and ROI statistics - Processing Kernel and rank filtering arithmeticlogic image and ROI calculators 2011-3-15 ProductionStable iMango 2009-12-31 ProductionStable Current Release Mango ProductionStable, ANALYZE, DICOM, End Users, Developers, MacOS, Windows XP, Windows Vista, SunOSSolaris, Linux, OS Independent, Freeware, Temporal Transformation, Websites, Atlas Application, Volumetric Analysis, Surface Analysis, Rendering, Platform or Development Environment, Web Environment, Console Text Based, Win32 MS Windows, Other Environment, English, Other Format, NIfTI-1, Java, Region of Interest, Registration, Statistical Operation http://www.nitrc.org/projects/mango/ martinezmj@uthscsa.edu NIDAG Yes Raymond Mar, mar@yorku.ca NITRC Yes Raymond Mar The NeuroImaging Data Access Group NIDAG is an informal working group dedicated to improving access to neuroimaging results in a free and open-access manner. Our current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete this will allow anyone to find all of the articles that report a coordinate or set of coordinates easily and without cost. Eventually we hope to expand this database to include not only coordinates but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited and also be a very useful tool for those interested in meta-analysis and hopefully clarify structure-function relationships. Please visit our website nidag.org and sign up to join our mailing list. We are interested in hearing from people who might be willing to contribute to our projects particularly those with programming experience. Neuroimaging Data Access Group Web Environment, English, Developers, End Users, Community, NIDAG http://www.nitrc.org/projects/nidag/ mar@yorku.ca Yes Haig Evans-Kavaldjian, haig@tcg.com NITRC OS Independent Yes Haig Evans-Kavaldjian This resource provides NITRC-wide facilities Forums Wiki Tracker and News. NITRC Community Web Environment, OS Independent, English, ProductionStable, Developers, End Users, Community, Database, Websites, Software http://www.nitrc.org/projects/nitrc/ haig@tcg.com DTI-TK license Yes Nagesh Adluru, nagesh.avr@gmail.com NITRC Nagesh Adluru Diffusion Tensor Imaging DTI studies of non-human primates NHP are becoming increasingly common. Recently many DTI analysis methodologies have been developed for human brain studies; however few are directly applicable to NHP. A prerequisite for most statistical DTI analyses to localize WM differences across populations is to spatially normalize the individual scans to a representative template. Here we report the development of a population-specific DTI template for young adolescent Rhesus Macaque Macaca mulatta monkeys using 271 high-quality scans. Using such a large number of animals in generating a template allows it to account for variability in the species. Our DTI template is based on the largest number of animals ever used in generating a computational brain template. It is anticipated that our DTI template will help facilitate voxel-based and tract specific WM analyses in non-human primate species which in turn may increase our understanding of brain function development and evolution. 2011-3-18 Template DTI-TEMPLATE-RHESUS-MACAQUES DTI-TK license http://www.nitrc.org/projects/rmdtitemplate/ nagesh.avr@gmail.com Freeware Yes Lars Forsberg, larsef@me.com NITRC Lars Forsberg NeuroPub is a NIfTI visualisation tool for the iPad. You can use it to store all your statistical images from your fMRIVBMTBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. You can download the app for free from the App Store 2010-12-02 NeuroPub Visualizer NeuroPub Visualizer Freeware http://www.nitrc.org/projects/neuropub/ larsef@me.com BRAINS License Yes Wen Li, wen-li@uiowa.edu NITRC MacOS,Linux,Windows Yes C,TclTk,Python,shbash Wen Li The BRAINS Brain Research Analysis of Images Networks and Systems image analysis software has been developed to study the brain thus providing a better understand of psychiatric and neurological disorders. 2011-5-17 Beta BRAINS3 Beta 3 2011-4-28 Beta BRAINS2-2011-04-27 2011-4-20 Beta BRAINS_20110420 2011-4-18 Beta Brains2-APR2011 2011-3-27 Beta BRAINS3 Beta 2010-12-20 Beta BRAINS3 Alpha 2010 2010-1-20 Beta BRAINS-JAN2010 2009-10-16 Beta BRAINS2-OCT2009 Release - RHEL5 2009-10-15 Beta BRAINS2-Oct2009 Release 2008-10-02 Beta BRAINS2-OCT2008 Release 2008-7-22 Beta 20080722 2008-2-25 Beta 20080225 BRAINS Workflow, Neural Network, Diffusion MR Fiber Tracking, Console Text Based, Other Environment, NIfTI-1, DICOM, Nrrd, ANALYZE, MGHMGZ, Other Format, C, TclTk, Resampling, Tensor Metric, KMeans, Image Display, Model Generation, Intersubject, Developers, End Users, Other Audience, BRAINS License, Windows, shbash, Python, MacOS, Linux, Intermodal, English, ProductionStable, Beta, Algorithm or Reusable Library, Mesh Generation, X11 Applications http://www.nitrc.org/projects/brains/ wen-li@uiowa.edu Yes R Bakker, erpuntbakker@gmail.com NITRC OS Independent Yes PHP R Bakker CoCoMac.org gives online access html or xml to structural connectivity wiring data on the Macaque brain. The database has become by far the largest of its kind with data extracted from more than four hundred published tracing studies. CoCoMac Brain Connectivity Database Tractography, Ontology, English, ProductionStable, End Users, Database Application, Atlas Application, Web Environment, PHP, OS Independent http://www.nitrc.org/projects/cocomac/ erpuntbakker@gmail.com Yes Jessica Turner, jturner@mrn.org NITRC Yes Jessica Turner This project will discuss debate develop and deploy ontological practices for the fMRI community. 2007-2-28 Planning 1.1 2007-1-17 Planning V0.3 Resource Ontology Discussion Group Ontology, Community, Planning, Domain Independent, Developers, English http://www.nitrc.org/projects/ontology/ jturner@mrn.org BSD License Yes Xavi Planes, xavier.planes@upf.edu NITRC POSIXUNIX-like,Windows C Xavi Planes GIMIAS is a workflow-oriented environment focused on biomedical image computing and simulation. The open source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation angiography imaging and simulation and neurology. 2011-12-05 Beta Gimias-1.4 2011-2-02 Beta Gimias-1.3.0 2010-10-20 Beta Gimias-1.2.0 GIMIAS Win32 MS Windows, X11 Applications, English, Beta, ANALYZE, DICOM, NIfTI-1, Other Format, C, Developers, End Users, Windows, POSIXUNIX-like, Application, Platform or Development Environment, BSD License http://www.nitrc.org/projects/gimias_fw/ xavier.planes@upf.edu Yes Feng Shi, fengshi@med.unc.edu NITRC MacOS,Linux,Microsoft Yes Feng Shi Keyword Infant; Pediatric; Template; Atlas; Longitudinal There are 3 atlases dedicated for neonates 1-year-olds and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model tissue probability maps and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods on a set of longitudinal images acquired from 95 normal infants 56 males and 39 females at neonate 1-year-old and 2-year-old. Please refer to the following article for the atlases Feng Shi Pew-Thian Yap Guorong Wu Hongjun Jia John H. Gilmore Weili Lin Dinggang Shenamp;quot;Infant Brain Atlases from Neonates to 1- and 2-year-oldsamp;quot; PLoS ONE 64 e18746 2011. For more information and download link please visit httpwww.med.unc.edubricideagroupfree-softwaresunc-infant-0-1-2-atlases 2011-11-12 UNCInfant012Atlases V2.0 2011-9-02 UNC Infant 0-1-2 Atlases 2009-3-28 Pediatric Atlas V2.0 2009-3-28 PediatricAtlas UNC 0-1-2 Infant Atlases Microsoft, MacOS, Linux, ANALYZE, English, Atlas Application, Developers, End Users http://www.nitrc.org/projects/pediatricatlas/ fengshi@med.unc.edu BSD License Yes Ravikiran Janardhana, ravikirn@cs.unc.edu NITRC Ravikiran Janardhana Used to analyze the fibers produced by ukf tractography Fiber Tracking Tool BSD License http://www.nitrc.org/projects/fiber-sig/ ravikirn@cs.unc.edu BSD License Yes Fang-Cheng Yeh, frank.yeh@gmail.com NITRC OS Independent C Fang-Cheng Yeh Template Image Processing Library TIPL is a lightweight C template library designed mainly for medical imaging processing. The design paradigm follows generic programming and the purpose is to provide an amp;quot;easy-to-useamp;quot; and also amp;quot;ready-to-useamp;quot; library. The code is template-based and only header files are needed to be included to the source code. This library provides the following functions 1.DICOM r Analyzer Nifti rw and MATLAB MAT V4 rw 2.numerical add multiply gradient. 3.interpolation linear gaussian radial basis 3.filters mean gaussian laplacian sobel anisotropic diffusion 4.morphological processing erosion expansion opening closing 5.template-based Fourier transform 6.linear coregistration rigid body affine transform least square fit mutual information 7.nonlinear coregistration The Large Deformation Diffeomorphic Metric Mapping LDDMM 2011-3-22 ProductionStable v1.3 2011-2-02 ProductionStable v1.21 2011-1-07 ProductionStable v1.0 2011-1-07 ProductionStable v1.2 2010-9-04 ProductionStable v1.12 2010-7-27 ProductionStable v1.11 2010-7-21 ProductionStable v1.1 2010-7-15 ProductionStable v1.0 Template Image Processing Library Win32 MS Windows, X11 Applications, English, ProductionStable, ANALYZE, DICOM, NIfTI-1, Other Format, C, Developers, OS Independent, Algorithm or Reusable Library, Segmentation, Spatial Transformation, Visualization, Format Conversion, BSD License http://www.nitrc.org/projects/tipl/ frank.yeh@gmail.com Yes Will Horton, hortonw@mir.wustl.edu NITRC POSIXUNIX-like Yes Java,Python Will Horton User contributions for XNAT. 2011-12-21 xnat_sync 0.21-alpha 2011-12-20 xnat_sync 0.2-alpha 2011-12-02 xnat_sync 0.1-alpha 2011-10-13 Extra jar for HTTPS XnatPipelineLauncher 2011-10-13 XNAT Tools 2011-10-12 FreeSurfer Uploader 2011-10-11 Metadata Uploader 2011-9-28 Freesurfer 2011-9-27 Xnnppx 2011-9-27 XNAT Workflow 2011-9-27 FreeSurfer 2011-9-08 pyxnat 2011-9-08 XNAT Rest Client XNAT Extras XNAT Pipeline, System Administrators, POSIXUNIX-like, Database Application, Java, Python, Developers, Web Environment, Console Text Based, Other Environment, English http://www.nitrc.org/projects/xnat_extras/ hortonw@mir.wustl.edu LONI Software License Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The Laboratory of Neuro Imaging strives to improve our understanding of the brain in health and disease. LONI develops advanced computational algorithms and scientific approaches for the comprehensive and quantitative mapping of brain structure and function. LONI aims to encourage communication between users and LONI software engineers in order to improve the effectiveness of computational brain mapping software and to promote its use by researchers worldwide. LONI software website httpwww.loni.ucla.eduSoftware includes downloadable and web-accessible tools training and support. Be sure to visit LONI Forums and discuss our tools with other end-users and LONI investigators. httpwww.loni.ucla.edu Laboratory of Neuro Imaging LONI LONI Software License http://www.nitrc.org/projects/loni/ iwaterpolo@gmail.com Creative Commons License Yes Niels van Strien, n.vanstrien@temporal-lobe.com NITRC Niels van Strien Existing knowledge of hippocampal - parahippocampal connections was integrated into an interactive diagram in which any connection can be turned on or off at the level of cortical layers. Project Goals To provide an overview of all known anatomical projections of the rat hippocampal - parahippocampal network. To provide a graphical interface with which users can turn on or off any connections at regional level down to the level of cortical layers. To make it easy to find references for a particular projection. Download the diagram for free at www.temporal-lobe.com. Temporal-lobe.com Creative Commons License http://www.nitrc.org/projects/connectivity/ n.vanstrien@temporal-lobe.com GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The Synchronized Histological Image Viewing Architecture httpwww.loni.ucla.eduSoftwareSHIVA is a Java-based visualization and analysis application. SHIVA can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets. SHIVA is distributed by the Laboratory of Neuro Imaging httpwww.loni.ucla.eduSoftwareSHIVA at UCLA. Synchronized Histological Image View Arc GNU General Public License GPL http://www.nitrc.org/projects/shiva/ iwaterpolo@gmail.com GNU General Public License GPL Yes Piotr Majka, pmajka@nencki.gov.pl NITRC Linux Python Piotr Majka 3d Brain Atlas Reconstructor 3dBAR httpwww.3dbar.org is a software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service httpservice.3dbar.org offering a variety of functions for the hosted datasets - downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings - previewing models as bitmap thumbnails and for webGL enabled browsers interactive manipulation zooming rotating etc. of the structures - downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. Check httpwww.3dbar.org for detailed description of the software and the latest releases. 2011-10-02 Beta 3dbar_v_0.1 3d Brain Atlas Reconstructor End Users, GNU General Public License GPL, English, Linux, Python, VRML, NIfTI-1, Other Format, Algorithm or Reusable Library, Atlas Application, Workflow, Web Service, Three Dimensional Display, Beta, Web Environment, Console Text Based, Developers, Gnome http://www.nitrc.org/projects/bar3d/ pmajka@nencki.gov.pl GNU Lesser General Public License LGPL Yes , NITRC lt;pgt;A 3d atlas of the mouse brain that allows multi-scale data to be visualized in a seamless way similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework.lt;pgt; Whole Brain Catalog Atlas Application, Beta, GNU Lesser General Public License LGPL http://www.nitrc.org/projects/incf_whole-brai/ BSD License Yes Christian Haselgrove, christian.haselgrove@umassmed.edu NITRC MacOS,POSIXUNIX-like Python Christian Haselgrove DFT is a loose collection of programs and configuration options that intend to make working with data more transparent to formats. Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand. 2011-7-19 Alpha Other 2011-7-19 Alpha DICOM 2011-7-18 Alpha v0.2.0 2011-6-30 Alpha Web and user fs v0.1 2011-6-30 Alpha file1 magic v0.1 Data Format Tools Console Text Based, Web Environment, English, Alpha, Python, Developers, End Users, System Administrators, MacOS, POSIXUNIX-like, Format Conversion, Visualization, Other Software Resource, DICOM, NIfTI-1, BSD License http://www.nitrc.org/projects/dft/ christian.haselgrove@umassmed.edu Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov PPMI includes a large and comprehensive set of correlated clinical data and biospecimens that is made available to the entire scientific community to help accelerate biomarker verification research. PPMI data and specimens have been collected in a standardized manner under strict protocols developed by the steering committee. The PPMI study dataset includes clinical biological and imaging data collected at PPMI clinical sites. The data have been aggregated into the PPMI study database which is managed by the PPMI Bioinformatics Core the Laboratory of NeuroImaging LONI at the University of California Los Angeles. httpwww.ppmi-info.orgaccess-data-specimens PPMI ANALYZE, DICOM, MINC, LONI Pipeline, Web Environment, English, Mature, End Users, Data, Database, Atlas Data http://www.nitrc.org/projects/ppmi/ iwaterpolo@gmail.com GNU General Public License GPL Yes Qianqian Fang, fangqq@gmail.com NITRC MacOS,POSIXUNIX-like,Windows Yes Other Programming Language,C Qianqian Fang Monte Carlo eXtreme or MCX is a Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units GPU based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card 14MP114Cores the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470. Monte Carlo eXtreme MCX English, Beta, Other Format, C, Other Programming Language, End Users, Windows, POSIXUNIX-like, MacOS, Monte Carlo, GNU General Public License GPL, Console Text Based, X11 Applications, Win32 MS Windows http://www.nitrc.org/projects/mcextreme/ fangqq@gmail.com Web Application - Free to use Yes Jesse Brown, jbrown81@gmail.com NITRC OS Independent Python Jesse Brown The UCLA Multimodal Connectivity Database - httpumcd.humanconnectomeproject.org - is a web-based analysis site and data repository for connectivity matrices that have been derived from neuroimaging data. The site is powered by the MGHUCLA Human Connectome Project. Anyone can browse and analyze connectivity matrices that researchers have shared on this site. The data comes from different imaging modalities fMRI DTI structural MRI EEG subject groups and studies. The website allows users to choose any network shared by another user compute graph theoretical metrics on the fly and visualize the results. UCLA Multimodal Connectivity Database Web Environment, English, ProductionStable, Python, OS Independent, Data, Web Resource, Image Display, Rendering, Web Application - Free to use http://www.nitrc.org/projects/umcd/ jbrown81@gmail.com BSD License Yes Jay Dubb, jdubb@nmr.mgh.harvard.edu NITRC MacOS,POSIXUNIX-like,Windows Yes C Jay Dubb tMCimg uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues e.g. white matter and weakly scattering tissues e.g. cerebral spinal fluid are supported. Using the anatomical information provided by MRI X-ray CT or ultrasound accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours depending on the optical properties and the computing resources available. Monte Carlo Simulation Software tMCimg Monte Carlo, Beta, Optical Imaging, MR, CT, Console Text Based, End Users, BSD License, English, MacOS, Windows, POSIXUNIX-like, C, Other Format http://www.nitrc.org/projects/tmcimg/ jdubb@nmr.mgh.harvard.edu Creative Commons License Yes Russell Poldrack, poldrack@mac.com NITRC Russell Poldrack The Cognitive Atlas httpwww.cognitiveatlas.org is a collaborative knowledge building project that aims to develop a knowledge base or ontology that characterizes the state of current thought in cognitive neuroscience. The goal is to develop a knowledge base that will support annotation of data in databases as well as supporting improved discourse in the community. It is open to all interested researchers. The Cognitive Atlas Creative Commons License http://www.nitrc.org/projects/cogatlas/ poldrack@mac.com Yes Anthony Kolasny, akolasny@jhu.edu NITRC Linux,Windows Yes C Anthony Kolasny LDDMM assigns a metric distances on the space of anatomical images LDDMM C, English, ProductionStable, Console Text Based, Win32 MS Windows, Shape Analysis, ANALYZE, Linux, Windows, End Users http://www.nitrc.org/projects/lddmm-volume/ akolasny@jhu.edu GNU Lesser General Public License LGPL Yes Joshua Stein, joshua.a.stein@vanderbilt.edu NITRC Joshua Stein GesTr is a cross platform open source gesture tracking program. You launch it from the web and use it to streamline the way you communicate with the computer. It allows for a more natural method of issuing commands than with keyboard shortcuts or GUI buttons. GesTr supports simple XML files to customize recognized gestures and their corresponding actions. GesTr also has experimental support for the Wii Remote used with an infrared pen as an alternative input device. GesTr GNU Lesser General Public License LGPL http://www.nitrc.org/projects/gestr/ joshua.a.stein@vanderbilt.edu GNU General Public License GPL Yes Xi-Nian Zuo, zuoxinian@gmail.com NITRC POSIXUNIX-like Yes shbash Xi-Nian Zuo BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis amplitude analysis and independent component analysis. Note this tool is just a plug-in for FSL AFNI and FreeSurfer. Thus you need have them before you use BASH4RfMRI. Of note most functions have been integrated in 1000 Functional Connectomes Project www.nitrc.orgprojectsfcon_1000. I do not update this package thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH4RfMRI shbash, NIfTI-1, GNU General Public License GPL, Console Text Based, Other Environment, X11 Applications, English, Alpha, Multivariate Analysis, Platform or Development Environment, Algorithm or Reusable Library, Information Theory, Spectral Analysis, Correlation, End Users, POSIXUNIX-like http://www.nitrc.org/projects/bash-rs-fcmri/ zuoxinian@gmail.com GNU General Public License GPL Yes Hongzhi Wang, wanghongzhi78@gmail.com NITRC POSIXUNIX-like Yes C Hongzhi Wang More and more automatic segmentation tools are publicly available to todays researchers. However when applied by their end-users these segmentation tools usually can not achieve the performance that the tool developer reported. Discrepancies between the tool developer and its users in manual segmentation protocols and imaging modalities are the main reasons for such inconsistency. In this project we will provide an open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the users manual segmentation using the image data and manual segmentation provided by the user. The motivation of this project is to bridge the gap between the segmentation tool developer and the tool users such that the existing segmentation tools can more effectively serve the community. 2012-1-25 Beta segAdapter_1.5 demo 2012-1-24 Beta segAdapter_1.4 demo 2012-1-23 Beta segAdapter_1.3 demo 2010-11-22 Beta segAdapter_1.2 demo 2010-9-28 Beta segAdapter_1.2 2010-7-21 Beta segadapter 1.1 2010-7-19 Beta segadapter 1.0 2010-7-13 Beta demo Automatic Segmentation Tool Adapter End Users, Console Text Based, English, Beta, NIfTI-1, ANALYZE, C, POSIXUNIX-like, Segmentation, Algorithm or Reusable Library, GNU General Public License GPL http://www.nitrc.org/projects/segadapter/ wanghongzhi78@gmail.com BSD License Yes Fang-Cheng Yeh, frank.yeh@gmail.com NITRC Linux,Windows C Fang-Cheng Yeh DSI Studio is a software for diffusion MR images analysis. The provided functions include reconstruction DTI QBI DSI and GQI deterministic fiber tracking and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. 2011-7-09 ProductionStable 20110710build win32 2011-6-07 ProductionStable NTU90 atlas Complete ODF MATLAB version 2011-6-07 ProductionStable NTU90 atlas Complete ODF FIB format 2011-5-24 ProductionStable NTU90 atlas QA Fiber orientation MATLAB version 2011-5-24 ProductionStable NTU90 atlas QA Fiber orientation FIB format 2011-5-24 ProductionStable DSI203 2.9 mm 2011-5-24 ProductionStable DSI203 1.9mm 2010-6-02 ProductionStable 20100602source for linux 2010-5-27 ProductionStable 20100527source for linux 2010-5-27 ProductionStable 20100527source for win32 DSI Studio Win32 MS Windows, Console Text Based, English, ProductionStable, NIfTI-1, DICOM, ANALYZE, Other Format, C, End Users, Windows, Linux, Image Reconstruction, Tensor Metric, Quantification, Diffusion MR Fiber Tracking, Visualization, Q-Ball, Diffusion Spectrum, BSD License http://www.nitrc.org/projects/dsistudio/ frank.yeh@gmail.com GNU General Public License GPL Yes Qianqian Fang, fangqq@gmail.com NITRC OS Independent Yes MATLAB Qianqian Fang amp;quot;Iso2meshamp;quot; is a MatlabOctave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scriptsprograms functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary segmented or gray-scale images such as those from MRI or CT scans making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling. URL httpiso2mesh.sf.net iso2mesh English, Beta, Other Format, MATLAB, End Users, OS Independent, Mesh Generation, GNU General Public License GPL http://www.nitrc.org/projects/iso2mesh/ fangqq@gmail.com Yes Maria Tass, mtassopoulos@rotman-baycrest.on.ca NITRC OS Independent Maria Tass The purpose of this project is to provide a community for the discussion of functional connectivity and all related topics. This includes discussion of related tools data sets methodological discussion related websites and publications etc. Functional Connectivity Community Web Environment, OS Independent, English, Beta, Developers, End Users, Community http://www.nitrc.org/projects/func_connect/ mtassopoulos@rotman-baycrest.on.ca GNU General Public License GPL Yes Qianqian Fang, fangqq@gmail.com NITRC POSIXUNIX-like Yes C Qianqian Fang Mesh-based Monte Carlo or MMC is a Monte Carlo MC solver for photon migration in 3D turbid media. Different from existing MC software designed for layered such as MCML or voxel-based media such as MMC or tMCimg MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smoothcomplex boundaries but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores. Mesh-based Monte Carlo MMC Console Text Based, English, Beta, Other Format, C, End Users, POSIXUNIX-like, Monte Carlo, GNU General Public License GPL http://www.nitrc.org/projects/mmc/ fangqq@gmail.com Attribution Yes Timothy Herron, tjherron@ebire.org NITRC MacOS,POSIXUNIX-like,Microsoft Yes C Timothy Herron CLEAVE is a UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large data sets with minimal memory use without loading all of the data into memory. It has been used for fMRI analysis e.g. CLEAVE adds the following to the standard ANOVA analyses 0 Unlimited numbers of factors can be analyzed. 1 Factor Correlation and Unequal Variance Corrections 2 Treatment Magnitudes omega^2 partial eta^2 and R^2 3 A convenient Ranking of Factors based upon treatment magnitudes and significance levels. 4 Post-Hoc Significance Tests 5 Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance. 6 Allows the use of Random Factors. 7 A Configuration File to make the program more tunable 8 A Histogram and Cell Line Diagrams which help the user to detect outliers. 9 Associated MATLAB functions port CLEAVE-style data sets in or out of MATLAB. Software is at httpwww.ebire.orghcnlabsoftwarecleave.html CLEAVE Large Data Set ANOVA MacOS, Microsoft, POSIXUNIX-like, Statistical Operation, Attribution, Other Format, Console Text Based, English, Mature, C, End Users http://www.nitrc.org/projects/cleave/ tjherron@ebire.org GNU General Public License GPL Yes Han Zhang, napoleon1982@gmail.com NITRC Linux,Windows MATLAB Han Zhang While the traditional temporally concatenated Group ICA TC-GICA adopting three steps of PCA reduction it could result in inconsistent and variable components when different subject orders were used both for the group- and individual-level results. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA SOI-GICA aims to fix this problem by producing stable and reliable GICA results. For details please see the paper amp;quot;Subject Order-Independent Group ICA SOI-GICA for Functional MRI Data Analysisamp;quot; Zhang et al. 2010 NeuroImagehttpdx.doi.org10.1016j.neuroimage.2010.03.039. MICA is the toolbox inplemented SOI-GICA for convenience of usage. 2010-7-28 Beta MICA_manual_beta1.2_20100729_en 2010-7-21 Beta MICA_beta1.2_20100718 2010-6-13 Beta MICA_manual_beta1.2_20100614_cn 2010-6-11 Beta MICA beta1.2 Subject Order-Independent Group ICA Win32 MS Windows, Gnome, KDE, English, Beta, GNU General Public License GPL, Independent Component Analysis, MATLAB, NIfTI-1, ANALYZE, Developers, End Users, Windows, Linux http://www.nitrc.org/projects/cogicat/ napoleon1982@gmail.com V3D License 2010-April Yes v3d list, v3d.list@gmail.com NITRC Windows NT2000,Windows Vista,MacOS,Linux,Cygwin,Windows 95982000,Windows XP Yes C,C v3d list Vaa3D 3D Visualization-Assisted Analysis is a handy fast and versatile 3D4D5D Image Visualization amp;amp; Analysis System for Bioimages amp;amp; Surface Objects. Vaa3D is a cross-platform Mac Linux and Windows tool for visualizing large-scale gigabytes and 64-bit data 3D4D5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis cell segmentation neuron tracing brain registration annotation quantitative measurement and statistics etc and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper 2010 284 pp.348-353 about Vaa3D and Vaa3D-Neuron an order of magnitude of performance improvement both reconstruction accuracy and speed was achieved compared to other tools. 2010-6-24 ProductionStable v2.475 2010-5-14 ProductionStable V3D 2.466 V3D-Neuron 2.0 Plugin Interface 0.92 Vaa3D and Vaa3D-Neuron Platform or Development Environment, Warping, Resampling, Image Display, V3D License 2010-April, Windows XP, Windows Vista, Windows NT2000, Linux, Cygwin, Algorithm or Reusable Library, Atlas Application, Neuronal Characterization, Surface Analysis, Position, Volumetric Analysis, Segmentation, Shape Analysis, Registration, Rendering, Fiber Tracking, Other Audience, MacOS, Windows 95982000, Developers, Win32 MS Windows, KDE, Gnome, Other Environment, English, ProductionStable, Other Format, C, C, End Users http://www.nitrc.org/projects/v3d/ v3d.list@gmail.com Commercial License OEI Yes Bruce Johnson, brucej@osmicenterprises.com NITRC Bruce Johnson The OEI OLFACT-fMRI olfactometer is a computerized odor delivery device that can be used for basic research applications including mapping olfactory centers cognitivelearning research neuro-marketing among other uses. Additional products including tests for odor threshold odor identification odor discrimination and odor memory. OEI fMRI compatible olfactometer Stimulus Presentation, Commercial License OEI http://www.nitrc.org/projects/oei/ brucej@osmicenterprises.com Yes Angelos Barmpoutis, abarmpou@cise.ufl.edu NITRC Angelos Barmpoutis This is an on-line tutorial on how to use MATLAB for Diffusion-Weighted MRI processing. The following subjects are covered in this tutorial Generation of Synthetic Diffusion-Weighted MRI datasets Diffusion Tensor DTI Estimation from DW-MRI DTI Visualization as a field of ellipsoids Higher-order Diffusion Tensor Estimation from DW-MRI Computing of Tensor Orientation Distribution Functions Tensor ODF Computing of Fiber Orientations Higher-order Diffusion Tensor Image Visualization as fields of spherical functions Multi-fiber reconstruction etc. The tutorial contains numerous illustrations figures and Matlab scripts embedded in the text. The readeruser can automatically generate Matlab script for a self-designed DW-MRI experiment by selecting which steps needs to be followed. The code that corresponds to the selected steps is then appropriately merged in the amp;quot;Matlab Script Generatoramp;quot; and the user can easily copy and paste the produced code directly to the Matlab command prompt. 2010-5-06 version1.0 MATLAB Tutorial on Diffusion Tensor MRI http://www.nitrc.org/projects/dwmri_in_matlab/ abarmpou@cise.ufl.edu dtiBrainScope Yes Dongrong Xu, dx2103@columbia.edu NITRC Dongrong Xu This is a software package for processing diffusion tensor imaging data. The following functions are included 1. Converting imaging data in DICOME format to ANALYZE format 2. Extracting binary brain mask for quick scalp-removing 3. Correcting eddy-current induced distortion 4. Optimized tensor estimation based on noisy diffusion-weighted imaging DWI data 5. Scalp removal using a brain mask image 6. Corregistering imaging data and generating deformation field for mapping images from individual spaces to a template or target space 7. Spatial Normalization and Warping DTI 8. Fiber tracking 9. Clustering fiber tracts 10. Identifying brain ventricles and generating binary masks for the baseline and DW imaging data 11. Deriving diffusion anisotropy indices DAIs and principal directions PD and the corresponding color-coded PD-map. dtiBrainScope dtiBrainScope http://www.nitrc.org/projects/brainscope/ dx2103@columbia.edu Yes Ayla Khan, ayla@sci.utah.edu NITRC MacOS,Linux,Windows 95982000 Yes C Ayla Khan map3d supports interactive visualization of surface based time signals such as high resolution EEG MEG and ECG. map3d Visualization, Forward - Inverse, EEGMEGECoG, Win32 MS Windows, X11 Applications, MacOS, Windows 95982000, Linux, C, Other Format http://www.nitrc.org/projects/map3d/ ayla@sci.utah.edu LONI Software License Yes Shantanu Joshi, shantanu.joshi@loni.ucla.edu NITRC Shantanu Joshi Fly through and interact with hundreds of human brains to compare structural differences or carefully inspect individual specimens. Introducing the “Informatics Visualization in Neuroimaging Invizian©” Project a 21st century visualization environment that enables you via your computer to display and interact with hundreds of neuroimaging data sets at once —bringing together brain image data from some of the world’s best neuroscience research teams. Invizian© empowers both researchers and students of neuroscience to explore and understand the human brain using Invizian’s© simple and powerful user interface for neuroimaging data exploration and discovery. Come back often to see how we are making continuing progress to make Invizian© even more amazing. INVIZIAN LONI Software License http://www.nitrc.org/projects/invizian/ shantanu.joshi@loni.ucla.edu Yes Vision Zheng, zheng.vision@gmail.com NITRC Vision Zheng Quadratically constrained quadratic programing QCQP technique in medical image analysis. QCQP based tools are provided for classification segmentation and bias field correction. QCQP http://www.nitrc.org/projects/qcqp/ zheng.vision@gmail.com MITX Consortium License Yes Christian Dansereau, christiandansereau@gmail.com NITRC POSIXUNIX-like Other Programming Language,Perl,MATLAB Christian Dansereau NIAK is a library of modules and pipelines for fMRI processing with Octave or Matlabr that can run in parallel either locally or in a supercomputing environment. Linux OS and MINC file format are supported. NIAK currently includes a T1 preprocessing pipeline a pipeline for correction of structured noise by component selection in ICA CORSICA as well as an fMRI preprocessing pipeline. NIAK features powerful pipeline management capabilities including parallel computing generation of detailed logs and automatic handling of pipeline failures or updates. 2011-1-17 Beta 0.6.4.1 2010-12-07 Beta 0.6.4 2010-12-07 Beta 0.6.4 2010-11-23 Beta 0.6.3.4 unstable 2010-10-28 Beta 1.0 2010-10-28 Beta 1.0 NeuroImaging Analysis Kit NIAK End Users, Console Text Based, English, Beta, MINC, MINC2, MATLAB, Perl, Other Programming Language, Developers, POSIXUNIX-like, Algorithm or Reusable Library, Independent Component Analysis, Workflow, Principal Component Analysis, Linear, Image-to-Template, Intermodal, Intrasubject, Quality Metrics, Resampling, Filtering, Artifact Removal, Intensity Non-uniformity Correction, Constrained Region Growing, MITX Consortium License http://www.nitrc.org/projects/niak/ christiandansereau@gmail.com Commercial License MAG Yes Ben Krasnow, ben@magconcept.com NITRC Ben Krasnow Mag Design and Engineering sells a variety of MEG- and fMRI-compatible hardware for research use. These items include typical response collection devices such as joysticks response pads mice as well as stimulation devices such as vibrotactile stimulators olfactometers and pressureforce generators. The company also offers custom design and production services for many different applications. Mag Design and Engineering Response Monitoring, Stimulus Presentation, Optical Imaging, Commercial License MAG http://www.nitrc.org/projects/magdande/ ben@magconcept.com Public Domain Yes Andrew Noske, anoske@ncmir.ucsd.edu NITRC Andrew Noske This is a venue for discussing and defining standard web interfaces for sharing images annotations and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure increase code reuse and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement extensible and cover the major tasks of developing tools for multiscale data on the web. Web Interfaces for Multiscale Images Public Domain http://www.nitrc.org/projects/webmscaleapi/ anoske@ncmir.ucsd.edu Attribution Share Alike Yes Chris Wyatt, clwyatt@vt.edu NITRC Chris Wyatt The vervet Chlorocebus aethiops sabaeus probabilistic atlas defines an anatomical space template with associated tissue and regional prior probability maps. The atlas was produced from whole head MRI of 10 normal adult animal subjects. The package consists of two atlases. The amp;quot;Biasedamp;quot; directory contains the average template and probabilistic atlases for selected tissue classes constructed by registering the training population to one subject. The amp;quot;Unbiasedamp;quot; directory contains the atlas constructed using unbiased estimation. The atlas is suitable for use in any segmentation tool using a probabilistic atlas for example those in Slicer. 2010-7-02 Vervet_Brain_Atlas_2_0 Vervet Probabilistic Atlas Atlas Data, Attribution Share Alike http://www.nitrc.org/projects/vervet_atlas/ clwyatt@vt.edu MITX Consortium License Yes Ayla Khan, ayla@sci.utah.edu NITRC Yes Ayla Khan SCIRun is a Problem Solving Environment PSE for modeling simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE as well as BioMesh3D. BioMesh3D is a free easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.5. SCIRun MITX Consortium License http://www.nitrc.org/projects/scirun/ ayla@sci.utah.edu GNU General Public License GPL Yes Jonathan Peirce, jon@peirce.org.uk NITRC FreeBSD,MacOS,Linux,Windows Python Jonathan Peirce PsychoPy - Psychology software in Python. PsychoPy is an open-source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience psychology and psychophysics experiments. It is intended as a free powerful alternative to Presentation or e-Prime. PsychoPy Console Text Based, Win32 MS Windows, English, Beta, Python, End Users, Developers, MacOS, Windows, Linux, FreeBSD, Experimental Control, GNU General Public License GPL http://www.nitrc.org/projects/psychopy/ jon@peirce.org.uk BSD License Yes Randall Frank, randall-frank@computer.org NITRC Randall Frank IOWA 3 Input Output time aWare Architecture IOWA 3 BSD License http://www.nitrc.org/projects/iowa3/ randall-frank@computer.org Yes Yaroslav Halchenko, yoh@onerussian.com NITRC FreeBSD,Linux,Other UNIX-like Yaroslav Halchenko This is a collaborative effort to package neuroscience-related software for the Debian operating system. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end the project offers a package repository that complements the main Debian and Ubuntu archive. NeuroDebian is not yet another Linux distribution but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. For example installing FSL looks like amp;quot;apt-get install fslamp;quot; There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian please drop us a note. 2011-2-06 ProductionStable Debian 7.0 wheezy 2010-10-12 ProductionStable Mac OS X 2010-10-12 ProductionStable Ubuntu 10.04 lucid 2010-10-12 ProductionStable Ubuntu 10.10 maverick 2010-4-28 ProductionStable Windows 2010-4-27 ProductionStable Ubuntu 8.10 intrepid 2010-4-27 ProductionStable Ubuntu 9.10 karmic 2010-4-27 ProductionStable Ubuntu 9.04 jaunty 2010-4-27 ProductionStable Debian 6.0 squeeze 2010-4-27 ProductionStable Debian unstable sid 2010-4-27 ProductionStable Debian 5.0 lenny 2010-1-29 ProductionStable Debian Stable NeuroDebian Console Text Based, Gnome, KDE, Web Environment, Other Environment, Developers, End Users, System Administrators, Linux, FreeBSD, Other UNIX-like, Other Software Resource, Platform or Development Environment, Mature, ProductionStable, AFNI BRIK, DICOM, MINC2, NIfTI-1, PDF - Portable Document Format, Other Format, bshortbfloat, Philips PARREC http://www.nitrc.org/projects/neurodebian/ yoh@onerussian.com GNU General Public License GPL Yes Srinivas Rachakonda, srachakonda@mrn.org NITRC MacOS,Linux,SunOSSolaris,Windows Yes MATLAB Srinivas Rachakonda Group ICA Toolbox is a MATLAB toolbox which implements multiple algorithms for independent component analysis of group magneto resonance imaging data GIFT and electro encephalogram data EEGIFT to group studies. 2010-9-19 Mature eegiftv1.0c 2010-9-19 Mature giftv1.3h Group ICA Toolbox GIFT and EEGIFT Win32 MS Windows, Gnome, KDE, English, Mature, ANALYZE, NIfTI-1, MATLAB, End Users, SunOSSolaris, Windows, MacOS, Linux, Linear, Algorithm or Reusable Library, Artifact Removal, Principal Component Analysis, Independent Component Analysis, GNU General Public License GPL http://www.nitrc.org/projects/gift/ srachakonda@mrn.org GPL-Style Open Source Yes Yogesh Rathi, yogesh@bwh.harvard.edu NITRC Yogesh Rathi This tool can be used as a command line module with 3D Slicer version 3 and above for the affine registration of image volumes. The registration toolbox has 2 options 1 a Mutual Information based registration 2 a Sum-of-Square differences registration method. The final output is in the same space as the fixed image. You do require to have CUDA v2.2 or greater installed on your system with atleast 256MB Nvidia GPU memmory card. All operating systems are supported but take a look at the CMakeLists.txt file for how to compile for you system. GPU based affine registration GPL-Style Open Source http://www.nitrc.org/projects/gpu-areg/ yogesh@bwh.harvard.edu MGH CSRL License Yes Ruopeng Wang, rpwang@nmr.mgh.harvard.edu NITRC MacOS,Linux,Windows Yes C Ruopeng Wang Diffusion Toolkit with TrackVis is a cross-platform software package that does reconstruction fiber tracking visualization and analysis on various diffusion imaging data. Features of the software include • Handles DTI DSI Q-Ball and HARDI imaging techniques. • Works on Windows Mac OS X and Linux with native look and feel. Native 64-bit support on Mac OS X and Linux. • Fast streamlined data processing. • Intuitive GUI front-end with command-line driven back-end. Thus allows advanced user to write their own scripts for automated multiple dataset processing. • Real-time fiber track visualization and analysis. Parameter adjustment applied to 3D render on the fly. Various tracking selection methods filters allows locating specific track bundle with ease. 2010-3-16 ProductionStable 0.6 2010-3-16 ProductionStable 0.5.1 2009-12-01 ProductionStable 0.5 2009-6-03 ProductionStable 0.4.3 2008-6-18 ProductionStable 0.4.2 Diffusion Toolkit TrackVis Console Text Based, Win32 MS Windows, X11 Applications, Other Environment, ANALYZE, DICOM, NIfTI-1, Diffusion MR Fiber Tracking, Visualization, English, ProductionStable, End Users, MGH CSRL License, MacOS, Windows, Linux, Image Reconstruction, C http://www.nitrc.org/projects/trackvis/ rpwang@nmr.mgh.harvard.edu Yes Rohith MV, rohithmv@udel.edu NITRC Rohith MV Structure from motion algorithms repository. Common interface for various sfm algorithms. SFMProject http://www.nitrc.org/projects/sfmproject/ rohithmv@udel.edu BSD License Yes Jarrod Millman, millman@berkeley.edu NITRC OS Independent Yes Python Jarrod Millman Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways with different underlying assumptions. However this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype an open-source community-developed initiative under the umbrella of Nipy is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages e.g. SPM FSL eases the design of workflows within and between packages and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. NIPY Pipeline and Interfaces Python, Developers, End Users, OS Independent, Workflow, BSD License, Beta http://www.nitrc.org/projects/nipype/ millman@berkeley.edu BSD License Yes Matthew Brett, matthew.brett@gmail.com NITRC Yes Matthew Brett Nipy aims to provide a complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging fMRI. NIPY Structural and Functional Analysis BSD License http://www.nitrc.org/projects/nipy/ matthew.brett@gmail.com Attribution Non-Commercial Yes Cameron Craddock, cameron.craddock@gmail.com NITRC Cameron Craddock These are the scripts used for the analyses reported in Craddock RC Holtzheimer PE 3rd Hu XP Mayberg HS. 2009 Disease state prediction from resting state functional connectivity. Magn Reson Med 6261619-28. Specifically included are scripts for performing t-test filter reliability filter recursive feature elimination and reliability recursive feature elimination feature selection methods. These make use of wrappers that perform .632 bootstrap and k-fold cross validation strategies. The scripts are written in matlab and require the Bioinformatics toolbox. If you do not have the bioinformatics toolbox the scripts can be easily modified to run with other matlab SVM toolboxes i.e. libsvm svmlight shogun etc.. Disease State Prediction Attribution Non-Commercial http://www.nitrc.org/projects/diseasestate/ cameron.craddock@gmail.com GNU General Public License GPL Yes Tom Close, t.close@brain.org.au NITRC MacOS,POSIXUNIX-like,Windows Yes C Tom Close NFG is a collection of tools that generate numerical fiber structures with the complexity of human white matter and simulate Diffusion-Weighted MR images that would arise from them. Its primary use is to enable the testing of tracking algorithms 2011-2-01 Beta nfg_1.1.1 2010-3-31 Beta Phantoms_A_to_I 2009-4-28 Beta nfg_1.1 2008-11-09 Beta default_10_v1.0.3 2008-11-06 Beta nfg_1.0.3 2008-11-05 Beta nfg_v1.0.2 2008-10-29 Beta nfg_1.0.1 2008-10-29 Beta default_10_v1.0.1 2008-10-22 Beta default_10_v1.0 2008-10-22 Beta nfg_1.0 2008-7-08 Beta nfg_0.9.5 Numerical Fibre Generator NFG MacOS, Tractography, GNU General Public License GPL, POSIXUNIX-like, English, Beta, Developers, C, Windows, ANALYZE, Console Text Based http://www.nitrc.org/projects/nfg/ t.close@brain.org.au Creative Commons License Yes David Kennedy, dave@dnkc.net NITRC Yes David Kennedy amp;quot;Best Practices for Software Development in the Imaging Community Users and Developers Uniteamp;quot; is a tutorial that will take place as part of MICCAI 2010 is the 13th International Conference on Medical Image Computing and Computer Assisted Intervention will be held from September 20-24 2010 in Beijing China. See httpwww.miccai2010.org This project will support community outreach and dialog between presenters and audience both before and after the tutorial session and is intended to engage the broader community in the deliberations on this important topic. amp;quot;Best Practicesamp;quot; will cover software engineering practices as well end-user installation and support practices. Best Practices for Software Development Community, Websites, Algorithm or Reusable Library, Beta, Domain Independent, Web Environment, Developers, End Users, Creative Commons License, English http://www.nitrc.org/projects/best_practices/ dave@dnkc.net GNU General Public License GPL Yes Christian Haselgrove, christian.haselgrove@umassmed.edu NITRC Linux C Christian Haselgrove This project is a simple Surface and Volumetric Visualization application that has been designed to facilitate rapid and flexible visualization from neuroanatomically segmented results. 2006-12-19 Alpha 20030113 SVV X11 Applications, End Users, GNU General Public License GPL, English, Linux, C, NIfTI-1, CT, MR, PETSPECT, Surface Rendering, Alpha http://www.nitrc.org/projects/dave1/ christian.haselgrove@umassmed.edu XNAT License Yes Will Horton, hortonw@mir.wustl.edu NITRC OS Independent Yes Java Will Horton XNAT is an open source imaging informatics platform designed to facilitate management and exploration of medical imaging and related data. XNAT includes a DICOM workflow a secure database backend and a rich web-based user interface. XNATs web services interface enables external applications to easily access XNAT-hosted data. 2011-5-15 ProductionStable 1.5 2010-4-06 ProductionStable 1.4 2007-10-03 ProductionStable 1.3.3 2007-6-30 ProductionStable 1.3 XNAT OS Independent, NIfTI-1, Web Environment, English, ProductionStable, Java, Database Application, Platform or Development Environment, DICOM, Developers, End Users, XNAT License http://www.nitrc.org/projects/xnat/ hortonw@mir.wustl.edu BSD License Yes Clement Vachet, cvachet@unc.edu NITRC MacOS,Linux Yes C Clement Vachet ARCTIC Automatic Regional Cortical ThICkness is an end-to-end application developped at UNC-Chapel Hill allowing individual regional analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module or directly as a command line. 2009-6-23 Mature ARCTIC_Batcmake_Wrapper_1.2 2009-6-23 Mature ARCTIC_Executables_1.2 2009-3-24 Mature ARCTIC_Executables_1.1 2009-3-20 Mature ARCTIC_Batcmake_Wrapper_1.1 2008-12-15 Mature ARCTIC_Batcmake_Wrapper_1.0 2008-12-15 Mature ARCTIC_Tutorial_example_1.0 2008-12-12 Mature ARCTIC_Executables_1.0 ARCTIC English, Mature, Nrrd, ANALYZE, Other Format, C, Workflow, End Users, Developers, Linux, MacOS, BSD License http://www.nitrc.org/projects/arctic/ cvachet@unc.edu WFU ANSIR License Yes Benjamin Wagner, bwagner@wfubmc.edu NITRC POSIXUNIX-like,Windows Yes MATLAB Benjamin Wagner WFU_PickAtlas provides a method for generating ROI masks based on the Talairach Daemon database. The atlases include Brodmann area Lobar Hemisphere Anatomic Label and Tissue Type. 2010-8-31 Mature 3.0.3 SPM8 revision 4010 Update 2010-8-24 Mature 2.5 2007-9-09 Mature 2.4 WFU_PickAtlas Win32 MS Windows, X11 Applications, Atlas Application, ANALYZE, Windows, POSIXUNIX-like, MATLAB, English, Mature, End Users, WFU ANSIR License http://www.nitrc.org/projects/wfu_pickatlas/ bwagner@wfubmc.edu BSD License Yes Matthew Brett, matthew.brett@gmail.com NITRC Matthew Brett The purpose of NIPY is to make it easier to do better brain imaging research. We believe that neuroscience ideas and analysis ideas develop together. Good ideas come from understanding; understanding comes from clarity and clarity must come from well-designed teaching materials and well-designed software. The software must be designed as a natural extension of the underlying ideas. We aim to build software that is clearly written clearly explained a good fit for the underlying ideas a natural home for collaboration NIPY Community BSD License http://www.nitrc.org/projects/nipy-community/ matthew.brett@gmail.com GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The ShapeViewer httpwww.loni.ucla.eduSoftwareShapeViewer is a simple portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions. Since it is written in Java it can run on a wide variety of computers. ShapeViewer is distributed by the Laboratory of Neuro Imaging httpwww.LONI.ucla.eduSoftwareShapeViewer at UCLA. ShapeViewer GNU General Public License GPL http://www.nitrc.org/projects/shapeviewer/ iwaterpolo@gmail.com 3D Slicer License Yes Sylvain Jaume, sylvainjaume@gmail.com NITRC Sylvain Jaume 3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City Jan 2010. SpineSegmentation module for 3DSlicer 3D Slicer License http://www.nitrc.org/projects/sylvainproject/ sylvainjaume@gmail.com GNU General Public License GPL Yes Bin He, luxxx273@umn.edu NITRC Windows XP MATLAB Bin He eConnectome Electrophysiological Connectome is an open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEGECoGMEG preprocessing source estimation connectivity analysis and visualization. Connectivity from EEGECoGMEG can be mapped over sensor and source domains. This package is designed for use by researchers in neuroscience psychology cognitive science clinical neurophysiology neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB. eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome amp;quot;La Sapienzaamp;quot;. 2011-5-31 eConnectome 2.0 beta 2010-8-18 eConnectome 1.0 full version 2010-3-12 eConnectome 1.0 beta eConnectome English, MATLAB, End Users, Windows XP, Forward - Inverse, Region of Interest, Visualization, Statistical Operation, Multivariate Analysis, GNU General Public License GPL http://www.nitrc.org/projects/econnectome/ luxxx273@umn.edu Freeware Yes Aaron Carass, aaron_carass+nitrc@jhu.edu NITRC Yes Aaron Carass The TOADS-CRUISE Brain Segmentation Tools are a collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical subcortical and cerebellar structures. The CRUISE algorithm produces inner central and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling lesion segmentation thickness computation surface visualization and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit both available on NITRC. They are therefore cross-platform and compatible with a wide variety of file formats. 2011-4-04 SPECTRE Atlases v2.0 .tar.gz 2011-3-23 SPECTRE Atlases v2.0 .zip 2010-12-06 Toads-Cruise 2010 December 6 R2a 2010-9-23 SPECTRE Atlases v1.0 2010-5-06 Toads-Cruise 2010 May 3 R1a 2010-3-08 GVF 2D Matlab - C CMEX Version 2010-3-08 GVF 2D Matlab - Windows v5.0 2010-3-08 GVF 2D Matlab - UNIX v4.2c 2010-3-08 Multi-Grid GVF Matlab - 1.0 TOADS-CRUISE Brain Segmentation Tools MR, Freeware http://www.nitrc.org/projects/toads-cruise/ aaron_carass+nitrc@jhu.edu Artistic License Yes Daniel Alexander, D.Alexander@cs.ucl.ac.uk NITRC MacOS,POSIXUNIX-like Yes Java,Unix Shell Daniel Alexander Camino is a free open-source object-oriented software package for analysis and reconstruction of Diffusion MRI data tractography and connectivity mapping. 2009-9-03 Latest version Camino English, Java, Unix Shell, Developers, End Users, MacOS, POSIXUNIX-like, Q-Ball, Tensor Metric, Diffusion MR Fiber Tracking, Artistic License, Console Text Based http://www.nitrc.org/projects/camino/ D.Alexander@cs.ucl.ac.uk Yes Christian Haselgrove, christian.haselgrove@umassmed.edu NITRC Yes Christian Haselgrove Licensing issues in software and data. All are invited to participate or join the project and contribute. 2011-7-12 Full Text Software Licenses Licensing http://www.nitrc.org/projects/licensing/ christian.haselgrove@umassmed.edu GNU General Public License GPL Yes Christian Habeck, ch629@columbia.edu NITRC Yes Christian Habeck Generalized Covariance Analysis a platform for any PCA-based analysis on functional neuroimaging data PET and fMRI. Includes - Ordinal Trend Canonical Variance Analysis for parametric designs C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data Ordinal Trend Analysis. Neural Computation 2005; 17 1602-1645 - Partial Least Squares for any design matrix - Subprofile Scaling Model for cross-sectional designs JR. Moeller Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;112A121-35. 2011-8-22 1.2 2010-4-13 1.1 2010-4-13 GCVA 1.1 Generalized Covariance Analysis gCVA GNU General Public License GPL, MR, PETSPECT http://www.nitrc.org/projects/gcva_pca/ ch629@columbia.edu FreeSurfer License Yes Nick Schmansky, nicks@nmr.mgh.harvard.edu NITRC MacOS,Linux Yes Nick Schmansky FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data and overlay of functional MRI data onto the reconstructed surface. 2009-8-10 ProductionStable Current v4.5.0 2008-10-14 ProductionStable Old Releases FreeSurfer Gaussian Curvature, Image Display, English, ProductionStable, End Users, FreeSurfer License, Console Text Based, X11 Applications, MGHMGZ, MacOS, Linux, Mean Curvature, Thickness, Surface Rendering, Spatial Transformation, Image Reconstruction, Anatomic http://www.nitrc.org/projects/freesurfer/ nicks@nmr.mgh.harvard.edu LONI Software License,BSDMIT-Style Open Source License,Public Domain Yes John Van Horn, jvanhorn@loni.ucla.edu NITRC MacOS,Linux,Windows XP Java,C,MATLAB,Unix Shell John Van Horn THE HUMAN CONNECTOME PROJECT HarvardMGH-UCLA The HCP is a multi-center project comprising two distinct consortia Mass. Gen. Hosp. and UCLA; and Wash. U. and the U. of Minn. seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods genomics architectonics mathematical approaches informatics and interactive visualization. This NITRC project site is dedicated to linking all listed connectivity analysis tools under one common heading HCP-related as well as independently created software packages. Please use this site to explore the variety of connectomics software tools available via NITRC as well well as valuable data resources forthcoming scientific meetings etc. Scroll down to view the list of useful tools. If you have such tools yourself please list them with NITRC and request to link with us See httpwww.humanconnectomeproject.org or httpwww.humanconnectome.org for details. HCP HarvardMGH-UCLA MEG, EEG, Scanner, Data, Database, Web Resource, Diffusion Spectrum, Q-Ball, Tensor Metric, Quantification, Shape Analysis, Spatial Transformation, Fiber Tracking, Visualization, Beta, Mature, Planning, EEGMEGECoG, MR, Web Environment, Developers, End Users, Other Audience, BSDMIT-Style Open Source License, LONI Software License, Public Domain, English, MacOS, Windows XP, Linux, LONI Pipeline, C, Java, MATLAB, Unix Shell, ANALYZE, NIfTI-1, DICOM, Other Format http://www.nitrc.org/projects/hcp_mgh-ucla/ jvanhorn@loni.ucla.edu GNU General Public License GPL Yes S. P. Mapping, spm@fil.ion.ucl.ac.uk NITRC OS Independent Yes MATLAB S. P. Mapping The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts or time-series from the same subject. The current release is designed for the analysis of fMRI PET SPECT EEG and MEG. 2009-4-02 Mature SPM8 2005-12-01 Mature SPM5 SPM Haemodynamic Response, Three Dimensional Display, Segmentation, Spatial Transformation, Time Domain Analysis, Forward - Inverse, Statistical Operation, Rendering, Workflow, Platform or Development Environment, Mature, MR, PETSPECT, EEGMEGECoG, Other Environment, End Users, GNU General Public License GPL, English, OS Independent, MATLAB, ANALYZE, GIfTI, DICOM, NIfTI-1 http://www.nitrc.org/projects/spm/ spm@fil.ion.ucl.ac.uk GNU General Public License GPL Yes Dominik Bach, d.bach@fil.ion.ucl.ac.uk NITRC OS Independent MATLAB Dominik Bach SCRalyze is a powerful software for model-based analysis of peripheral psychophysiology e.g. skin conductance heart rate pupil size etc.. General linear modelling and dynamic causal modelling of these signals provide for inference on neural statesprocesses. SCRalyze includes flexible data import and display statistical inference and results display and export. Easy programming of add-ons for new data formats signal channels and models. SCRalyze Modeling, Quantification, Time Domain Analysis, Other Software Resource, GNU General Public License GPL, English, Beta, MATLAB, End Users, OS Independent http://www.nitrc.org/projects/scralyze/ d.bach@fil.ion.ucl.ac.uk GNU General Public License GPL Yes , NITRC General-purpose unsupervised data-analysis tool most often used for brain imaging data. FastICA GNU General Public License GPL, ProductionStable, Independent Component Analysis http://www.nitrc.org/projects/incf_fastica/ MITX Consortium License Yes Maxwell Collins, mcollins@cs.wisc.edu NITRC Maxwell Collins With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools. This package allows interoperability between CAMINO and TRACKVIS. CAMINO is a leading software package in DTI processing. The package is from University of College London. TRACKVIS is a tract visualizing utility with capability of visualizing up to and over a million white matter tracts seamlessly. The package is from Massachusetts General Hospital. The tools in this package allow conversion of tracts from one format to another in a very effective way with ability to handle over a million tracts. CAMINO-TRACKVIS MITX Consortium License http://www.nitrc.org/projects/camino-trackvis/ mcollins@cs.wisc.edu BSD License Yes Brian Avants, stnava@gmail.com NITRC Brian Avants ANTsR is an R extension to ANTs that performs multivariate statistical parametric mapping of DTI T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs and other image processing methodologies. ANTsR depends upon the R statistical language bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and in that case ANTsR will provide a 100% reproducible neuroimaging study on that data. ANTsR BSD License http://www.nitrc.org/projects/antsr/ stnava@gmail.com Academic Free License amp;quot;AFLamp;quot; Yes Chao-Gan YAN, ycg.yan@gmail.com NITRC OS Independent,MacOS,Linux,Windows MATLAB Chao-Gan YAN REsting State fMRI data analysis Toolkit REST is a user-friendly convenient toolkit to calculate Functional Connectivity FC Regional Homogeneity ReHo Amplitude of Low-Frequency Fluctuation ALFF Fractional ALFF fALFF Gragner causality and perform statistical analysis. You also can use REST to view your data perform Monte Carlo simulation similar to AlphaSim in AFNI calculate your images regress out covariates extract ROI time courses reslice images and sort DICOM files. Most recent version and any questions could also be checked out in httpwww.restfmri.net. REST a toolkit for resting-state fMRI Win32 MS Windows, Gnome, KDE, Console Text Based, English, Beta, ANALYZE, NIfTI-1, MATLAB, End Users, Developers, Other Audience, OS Independent, Windows, Linux, MacOS, Modeling, Algorithm or Reusable Library, Resampling, Statistical Operation, Fourier Time-domain Analysis, Spectral Analysis, Cross-correlation, Two Dimensional Display, Academic Free License amp;quot;AFLamp;quot; http://www.nitrc.org/projects/rest/ ycg.yan@gmail.com BSD License Yes Steven Dunn, stevendunn@gmail.com NITRC C Steven Dunn NOTE All active development of BRAINSMush is now being stored in a Git repository at github.com. Please go to httpsgithub.comBRAINSiaBRAINSStandAlone Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura skull eyes etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. BRAINSMush BSD License, Segmentation, NIfTI-1, Nrrd, ANALYZE, DICOM, Console Text Based, English, ProductionStable, C http://www.nitrc.org/projects/brainsmush/ stevendunn@gmail.com Yes Samuel Won, samwon@ucdavis.edu NITRC OS Independent Python Samuel Won UC Davis IDeA Lab Applications for Management Of Neuroimaging Data - View dicom files and assemble them into 3D volumes. View and convert between Analyze Nifti and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans. 2011-2-13 Beta 1.1.2 DIAMOND Python, X11 Applications, English, Beta, DICOM, ANALYZE, NIfTI-1, End Users, OS Independent, Image Reconstruction, Format Conversion, Image Display, Workflow, Database Application, Algorithm or Reusable Library http://www.nitrc.org/projects/diamond/ samwon@ucdavis.edu BSD License Yes Bertrand Thirion, bertrand.thirion@inria.fr NITRC MacOS,POSIXUNIX-like,Windows Python Bertrand Thirion scikit-learn machine learning in Python scikit-learn English, ProductionStable, Python, Developers, End Users, MacOS, Windows, POSIXUNIX-like, Algorithm or Reusable Library, Modeling, Discriminant Analysis, Independent Component Analysis, Principal Component Analysis, Linear, Nonlinear, BSD License http://www.nitrc.org/projects/scikit-learn/ bertrand.thirion@inria.fr GNU General Public License GPL Yes edward herskovits, ehh@ieee.org NITRC MacOS,HP-UX,Linux,Cygwin,Windows Yes C,C edward herskovits GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification. We designed and implemented a Bayesian multivariate nonparametric suite of algorithms for analyzing neuroimaging data. The GAMMA suite can be used for brain morphometric analysis lesion-deficit analysis and functional MR data analysis. 2011-12-19 Beta GAMMA v1.2 2010-12-16 Beta GAMMA suite v1.1 program 2010-12-16 Beta GAMMA suite v1.1 source code 2010-12-16 Beta GAMMA suite v1.1 test data GAMMA GNU General Public License GPL, Console Text Based, Win32 MS Windows, X11 Applications, Other Environment, English, Beta, ANALYZE, NIfTI-1, Other Format, C, C, End Users, Developers, Linux, HP-UX, MacOS, Windows, Cygwin, Algorithm or Reusable Library, Modeling, Statistical Operation, Volumetric Analysis http://www.nitrc.org/projects/gamma_suite/ ehh@ieee.org Yes Psychology Software Tools, gretchen.archer@pstnet.com NITRC Psychology Software Tools The MRI Digital Projection System uses Digital Light Processing® DLP technology that provides microsecond pixel rise times outstanding contrast with all-digital fiber optic control that allows you to project crystal clear sharp images. Includes High resolution 1024x768 DLP Projector with RF filtered enclosure custom lens assembly digital video DVI over fiber high flow fans internal thermal sensor Control room device to perform DVI to Fiber conversion remotely power down the projector and allow use of projector remote control from control room 30 meter fiber optic cable that runs between the projector and projector control station Heavy duty magnet compatible projector stand assembly required Heavy duty magnet compatible mirror stand with mirror assembly required High resolution lenticular pitch rear projection screen for high quality image reproduction Optional VGA to DVI converter native DVI video cards on Windows or Macintosh recommended MRI Digital Projection System Stimulus Presentation, Mature http://www.nitrc.org/projects/projector/ gretchen.archer@pstnet.com GNU General Public License GPL Yes Cyril Pernet, cyril.pernet@ed.ac.uk NITRC OS Independent MATLAB Cyril Pernet LIMO EEG is a matlab toolbox EEGlab compatible allowing the processing of MEEG data using single trials and hierarchical linear models. Almost all statistical designs can be analyzed with our tool. Across subject analyses are performed using bootstrap offering robust inferences. LIMO EEG English, ProductionStable, End Users, OS Independent, Time Domain Analysis, Algorithm or Reusable Library, Other Format, GNU General Public License GPL, MATLAB http://www.nitrc.org/projects/limo_eeg/ cyril.pernet@ed.ac.uk OtherProprietary License Yes Joost Mulders, mulders@brainvoyager.com NITRC MacOS,Linux,Windows Yes MATLAB Joost Mulders BVQXtools is a Matlab-based toolbox for the reading writing and processing of BrainVoyager QX files in Matlab. The toolbox is freely available. BVQXtools English, Beta, MATLAB, Workflow, MacOS, Windows, Linux, ANALYZE, Other Format, Other Software Resource, Format Conversion, Statistical Operation, Time Domain Analysis, OtherProprietary License, Developers, End Users http://www.nitrc.org/projects/bvqxtools/ mulders@brainvoyager.com Commercial license from Brain Innovation B.V. Maastricht The Netherlands Yes Rainer Goebel, rainergoebel@mac.com NITRC Windows Vista,MacOS,Linux,Windows XP Yes C Rainer Goebel BrainVoyager QX is a powerful neuroimaging software package. It started as a tool for the analysis of anatomical and functional MRI data sets but has evolved over the years into a multi-modal analysis tool for fMRI DTI TMS EEG and MEG data. The software is highly optimized and user friendly running on all major computer platforms including Windows XPVista7 Linux i.e. Ubuntu SUSE Fedora and Mac OS X 10.4 or higher including Snow Leopard. 2010-11-10 Mature 2.2.1 2009-12-10 Mature 2.1 BrainVoyager QX Segmentation, Volume Measurement, Spatial Transformation, MEG Modeling, Mesh Generation, Platform or Development Environment, Statistical Operation, Thickness, Time Domain Analysis, Fiber Tracking, Visualization, EEG Modeling, Mature, MR, EEGMEGECoG, End Users, Developers, Commercial license from Brain Innovation B.V. Maastricht The Netherlands, English, MacOS, Windows XP, Windows Vista, Linux, C, DICOM, Philips PARREC, ANALYZE, NIfTI-1, GIfTI http://www.nitrc.org/projects/bvqx/ rainergoebel@mac.com Freeware Yes Rainer Goebel, rainergoebel@mac.com NITRC Windows XP C Rainer Goebel BrainVoyager Brain Viewer allows to browse and inspect essential BrainVoyager data files. In addition the program supports viewing the header and content of DICOM files. The Viewer also supports standard image files JPEG GIF PNG TIFF BMP allowing to inspect snapshots figures or photos. The program offers an elegant user interface with fluid navigation abilities inspired by Apples amp;quot;Cover Flowamp;quot; and the iPhone interface. The program can be downloaded and distributed freely. 2010-11-10 ProductionStable BrainVoyager Viewer 1.8 BrainVoyager Viewer Freeware, Other Format, Win32 MS Windows, English, ProductionStable, Windows XP, DICOM, End Users, C, Visualization http://www.nitrc.org/projects/bvviewer/ rainergoebel@mac.com MGH CSRL License Yes Gary Boas, gboas@nmr.mgh.harvard.edu NITRC OS Independent Yes Gary Boas The Center for Functional Neuroimaging Technologies CFNT is a Regional Resource located at the Athinoula A. Martinos Center for Biomedical Imaging at the Massachusetts General Hospital. The primary mission of the Center is to expand understanding of the human brain in health and disease through the development and dissemination of innovative multimodal Magnetic Resonance MR-based neuroimaging techniques and technologies. The Resource is sponsored by the National Center for Research Resources of the NIH. 2008-10-21 ProductionStable PMI Toolbox 2008-10-21 ProductionStable OPTseq2 2008-10-21 ProductionStable MNE 2008-10-21 ProductionStable HomER 2008-10-21 ProductionStable HF-1 2008-10-21 ProductionStable Freesurfer amp;amp; FS-Fast Center for Functional Neuroimaging Tech Knowledge Environment, ProductionStable, EEGMEGECoG, MR, Optical Imaging, Web Environment, Developers, End Users, MGH CSRL License, English, OS Independent http://www.nitrc.org/projects/cfnt/ gboas@nmr.mgh.harvard.edu GNU General Public License GPL Yes Dustin Scheinost, dustin.scheinost@yale.edu NITRC Windows NT2000,BSD,MacOS,Linux,SunOSSolaris,IRIX Yes C,TclTk Dustin Scheinost BioImage Suite is a general purpose registrationsegmentationvisualization suite. It also has facilities for DTI and fMRI processing. 2011-3-18 ProductionStable BioImage Suite 3.01 2008-1-30 ProductionStable BioImage Suite 2.5 2008-1-16 ProductionStable 2.5RC2 2007-10-17 ProductionStable 2.5 RC1 2007-9-26 ProductionStable Introduction to Programming for Image Analysis with VTK 2007-9-26 ProductionStable NonLinear MNI 2 Talairach 1.0 2007-9-26 ProductionStable BioImage Suite 2.0 BioImage Suite Intersubject, Image-to-Template, Fiber Tracking, Animation, Three Dimensional Display, Volume Rendering, Web Resource, English, GNU General Public License GPL, ProductionStable, Expectation Minimization, Linux, BSD, SunOSSolaris, IRIX, ANALYZE, Intermodal, C, TclTk, MacOS, Windows NT2000, NIfTI-1, MINC2, Console Text Based, Win32 MS Windows, X11 Applications, Morphology, Volumetric Analysis, Active Contour, End Users, Developers http://www.nitrc.org/projects/bioimagesuite/ dustin.scheinost@yale.edu MITX Consortium License Yes Ayla Khan, ayla@sci.utah.edu NITRC Yes Ayla Khan BioMesh3D is a free easy to use program for generating quality meshes for use in biological simulations. It is included when downloading SCIRun v4.5. BioMesh3D MITX Consortium License http://www.nitrc.org/projects/biomesh3d/ ayla@sci.utah.edu BSD License Yes Jarrod Millman, millman@berkeley.edu NITRC Yes Jarrod Millman Nitime is a library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains a set of container objects to represent time-series and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code. NIPY Timeseries Analysis BSD License http://www.nitrc.org/projects/nitime/ millman@berkeley.edu GNU Lesser General Public License LGPL Yes Carl Lederman, clederma@math.ucla.edu NITRC Yes Carl Lederman TetraMetrix is an open-source software project for distributed Tetrahedral Mesh Modeling and Analysis TMMA of multidimensional data. Tetrahedra are 3D space filling geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images e.g. 3D MRI brain images. Tetrahedra are a natural extension of lines 1D and surface triangulations 2D which enable finite element analysis of irregular shapes and permit a greater range of morphometric characterization of multidimensional objects. The project is being developed by researchers at UCLA Laboratory of Neuro Imaging httpwww.LONI.ucla.edu and Department of Mathematics httpwww.math.ucla.edu. A beta version of the program is available for download. Please see the very brief instructions on the Docs tab on the left. TetraMetrix is distributed by the Laboratory of Neuro Imaging at UCLA. 2011-2-19 v1.03_beta_windows_executables 2011-2-19 v1.03_beta_linux_code 2011-2-19 v1.03_beta_windows_code 2011-2-17 v1.02_beta_pipeline 2011-2-17 v1.02_beta_executables 2011-2-17 v1.02_beta 2010-11-19 v1.01_beta 2010-11-19 v1.01_beta_executables 2010-11-07 v1.0_beta_executables 2010-11-07 v1.0_beta_pipeline 2010-11-07 v1.0_beta TetraMetrix GNU Lesser General Public License LGPL http://www.nitrc.org/projects/tmma/ clederma@math.ucla.edu GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The ShapeTools library is a collection of Java classes that enable Java programmers to model manipulate and visualize geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines. ShapeTools are distributed by the Laboratory of Neuro Imaging httpwww.LONI.ucla.eduSoftwareShapeTools at UCLA. ShareTools GNU General Public License GPL http://www.nitrc.org/projects/shapetools/ iwaterpolo@gmail.com 3D Slicer License Yes Lucile Bompard, lucile.bompard@gmail.com NITRC MacOS,POSIXUNIX-like,Windows Yes C Lucile Bompard Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures. SPHARM-PDM is a tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at specific locations. 2011-9-19 ProductionStable spharm-pdm_v1.10.12_linux64 2011-8-01 ProductionStable spharm-pdm_v1.10.11_linux64 2011-6-22 ProductionStable v.1.10.10 2011-6-17 ProductionStable v1.10.9 2011-6-03 ProductionStable v1.10.8 2011-5-02 ProductionStable v.1.10.7 2011-4-15 ProductionStable v.1.10.6 2011-3-28 ProductionStable v.1.10.5 2011-3-23 ProductionStable v.1.10.4 2011-2-21 ProductionStable v.10.3 2011-2-07 ProductionStable v1.10.2 2010-10-11 ProductionStable v1.10 2010-5-20 ProductionStable v1.9 2010-1-14 ProductionStable v1.8 SPHARM-PDM Toolbox X11 Applications, Win32 MS Windows, Console Text Based, English, ProductionStable, C, ANALYZE, NIfTI-1, Nrrd, Other Format, Developers, End Users, MacOS, POSIXUNIX-like, Spherical Harmonics, Surface Analysis, Quantitative Shape Analysis, 3D Slicer License, Windows http://www.nitrc.org/projects/spharm-pdm/ lucile.bompard@gmail.com Yes Owen Carmichael, ocarmichael@ucdavis.edu NITRC OS Independent Python Owen Carmichael UC Davis IDeA Lab Applications for Management Of Neuroimaging Data -- A collection of tools used for processing and organizing MRI data. The Dicom Importer allows you to to view assemble and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks. 2009-12-11 Beta 1.1.0 2009-8-21 Beta 1.0.0 Subject Library Beta, Console Text Based, X11 Applications, English, Database Application, Python, ANALYZE, End Users, OS Independent, Workflow, Other Software Resource, Algorithm or Reusable Library http://www.nitrc.org/projects/subjectlibrary/ ocarmichael@ucdavis.edu BSD License Yes Benjamin Yvernault, byvernault@gmail.com NITRC Yes Benjamin Yvernault Corpus Callosum Segmentation Tool CCSeg is an open-source C-based application developed at UNC-Chapel Hill that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface CCSeg also performs semi-automatic segmentation. 2011-5-17 CCSeg_1.2.1 2011-4-14 CCSeg_1.2 2011-4-07 CCSeg_Atlas_1.0 2011-4-06 CCSeg_1.1 2011-4-05 CCSeg_1.0 CCSeg BSD License http://www.nitrc.org/projects/ccseg/ byvernault@gmail.com Yes Vision Zheng, zheng.vision@gmail.com NITRC Vision Zheng Tools to make easier on using spm pipedream dti-tk and other softwares to analyze t1 or dti images. factory_t1_dti http://www.nitrc.org/projects/factory4t1ndti/ zheng.vision@gmail.com UCSF NCL Software License Yes Yiou Li, liyiou@gmail.com NITRC Yiou Li Microstructural correlation toolbox MSC is a Matlab-based software library to perform independent component analysis on group white matter skeleton generated by FSL TBSS. The script produces stable estimates of the white matter tract or tract segments that resemble highly correlated variation profiles across a group of subjects. Please refer to the following publication for detailed information Li YO et al. amp;quot;Independent component analysis of DTI reveals multivariate microstructural correlations of white matter in the human brainamp;quot; Hum Brain Mapp.2011. 2011-11-11 MSC v0.1 Microstructural correlation toolbox UCSF NCL Software License http://www.nitrc.org/projects/msc_toolbox/ liyiou@gmail.com GNU General Public License GPL Yes Gary Hui Zhang, garyhuizhang@gmail.com NITRC MacOS,Linux,Windows Yes C Gary Hui Zhang ITK-SNAP is an open-source software application for medical image segmentation. Its primary use is for delineating anatomical structures and regions in MRI CT and other 3D biomedical imaging data. ITK-SNAP is actively developed by Paul Yushkevich Hui Zhang and colleagues at the Penn Image Computing and Science Laboratory at the University of Pennsylvania. 2011-5-04 Mature 2.2.0 2010-10-20 Mature 2.1.4-rc1 2009-11-18 Mature 0.8.2 2009-11-18 Mature 2.0.0 2009-11-12 Mature ITK-SNAP 2.0 2009-11-04 Mature NIGHTLY 2009-11-04 Mature NIGHTLY 2009-5-11 Mature 1.0 2009-5-11 Mature 1.8.0 ITK-SNAP NIfTI-1, Nrrd, Other Format, C, MacOS, Windows, Linux, Manual, Active Contour, Anatomic, X11 Applications, Win32 MS Windows, ANALYZE, DICOM, End Users, GNU General Public License GPL, Volumetric Analysis, English, Mature http://www.nitrc.org/projects/itk-snap/ garyhuizhang@gmail.com LONI Software License Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The LONI Pipeline Neuroimaging Virtual Environment PNVE is a self-contained virtual machine that can be executed on a common laptop or desktop enabling the Pipeline to run virtually anywhere. Neophytes to the Pipeline can have their own private server running in minutes software engineers and workflow designers can use the PNVE as a sandbox and those without access to grid computing facilities can now take full advantage of the Pipeline processing environment. PNVE is distributed by the Laboratory of Neuro Imaging httppipeline.loni.ucla.eduPNVE at UCLA. Pipeline Neuroimaging VirtualEnvironment LONI Software License http://www.nitrc.org/projects/pnve/ iwaterpolo@gmail.com LONI Software License Yes David Shattuck, shattuck@loni.ucla.edu NITRC Windows NT2000,Windows Vista,MacOS,Linux,Windows XP C David Shattuck BrainSuite is a suite of image analysis tools designed to process magnetic resonance images MRI of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. 2011-5-18 ProductionStable Brainsuite11a Windows GUI 2011-5-02 ProductionStable BrainSuite11a Command Line Mac OSX 2011-5-02 ProductionStable BrainSuite11a Command Line Linux 32-bit 2011-5-02 ProductionStable BrainSuite11a Command Line Linux 2009-8-24 ProductionStable BrainSuite09.R1 BrainSuite Console Text Based, LONI Software License, Windows NT2000, Windows XP, Windows Vista, MacOS, Linux, Win32 MS Windows, English, ProductionStable, LONI Pipeline, Mesh Generation, Volumetric Analysis, Two Dimensional Display, Surface Rendering, Three Dimensional Display, Clipping, C, ANALYZE, NIfTI-1, End Users http://www.nitrc.org/projects/brainsuite/ shattuck@loni.ucla.edu Public Domain Yes Thomas Nichols, t.e.nichols@warwick.ac.uk NITRC MacOS,Linux,SunOSSolaris,Windows Yes MATLAB Thomas Nichols The Statistical nonParametric Mapping toolbox provides an extensible framework for voxel level non-parametric permutationrandomisation tests of functional Neuroimaging experiments with independent observations. 2007-8-08 Mature SnPM5b 2007-8-08 Mature SnPM2 2007-8-08 Mature SnPM99 2007-8-08 Mature SnPM3 SnPM Linear, ANALYZE, MacOS, Windows, Linux, SunOSSolaris, Mature, Public Domain, English, NIfTI-1, MATLAB, End Users http://www.nitrc.org/projects/snpm/ t.e.nichols@warwick.ac.uk BSD License Yes Jean-Baptiste BERGER, jibberger@gmail.com NITRC Linux,Microsoft Yes C Jean-Baptiste BERGER Light version of the existing tool Fiber Viewer. It includes every clustering methods of Fiber Viewer such as Lenght Gravity Hausdorff and Mean methods but also a Normalized Cut algorithm. As in the full version you can also display a plane on the fiber. This tool works faster than the full version due to simplified visualizations. 2011-11-14 FiberViewerLight_1.1_linux64 2011-11-14 FiberViewerLight_1.0_linux64 FiberViewerLight Application, BSD License, English, Microsoft, Linux, C http://www.nitrc.org/projects/fvlight/ jibberger@gmail.com Academic Free License amp;quot;AFLamp;quot; Yes Jorge Luis Bernal Rusiel, jbernal0019@yahoo.es NITRC OS Independent Yes MATLAB Jorge Luis Bernal Rusiel So far there is a lack for Random Field TheoryRFT-based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley’s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer’s matlab subdirectory in the Matlab’s search path. In addition this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses Neuroimage 52 158-171. 2011-2-28 1.01 2011-1-18 1.00 RFT_FDR Console Text Based, Gnome, KDE, Other Environment, English, MGHMGZ, MATLAB, Academic Free License amp;quot;AFLamp;quot;, Thickness, Surface Rendering, Modeling, Statistical Operation, End Users, OS Independent http://www.nitrc.org/projects/rft_fdr/ jbernal0019@yahoo.es TORTOISE License Yes Lin-Ching Chang, changl@cua.edu NITRC Lin-Ching Chang The TORTOISE software package is for processing diffusion MRI data. It contains two main modules DIFF_PREP and DIFF_CALC. DIFF_PREP - software for image resampling motion eddy current distortion and susceptibility induced EPI distortion corrections and for re-orientation of data to a common space DIFF_CALC - software for tensor fitting error analysis color map visualization and ROI analysis Software and sample data downloads as well as documentation for the software are available at httpwww.tortoisedti.org. TORTOISE MR, TORTOISE License, Tensor Metric http://www.nitrc.org/projects/tortoise/ changl@cua.edu LONI Software License Yes John Van Horn, jvanhorn@loni.ucla.edu NITRC John Van Horn Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources. Parkinsons Disease Discovery Database LONI Software License http://www.nitrc.org/projects/pd3/ jvanhorn@loni.ucla.edu Open Data Commons Public Domain Dedication and License 1.0 Yes Russell Poldrack, poldrack@mac.com NITRC Russell Poldrack OpenFMRI is a data sharing resource for task-based fMRI data. It aims to provide a resource for any fMRI researcher who wishes to share their data openly. Currently it provides access to raw fMRI datasets along with associated metadata. In the future it will also provide access to processed datasets. OpenFMRI Open Data Commons Public Domain Dedication and License 1.0 http://www.nitrc.org/projects/openfmri/ poldrack@mac.com Yes Erik Anderson, eranders@sci.utah.edu NITRC OS Independent Yes Python,C Erik Anderson Geometry format under the Neuroimaging Informatics Technology Initiative NIfTI. 2011-1-14 Beta GIFTI File Format January 14 2011 2010-6-28 Beta GIFTI Clibs source tree 2010-3-16 Beta gifti.dtd 2010-3-09 Beta Left and Right Examples 2010-3-03 Beta Freesurfer annotation as gifti LabelTable 2010-2-25 Beta Dset_with_LabelTable 2009-11-09 Beta 1.0.4 2009-11-03 Beta Image of Labels On Surface 2009-6-20 Beta GIFTI converter plugin v1.0 2009-5-08 Beta freesurfer_to_gifti 2008-10-07 Beta Poster in JPEG Format 2008-10-07 Beta Poster in PDF Format 2008-9-18 Beta Brainvisa GIFTI samples v1.3 2008-7-24 Beta Right hemisphere 2008-5-31 Beta Python Examples 2008-5-31 Beta Python Bindings 2008-5-03 Beta Freesurfer GIFTI samples v1.0 2008-4-21 Beta Brainvisa GIFTI samples v1.2 2008-4-15 Beta GIFTI DTD 2008-4-15 Beta Brainvisa GIFTI samples v1.1 2008-4-08 Beta Vistrails White Matter 2008-3-20 Beta AFNISUMA GIFTI samples v1.0 2008-2-21 Beta gifti.xsd 2008-1-22 Beta VisTrails SPX surface Bin64 2008-1-22 Beta VisTrails SPX surface GIFTI English, Beta, Algorithm or Reusable Library, OS Independent, Other Information Resource, C, Python, GIfTI, End Users, Developers http://www.nitrc.org/projects/gifti/ eranders@sci.utah.edu Yes Julianne Rovesti, jrovesti@apa.org NITRC Julianne Rovesti If you are interested in finding books related to neuroscience you have come to the right place Books is a bibliography of books addressing the topic of functional and structural neuroimaging. Books Books, Domain Independent, End Users, Developers, Other Audience, English http://www.nitrc.org/projects/books/ jrovesti@apa.org GNU Lesser General Public License plus Addendum Yes Maarten Van de Velde, mvelde@ant-neuro.com NITRC Maarten Van de Velde The LIBEEP library deals with reading and writing RIFF-format CNTAVR-files. This file format is also called amp;quot;EEProbe data formatamp;quot; and is used in the software packages EEProbe ASA ASA-Lab Cognitrace eemagine EEG Visor by ANT Neuro B.V. The Netherlands. The file format provides for storage of EEGERPMEG data as 32-bit values and includes a very efficient compression algorithm. Encodingdecoding from the compressed data is performed automatically through the LIBEEP interface functions. LIBEEP GNU Lesser General Public License plus Addendum http://www.nitrc.org/projects/libeep/ mvelde@ant-neuro.com E-Prime License Yes Psychology Software Tools, gretchen.archer@pstnet.com NITRC Windows Vista,Windows XP Visual Basic Psychology Software Tools E-Prime® is a suite of applications to fulfill all of your computerized experiment needs. Used by more than 15000 professionals in the research community E-Prime® provides a truly easy-to-use environment for computerized experiment design data collection and analysis. E-Prime® provides millisecond precision timing to ensure the accuracy of your data. E-Prime’s flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime® suite of applications includes •E-Studio – Drag and drop graphical interface for experiment design •E-Basic – Underlying scripting language of E-Prime •E-Run – Once the experiment is generated with a single click E-Run affords you the millisecond precision of stimulus presentation synchronizations and data collection. •E-Merge – Merges your single session data files for group analysis •E-DataAid – Data management utility •E-Recovery – Recovers data files E-Prime 2.0 Win32 MS Windows, English, ProductionStable, E-Prime License, Visual Basic, Other Format, End Users, Developers, Windows XP, Windows Vista, Experimental Control http://www.nitrc.org/projects/eprime/ gretchen.archer@pstnet.com GNU General Public License GPL Yes Christopher Adamson, chris.adamson@mcri.edu.au NITRC Christopher Adamson DFBIdb is a suite of tools for efficient management of neuroimaging project data. Specifically DFBIdb was designed to allow users to quickly perform routine management tasks of sorting archiving exploring exporting and organising raw data. DFBIdb was implemented as a collection of Python scripts that maintain a project-based centralised database that is based on the XCEDE 2 data model. Project data is imported from a filesystem hierarchy of raw files which is an often-used convention of imaging devices using a single script that catalogues meta-data into a modified XCEDE 2 data model. During the import process data are reversibly anonymised archived and compressed. The import script was designed to support multiple file formats and features an extensible framework that can be adapted to novel file formats. Graphical user interfaces are provided for data exploration. DFBIdb includes facilities to export convert and organise customisable subsets of project data according to user-specified criteria. 2010-9-27 1.0rc1.1 2010-9-27 1.0rc1 DFBIdb GNU General Public License GPL http://www.nitrc.org/projects/dfbidb/ chris.adamson@mcri.edu.au LONI Software License Yes Bruce Liu, chengyiliu@gmail.com NITRC Windows NT2000,Windows Vista,Linux Yes C,shbash Bruce Liu BrainSolution is a collection of tools for MRI T1 brain image segmentation in the Windows® environment. It helps construct a complete pipeline with necessary preprocessing and postprocessing procedures besides brainparser the core program of our fast brain segmentation. The execution of the whole pipeline can be completed in 2 hours with good segmentation results. 2009-12-18 Alpha 20091218 2009-12-18 Alpha 20091218 2009-12-18 Alpha 20091218 BrainSolution Console Text Based, English, Alpha, LONI Software License, Labeling, Workflow, C, shbash, ANALYZE, End Users, Windows NT2000, Windows Vista, Linux http://www.nitrc.org/projects/brainsolution/ chengyiliu@gmail.com BSD License Yes Ryan Wyse, ryan-wyse@uiowa.edu NITRC Ryan Wyse Huntington Disease Nueroimaging Initiative HDNI is an international effort to establish resources necessary to study the application of neuroimaging measures as surrogate biomarkers in HD. The primary aims are to develop and apply software tools imaging protocols quality control procedures data archiving data distribution and participation guidelines that will accelerate existing and prospective imaging studies. HD Neuro-Informatics BSD License http://www.nitrc.org/projects/hdni/ ryan-wyse@uiowa.edu BSD License Yes Bennett Landman, bennett.landman@vanderbilt.edu NITRC Yes Bennett Landman The Framework for Open Programmatic Access FOPA aims to provide a standardized framework for communication and data exchange between medical imaging applications with particular focus on neuroimaging technologies. FOPA is an attempt to design and implement a common protocol for network and command line communication with either file-system or imbedded data structures. Initial reference implementations will support interoperability between ITK VTK and Java platforms. Contributions are welcome from other neuroimaging development communities. This project is an open community effort under the BSD license. Framework for Open Programmatic Access BSD License http://www.nitrc.org/projects/fopa/ bennett.landman@vanderbilt.edu GNU General Public License GPL Yes Ze Wang, redhatw@gmail.com NITRC MacOS,Linux,Windows MATLAB Ze Wang This tool box is for arterial spin labeled perfusion MRI data processing. It is based on SPM copyright by Wellcome Department London and Matlab MathWorks Inc. A more detailed documentation could be found in asl_perf_subtract.m the main function for calculating CBF value. The current version support 3D or 4D Analyze or Nifiti format and support PASL CASL and PCASL data. It currently contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis. I will include some toolkits for data quality checking and data visualization. Sample data will be also provided in my webpage httpcfn.upenn.edu~zewang. ASL data processing tool box Curses, English, Alpha, ANALYZE, NIfTI-1, MATLAB, End Users, Developers, Linux, Windows, MacOS, Statistical Operation, Quantification, GNU General Public License GPL http://www.nitrc.org/projects/asltbx/ redhatw@gmail.com Attribution Non-Commercial Share Alike Yes Clementine Ouziel, clementine.ouziel@gmail.com NITRC Clementine Ouziel Human brain atlases have been generated at UNC-Chapel Hill for adult pediatric and elderly populations by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images tissue priors WMGMCSF lobar parcellation maps and subcortical structures. Current available atlases - Adult atlas Symmetric atlas generated from 50 healthy adult subjects 20-59 year old. - UNC-MNI Pediatric 1-year-old atlas Symmetric atlas generated from 104 1-year-old subjects combining children at high familial risk of autism and controls. - Pediatric 4-year-old atlas Symmetric atlas generated from 10 4-year-old healthy subjects. - Elderly atlas Atlas generated from 27 healthy elderly subjects 60 years old. Additional information and acknowledgment for their usage can be found by clicking on the release notes. 2011-10-19 UNC-MNI_Pediatric_1year_Brain_Atlas 2011-6-16 UNC_Pediatric_Brain_Atlas_2 2011-6-16 UNC_Adult_Brain_Atlas_2 2009-10-26 UNC_Elderly_Brain_Atlas_1 2009-10-26 UNC_Adult_Brain_Atlas_1 2009-10-26 UNC_Pediatric_Brain_Atlas_1 UNC Human Brain Atlas Data, Atlas Data, End Users, Attribution Non-Commercial Share Alike, Nrrd http://www.nitrc.org/projects/unc_brain_atlas/ clementine.ouziel@gmail.com BSD License Yes Jiahui Wang, jh_wang@ieee.org NITRC MacOS,Linux,Microsoft C Jiahui Wang NIRAL Utilities are open-source applications developped at UNC-Chapel Hill in the Neuro Image Research and Analysis Lab NIRAL. These utilities are C based command line applications that allow image analysis and processing using ITK or VTK libraries. NIRAL Utilities ANALYZE, Nrrd, Other Format, C, Application, Developers, End Users, Console Text Based, English, Mature, Linux, MacOS, Microsoft, BSD License http://www.nitrc.org/projects/niral_utilities/ jh_wang@ieee.org LONI Software License Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The LONI Provenance Editor httpwww.loni.ucla.eduSoftwareProvenanceEditor is a self-contained platform-independent application that automatically extracts the provenance information from an image header such as a DICOM image and generates a data provenance XML file with that information. Provenance Editor is distributed by the Laboratory of Neuro Imaging httpwww.LONI.ucla.eduSoftwareProvenanceEditor at UCLA. LONI Provenance Editor LONI Software License http://www.nitrc.org/projects/provenance/ iwaterpolo@gmail.com Yes Psychology Software Tools, gretchen.archer@pstnet.com NITRC Psychology Software Tools The Psychology Software Tools MRI Simulator provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less daunting than a real scanner. Special populations such as children the elderly and psychiatric patients are often prone to claustrophobia and anxiety in the bore of a magnet and consequently have a much higher rate of terminating the experiment or scan session before its completion. Some centers that have dealt with these populations estimate a 50%-80% failure rate. With the use of the MRI Simulator this failure rate can often be reduced below 5% improving cost effectiveness. PST MRI Simulator English, Mature, Training, Experiment Control http://www.nitrc.org/projects/mri_simulator/ gretchen.archer@pstnet.com Public Domain Yes , NITRC Yes Java From httprsbweb.nih.govijdocsintro.html ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs either as an online applet or as a downloadable application on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows Mac OS Mac OS X and Linux. It can display edit analyze process save and print 8-bit 16-bit and 32-bit images. It can read many image formats including TIFF GIF JPEG BMP DICOM FITS and quot;rawquot;. It supports quot;stacksquot; a series of images that share a single window. It is multithreaded so time-consuming operations such as image file reading can be performed in parallel with other operations. 2008-6-16 ProductionStable Download All Versions 2008-4-12 ProductionStable ImageJ 1.36 2008-4-12 ProductionStable ImageJ 1.40 ImageJ Public Domain, ProductionStable, Java http://www.nitrc.org/projects/incf_imagej/ GNU General Public License GPL Yes , NITRC Yes LONI_Viz is a versatile 1D 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a portable Java-based software which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. It reads Analyze Raw-binary and NetCDF volumetric data as well as Multi-Contour Files MCF LWOLWSDXF surfaces and atlas hierarchical brain-region labelings Hyperbolic BrainGraph Model Display. LONI_Viz allows the user to interactively overlay and browse through several data volumes zoom in and out in the axial sagittal and coronal views and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest e.g. sulcal curves on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. 2008-6-11 Beta Download link LONI Viz GNU General Public License GPL, Beta, Atlas Application, Surface Analysis http://www.nitrc.org/projects/incf_loni-viz/ GNU General Public License GPL Yes , NITRC This software can be used to analyze EEG data either using a graphical interface GUI or using Matlab scripts which make use of the functions provided by the MeanMachine. As compared to other libraries MeanMachine can handle even very large data sets like for example 256 channels recorded at 2KHz. Mean Machine GNU General Public License GPL, Beta http://www.nitrc.org/projects/incf_mean-machi/ OtherProprietary License Yes , NITRC Free-D allows the reconstruction of 3D models from image stacks segmentation registration surface reconstruction 3D rendering. It is designed in the goal of non-linear spatial normalization and averaging of collections of individual 3D models this module is currently in alpha version only and not included in the distributed version. Free-D OtherProprietary License, Beta http://www.nitrc.org/projects/incf_free-d/ Yes Vision Zheng, zheng.vision@gmail.com NITRC Vision Zheng Tools processing MRI data with a number of techniques from cvpr conference including segmentation matching features and classification. MRI_CVPR http://www.nitrc.org/projects/medical_cvpr/ zheng.vision@gmail.com 3D Slicer License Yes Mahnaz Maddah, mmaddah@alum.mit.edu NITRC OS Independent C Mahnaz Maddah The Quantitative Diffusion Tools provide Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts summarizing measures over tract clusters etc. 2010-4-26 Fiber clustering tutorial and data - Version 1.3 2009-12-29 Fiber clustering tutorial and data - Version 1.2 2009-10-02 Fiber clustering tutorial and data - Version 1.1 2009-9-10 Fiber clustering tutorial and data - Version 1.0 Quantitative Diffusion Tools Other Format, C, End Users, Developers, OS Independent, Quantification, Tractography, Segmentation, 3D Slicer License http://www.nitrc.org/projects/quantitativedti/ mmaddah@alum.mit.edu Yes Daniel Marcus, dmarcus@wustl.edu NITRC OS Independent Yes Daniel Marcus Brainscape is a database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain evaluating neuroanatomical models and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal. 2009-8-04 Beta BETA2 Brainscape Beta, Data, Database, Statistical Operation, Correlation, End Users, DICOM, Web Environment, English, OS Independent http://www.nitrc.org/projects/brainscape/ dmarcus@wustl.edu Attribution Share Alike Yes Clementine Ouziel, clementine.ouziel@gmail.com NITRC Clementine Ouziel This symmetric atlas of the primate brain has been created using 18 cases of rhesus macaques aged 16-34 months. It includes the T1-weighted image with and without skull and also tissue segmentation probability maps white matter gray matter CSF rest subcortical structures segmentation amygdala caudate hippocampus pallidus putamen and a lobar parcellation map. You can find more details about the creation of this atlas in the following paper M. Styner R. Knickmeyer S. Joshi C. Coe S. J. Short and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512 Medical Imaging 2007 pp. 65122 L1-8 2009-2-13 Primate_Brain_Atlas UNC Primate Brain Atlas Data, Atlas Data, End Users, Attribution Share Alike, Nrrd http://www.nitrc.org/projects/primate_atlas/ clementine.ouziel@gmail.com BSD License Yes Brian Avants, stnava@gmail.com NITRC OS Independent Yes C Brian Avants Advanced Normalization Tools ANTS Image registration with variable transformation models elastic diffeomorphic unbiased and similarity metrics landmarks cross-correlation mutual information optical flow. Designed for neuroscience and medical imaging researchers and users. Special capabilities include symmetric diffeomorphic normalization optimal template creation and user-guided normalization. Advanced Normalization Tools NIfTI-1, Other Format, English, ProductionStable, OS Independent, ANALYZE, DICOM, C, End Users, Algorithm or Reusable Library, Atlas Application, Morphology, Temporal Transformation, Segmentation, Registration, BSD License http://www.nitrc.org/projects/ants/ stnava@gmail.com FreeSurfer License Yes Nick Schmansky, nicks@nmr.mgh.harvard.edu NITRC MacOS,Linux Yes Nick Schmansky Tool to remove facial features from an MRI structural image for the purpose of de-identification. 2009-7-22 ProductionStable 1.22 2009-7-22 ProductionStable Support Files MRI Defacer English, ProductionStable, FreeSurfer License, Surface Analysis, Intensity Operations, Resampling, End Users, Linux, MacOS, MGHMGZ, Console Text Based http://www.nitrc.org/projects/mri_deface/ nicks@nmr.mgh.harvard.edu GNU Lesser General Public License LGPL Yes Alexandr Opanasenko, skivr@yandex.ru NITRC Yes Alexandr Opanasenko Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system. Typically an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function. The goal of the proposed work is to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many minimally-trained raters. The proposed research investigates extension of established practices for volumetric labeling and web- based collaboration to create an innovative infrastructure for labeling. 2010-3-31 Virtual Server Demonstration 1.2 GB Web Game for Collaborative Labeling GNU Lesser General Public License LGPL http://www.nitrc.org/projects/webmill/ skivr@yandex.ru GNU General Public License GPL Yes Finn Nielsen, fn@imm.dtu.dk NITRC OS Independent Yes Finn Nielsen The Brede Wiki is a semantic wiki with structured information from neuroscience. It contains listing of results from neuroimaging studies such as Talairach coordinates and brain volume measurements as well as items for researchers software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. Search on Talairach coordinates in the database is available from an external specialized search engine. Brede Wiki OS Independent, Web Environment, English, Beta, Knowledge Environment, Data, Websites, End Users, GNU General Public License GPL http://www.nitrc.org/projects/bredewiki/ fn@imm.dtu.dk Yes Psychology Software Tools, gretchen.archer@pstnet.com NITRC Windows Vista,Windows XP Psychology Software Tools Designed for use in an MRI simulator MoTrak software uses Ascension Technology’s Flock of Birds. The sensor attaches to the subject’s head and determines the position of the head in space relative to the transmitter. The sensor records angular rotations as well as positional displacements from an initially calibrated position. This information is displayed and logged by the program in real-time allowing observation of head motion in an MRI simulator. In the simulator the participant can simultaneously be habituated to the MRI environment while being trained to remain still via feedback from the MoTrak system. MoTrak - Head Motion Tracking System Win32 MS Windows, English, Mature, End Users, Windows XP, Windows Vista, Experiment Control, Training, Application http://www.nitrc.org/projects/motrak/ gretchen.archer@pstnet.com OASIS Yes Daniel Marcus, dmarcus@wustl.edu NITRC OS Independent Yes Daniel Marcus The Open Access Series of Imaging Studies OASIS is a project aimed at making MRI data sets of the brain freely available to the scientific community. By compiling and freely distributing MRI data sets we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS is made available by the Washington University Alzheimer’s Disease Research Center Dr. Randy Buckner at the Howard Hughes Medical Institute HHMI at Harvard University the Neuroinformatics Research Group NRG at Washington University School of Medicine and the Biomedical Informatics Research Network BIRN. OASIS currently includes two data sets. A cross-sectional set includes 416 subjects aged 18 to 96 100 of whom were clinically diagnosed with Alzheimers disease. A longitudinal release includes 150 subjects aged 60 to 96 many diagnosed with Alzheimers disease at some point during their participation. 2010-2-24 ProductionStable Data access tools 2010-2-24 ProductionStable Home OASIS Data, ProductionStable, MR, Web Environment, End Users, OASIS, English, OS Independent, DICOM http://www.nitrc.org/projects/oasis/ dmarcus@wustl.edu BSD License Yes Aditya Gupta, adigupta@med.unc.edu NITRC MacOS,POSIXUNIX-like,Windows C Aditya Gupta DTIProcess is a DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim dtiprocess dtiaverage fibertrack fiberprocess et al.. DTIProcess ToolKit Console Text Based, English, Beta, Nrrd, C, Developers, End Users, MacOS, POSIXUNIX-like, Windows, Tractography, Resampling, Tensor Metric, BSD License http://www.nitrc.org/projects/dtiprocess/ adigupta@med.unc.edu GNU General Public License GPL Yes , NITRC MacOS,Linux,Windows C VoxBo is a highly modular and interoperable collection of free tools for brain image manipulation and analysis focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. 2011-6-15 Beta 1.8.5 2011-1-18 Beta 1.8.5pre14 2010-5-06 Beta 1.8.5pre8 2010-1-05 Beta 1.8.5pre7 2008-6-06 Beta 1.8.5pre3 VoxBo NIfTI-1, C, End Users, Linux, MacOS, Windows, Linear, Three Dimensional Display, Workflow, Format Conversion, English, Beta, ProductionStable, Other Format, ANALYZE, DICOM, Overlap Metrics, Sinc Function Interpolation, GNU General Public License GPL, No InputOutput Daemon, Console Text Based, X11 Applications http://www.nitrc.org/projects/voxbo/ Attribution Yes Stephan Gerhard, connectome@unidesign.ch NITRC Stephan Gerhard ConnectomeWiki is a knowledge base for macro- and mesoscale brain region and brain connectivity information across species. It is built using modern semantic wiki technology meaning that it is a resource added to and maintained by a community of users. Sophisticated semantic search queries references to relevant papers about regions and connectivity links to other databases different brain partition schemes and their relation are some of its features. ConnectomeWiki Knowledge Base Web Environment, English, ProductionStable, End Users, Bibliographic Resource, Database, Tractography, Web Service, Websites, Atlas Application, Ontology, Community, Attribution http://www.nitrc.org/projects/connectomewiki/ connectome@unidesign.ch CeCill v2 Yes Denis Rivière, denis.riviere.gm@gmail.com NITRC MacOS,Linux,Windows C,Python Denis Rivière BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developped for BrainVISA T1 MRI sulcal identification and morphometry cortical surface analysis diffusion imaging and tractography fMRI nuclear imaging EEG and MEG TMS histology and autoradiography etc.. BrainVISA main features are - Harmonization of communications between different software. For instance BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer FSL SPM nipy R-project Matlab etc. - Ontology-based data organization allowing database sharing and automation of mass of data analysis. - Fusion and interactive visualization of multimodal data using Anatomist software. - Automatic generation of graphical user interfaces. - Workflow monitoring and data quality checking. - Full customization possible. - Runs on Linux Mac and Windows. 2011-7-04 Mature brainvisa 4.1 2010-6-15 Mature brainvisa 4.0.0 2010-1-28 Mature brainvisa 3.2.1 2009-11-04 Mature brainvisa 3.2.0 BrainVISA Platform or Development Environment, Database, Tensor Metric, Morphology, Quantitative Shape Analysis, Segmentation, Spatial Transformation, Surface Analysis, Visualization, Diffusion MR Fiber Tracking, Mature, MR, EEGMEGECoG, KDE, End Users, Developers, CeCill v2, English, French, Linux, MacOS, Windows, Python, C, GIfTI, Other Format, NIfTI-1, DICOM, ANALYZE, MINC http://www.nitrc.org/projects/brainvisa/ denis.riviere.gm@gmail.com Yes Judith Rumsey, jrumsey@mail.nih.gov NITRC OS Independent Yes Judith Rumsey The NIH Pediatric MRI Data Repository contains longitudinal structural MRIs spectroscopy DTI and correlated clinicalbehavioral data from approximately 500 healthy normally developing children ages newborn to young adult. 2008-4-07 ProductionStable 1.0 NIH Pediatric MRI Data Repository Data, Database, Websites, ProductionStable, MR, Web Environment, End Users, Developers, English, OS Independent, MINC, MINC2 http://www.nitrc.org/projects/pediatric_mri/ jrumsey@mail.nih.gov GNU General Public License GPL Yes , NITRC Example implementation of SignaML metadescription of formats of biomedical time series allowing to read data in new formats base upon standardized XML description. Also open platform for implementing advanced signal processing methods in user-friendly environment at the moment interfacs for Java code standalone executables and Matlab code via Matlab Builder for Java. signalml EEG Modeling, MEG Modeling, Pre-Alpha, EEGMEGECoG, GNU General Public License GPL http://www.nitrc.org/projects/incf_signalml/ Yes Mika Rubinov, mikarubi@gmail.com NITRC OS Independent MATLAB Mika Rubinov The brain connectivity toolbox provides an easy access to a large selection of state of the art complex network measures which characterize brain connectivity by easily computable and neurobiologically meaningful statistics and are increasingly utilized in the description of large structural and functional connectivity datasets. The toolbox is available online at httpwww.brain-connectivity-toolbox.net and runs in Matlab. Network measures include those based on degree clustering distance centrality modularity and motif count. Most measures have weighted and directed variants. In addition the toolbox contains multiple cortical connectivity datasets acquired using tract tracing and diffusion MRI techniques. There is also a selection of methods for the generation of reference random and ordered networks. Brain Connectivity Toolbox OS Independent, Other Format, Console Text Based, ProductionStable, MATLAB, End Users, Statistical Operation http://www.nitrc.org/projects/bct/ mikarubi@gmail.com Public Domain Yes Jim McKay, jbmckay@telus.net NITRC Jim McKay A discussion group for those actively involved in research into or applications of biomagnetism and magnetoencephalography MEG. Continuing in the tradition of the first biomagnet host based in Gothenburg Sweden which was followed by a host maintained by CTF Systems Inc. in Coquitlam BC Canada this is an electronic forum for discussion of topics in biomagnetism and for maintaining a database for archival and dissemination of shared information. To get to the discussion group page click on menu item at left or copy the following to your browser address field httptech.groups.yahoo.comgroupbiomag Biomag Discussion Group on Yahoo Public Domain http://www.nitrc.org/projects/biomag_group/ jbmckay@telus.net Commerical Software Yes A. Mark Mento, mark.mento@smivision.com NITRC A. Mark Mento The iView X MRI-LR is a non-invasive long-range eye tracking system for use in the fMRI environment. Some features of the system include - Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. - Includes stimulus presentation software “Experiment Center” and is compatible with 3rd party products such as “Presentation” by NeuroBS. - Utilizes mirror box customized for large field of view. - Includes powerful analysis software “BeGaze2” for graphical and statistical analysis of eye movements. - Includes fixation saccade and blink detection and area-of-interest based statistics - Real-time data available via digital or analog output iView X MRI-LR - Eye Tracking for fMRI Commerical Software http://www.nitrc.org/projects/iviewx_mri-lr/ mark.mento@smivision.com Yes Psychology Software Tools, gretchen.archer@pstnet.com NITRC Psychology Software Tools The Fiber Optic Button Response System accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact chemical resistant medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant’s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed. Fiber Optic Button Response System Mature, Response Monitoring http://www.nitrc.org/projects/fobrs/ gretchen.archer@pstnet.com WFU ANSIR License Yes Benjamin Wagner, bwagner@wfubmc.edu NITRC POSIXUNIX-like,Windows Yes MATLAB Benjamin Wagner The WFU Biological Parametric Mapping WFU_BPM toolbox performs SPM analysis with voxel-wise imaging covariates. 2007-9-10 Beta wfu_bpm user manual 2007-9-10 Beta wfu_bpm link WFU_BPM ANALYZE, NIfTI-1, Win32 MS Windows, X11 Applications, Statistical Operation, End Users, WFU ANSIR License, Windows, POSIXUNIX-like, MATLAB, English, Beta http://www.nitrc.org/projects/wfu_bpm/ bwagner@wfubmc.edu Open Software License 3.0 Yes Simon Warfield, simon.warfield@childrens.harvard.edu NITRC MacOS,Linux,Windows Yes C Simon Warfield STAPLE is an algorithm for the Simultaneous Truth and Performance Level Estimation which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation by combination of the output of a group of segmentation algorithms and for segmentation by registration and template fusion. Further information is available at httpwww.crl.med.harvard.edu 2009-2-28 ProductionStable Version 1.4 STAPLE Linux, MacOS, Windows, Nrrd, GIfTI, ANALYZE, ProductionStable, C, Algorithm or Reusable Library, DICOM, NIfTI-1, Console Text Based, X11 Applications, Win32 MS Windows, English, Quantification, Segmentation, Image Display, Surface Rendering, End Users, Developers, Open Software License 3.0 http://www.nitrc.org/projects/staple/ simon.warfield@childrens.harvard.edu Brede Toolbox License Yes Finn Nielsen, fn@imm.dtu.dk NITRC OS Independent Yes MATLAB Finn Nielsen The Brede Toolbox is a package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization neuroimaging analysis of voxel or regional data. Among the algorithms implemented are kernel density estimation for coordinate-based meta-analysis independent component analysis non-negative matrix factorization k-means clustering singular value decomposition partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies and ontologies for e.g. brain function and brain regions. Brede Toolbox OS Independent, ANALYZE, Console Text Based, X11 Applications, Win32 MS Windows, English, ProductionStable, MATLAB, Independent Component Analysis, Ontology, Database Application, Principal Component Analysis, Regression, Brede Toolbox License, End Users, Developers http://www.nitrc.org/projects/bredetoolbox/ fn@imm.dtu.dk GNU Lesser General Public License LGPL Yes Elliot Hall, elliot.t.hall@vanderbilt.edu NITRC OS Independent,BSD,MacOS,Linux,SunOSSolaris,Windows Yes Java Elliot Hall Java Image Science Toolkit JIST provides a native Java-based imaging processing environment similar to the ITKVTK paradigm. Initially developed as an extension to MIPAV CIT NIH Bethesda MD the JIST processing infrastructure provides automated GUI generation for application plug-ins graphical layout tools and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. To participate in this consortium or seek assistance in integrating JIST modules in your application please contact us at jist-adminwww.nitrc.org. JIST was originally developed at IACL and MedIC Johns Hopkins University and is now also supported by MASI Vanderbilt University. 2012-5-09 Beta JIST Nightly Build automated 2011-5-09 Beta CRUISE-JIST Bundle for MIAPV 5.0.0-5.2.1 2011-5-09 Beta JIST BASE Bundle for MIAPV 5.0.0-5.2.1 2011-5-09 Beta JIST Bundle for MIAPV 5.0.0-5.2.1 2010-9-14 Beta 1.0 2010-8-19 Beta 2.0 2010-7-28 Beta Single Module CATNAP 2010-6-03 Beta Jist Beta 1.10 for MIPAV Nightly Release June 3 2010 or NEWER 2010-4-14 Beta JIST Beta 1.9 2010-4-05 Beta JIST Beta 1.8 2010-1-06 Beta CATNAP for JIST 1.6 2010-1-06 Beta Beta 1.6 2009-11-19 Beta Beta 1.5 2009-10-10 Beta Beta 2009-10-10 Beta Beta 1.4 2009-9-15 Beta Public Data 2009-9-15 Beta Pre-Beta 1.3 2009-9-14 Beta Initial Release 2009-8-27 Beta Pre-Beta 1.2 2009-8-27 Beta jist-Noise Field Estimation 2009-8-17 Beta Pre-Beta 1.1 2009-8-17 Beta JIST- CATNAP - Pre-Beta 2009-8-10 Beta Pre-Beta 1.0 JIST Java Image Science Toolkit Philips PARREC, X11 Applications, Other Environment, Console Text Based, English, Beta, Java, AFNI BRIK, ANALYZE, COR, DICOM, GIfTI, MGHMGZ, MINC, MINC2, NIfTI-1, Nrrd, Other Format, Experimental Control, Workflow, Segmentation, Developers, End Users, OS Independent, MacOS, Windows, Linux, BSD, SunOSSolaris, Quantification, Modeling, Spatial Transformation, Shape Analysis, GNU Lesser General Public License LGPL, Win32 MS Windows http://www.nitrc.org/projects/jist/ elliot.t.hall@vanderbilt.edu Yes John Bogovic, bogovic@jhu.edu NITRC John Bogovic This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available but it is not intended for any specific purpose. 2009-9-24 Binary Release all platforms JHU Proj. in Applied Medical Imaging http://www.nitrc.org/projects/iaclmedic/ bogovic@jhu.edu BIRN License Yes Daren Lee, dlee@loni.ucla.edu NITRC OS Independent Yes Java Daren Lee MBAT provides a workflow environment bringing together heterogenous online biological image resources a user’s image data and biological atlases in a concise unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it’s plugin architecture. MBAT integrates three distinct workspaces for online search image alignment registration and image display Search Workspace able to submit a query to multiple databases simultaneously and online literature searches. Registration Workspace performs 2D landmark based registration. Viewer Workspace displays amp;amp; composites images and image volumes using high performance graphics hardware. Atlas Viewer allows navigation and interrogation of volumetric atlases. Hierarchy Editor create logical groupings of atlas labels. 2008-1-24 Beta MBAT 2.0.13 MouseBIRN Atlasing Toolkit MBAT Information Resource, Beta, MR, Other Environment, Win32 MS Windows, Gnome, KDE, End Users, BIRN License, English, OS Independent, Java, ANALYZE, NIfTI-1 http://www.nitrc.org/projects/mbat/ dlee@loni.ucla.edu Presentation License Yes Neurobehavioral Systems Inc. , nbsweb@neurobs.com NITRC Windows NT2000,Windows Vista,Windows 95982000,Windows XP Yes Other Programming Language,C Neurobehavioral Systems Inc. Presentation® is a precise and powerful stimulus delivery and experimental control program for neuroscience. Presentation® runs on any Windows PC and delivers auditory visual and multimodal stimuli with sub-millisecond temporal precision. Presentation® includes special features for experiments using psychophysics eye movements fMRI ERP MEG single neuron recording and more. Presentation Experimental Control, Platform or Development Environment, Mature, MR, EEGMEGECoG, Win32 MS Windows, Developers, End Users, Presentation License, Windows 95982000, Windows NT2000, Windows Vista, Windows XP, C, Other Programming Language http://www.nitrc.org/projects/presentation/ nbsweb@neurobs.com GNU Lesser General Public License LGPL Yes I Dinov, iwaterpolo@gmail.com NITRC OS Independent Yes Java I Dinov The Statistics Online Computational Resources SOCR include the following suite of web-based Java applets Distributions interactive graphs and calculators Experiments virtual computer-generated games and processes Analyses collection of common web-accessible tools for statistical data analysis Games interfaces and simulations to real-life processes Modeler tools for distribution polynomial and spectral model-fitting and simulation Graphs Plots and Charts comprehensive web-based tools for exploratory data analysis Additional Tools other statistical tools and resources SOCR Java-based Statistical Computing Libraries. In addition SOCR provides a suite of tools for volume-based statistical mapping httpwiki.stat.ucla.edusocrindex.phpSOCR_EduMaterials_AnalysesCommandLine via command-line execution and via the LONI Pipeline workflows httpwww.nitrc.orgprojectspipeline. Statistics Online Computational Resource OS Independent, Other Format, Web Environment, English, Mature, End Users, LONI Pipeline, Java, Web Resource, GNU Lesser General Public License LGPL http://www.nitrc.org/projects/socr/ iwaterpolo@gmail.com WFU ANSIR License Yes Benjamin Wagner, bwagner@wfubmc.edu NITRC Linux Yes C,MATLAB,Unix Shell Benjamin Wagner The WFU SPM5 Pipeline is a fully automated method for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer archiving real-time SPM5 batch script generation with distributed grid processing automated error-recovery procedures full data-provenance email notifications optional conversion back to DICOM Digital Imaging and Communications in Medicine and picture archiving and communications systems PACS insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition. 2009-2-11 ProductionStable Installation Archive 2009-2-11 ProductionStable Sample Data 2009-2-11 ProductionStable User Manual WFU_Pipeline Linux, NIfTI-1, DICOM, ANALYZE, Console Text Based, X11 Applications, English, ProductionStable, MATLAB, Unix Shell, C, Workflow, WFU ANSIR License http://www.nitrc.org/projects/wfu_pipeline/ bwagner@wfubmc.edu Attribution Yes Timothy Herron, tjherron@ebire.org NITRC Yes Timothy Herron C8 is a small stand-alone MatLab toolbox that measures sagittal cross-section thickness and area of the human corpus callosum from high-resolution T1 in vivo MR images. C8 takes as input affine normalized white matter segmentations derived from high-resolution in-plane T1 images and outputs both regional callosal thicknesses in three different formats and geometrically-defined regional areas in three different configurations. It is a small package that is easily configurable and modifiable and it measures callosa at the rate of several per minute. 2011-7-29 July_2011 2011-5-05 May_5_2011 C8 Corpus Callosum Computations Attribution http://www.nitrc.org/projects/c8c8/ tjherron@ebire.org Yes Christian Haselgrove, ch@neuromorphometrics.com NITRC OS Independent Yes PHP Christian Haselgrove The IBVD provides a web-based searchable database of brain neuroanatomic volumetric observations. This is designed to access both group volumetric results as well as volume observations in individual cases. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies as well as meta-analysis. Extensions that permit pre-published non-published and other representation are planned again to facilitate comparative analyses. 2009-5-12 ProductionStable Stable_V1.0 Internet Brain Volume Database IBVD Database, Web Service, Volumetric Analysis, ProductionStable, CT, MR, Web Environment, End Users, English, OS Independent, PHP http://www.nitrc.org/projects/ibvd/ ch@neuromorphometrics.com NC-ICT Fast Imaging Library Contribution and Software License Yes Scott Hoge, shoge@bwh.harvard.edu NITRC MacOS,Linux,Windows C Scott Hoge This software provides algorithms for the reconstruction of raw MR data. In particular it supports the reconstruction of accelerated data acquisitions where k-space is subsampled and the Fourier domain encoding is complemented by temporal encoding spatial encoding or andor a constrained reconstruction. This library of functions provides a number of reconstruction algorithms that accurately employ advanced MR imaging methods including UNFOLD; parallel imaging methods such as SENSE and GRAPPA; Homodyne processing of partial-Fourier data and gradient field inhomogeneity correction. The target audience is research groups who may be interested in exploring or employing advanced MR reconstruction techniques but dont have the necessary expertise in-house. Inquires may be directed to ncigt-imaging-toolkit -at- bwh.harvard.edu NC-IGT Fast Imaging Library MacOS, Linux, Other Format, Windows, X11 Applications, Console Text Based, Other Environment, English, Beta, C, NC-ICT Fast Imaging Library Contribution and Software License, Image Reconstruction, Algorithm or Reusable Library, Developers http://www.nitrc.org/projects/igt_fil/ shoge@bwh.harvard.edu GNU General Public License GPL Yes Keiji Harada, kharada@atr.jp NITRC MacOS,Linux,Windows Yes MATLAB Keiji Harada Brain Decoder Toolbox performs “decoding” of brain activity by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent. 2011-8-03 Mature 1.0 2011-8-03 Mature 1.0 2011-8-03 Mature 1.2.1 BrainDecoderToolbox Console Text Based, Japanese, English, Mature, MATLAB, End Users, Other Audience, MacOS, Windows, Linux, Application, ANALYZE, Other Format, GNU General Public License GPL http://www.nitrc.org/projects/bdtb/ kharada@atr.jp NEMO License Yes Gwen Frishkoff, gfrishkoff@gsu.edu NITRC Yes Gwen Frishkoff We first provide a NEMO_spatial ontology for the public to annotate their EEGERP data. The URL is httpaimlab.cs.uoregon.eduNEMOontology1.0NEMO_spatial.obo Neural ElectroMagnetic Ontologies NEMO License http://www.nitrc.org/projects/nemo/ gfrishkoff@gsu.edu Yes Carolyn Lauzon, clauzon1@gmail.com NITRC Carolyn Lauzon The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically we are interested in population characterization with magnetic resonance imaging MRI multi-parametric studies DTI sMRI qMRI and shape modeling. This repository stores and provides opportunities for collaboration through Matlab code libraries and configuration information for projects in early stage development. 2011-7-07 SIMEX_DTI_DEMO 2011-2-10 label-fusion-v1 MASIMatlab http://www.nitrc.org/projects/masimatlab/ clauzon1@gmail.com LONI Software License Yes I Dinov, iwaterpolo@gmail.com NITRC Java,JavaScript I Dinov The Mouse Connectome Project MCPhttpwww.mouseconnectome.org aims to create a three-dimensional digital connectome atlas of the C57Black6J mouse brain. MCP offers a catalog of neural tracer injection cases which is updated continuously to eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome browser. Sample data set is available to explore in iConnectome. The data set features 5 layers which may be turned on off or adjusted for transparency and split window features are available for comparing data sets. The MCP project is housed at the Laboratory of Neuro Imaging at UCLA. Mouse Connectome Project MCP Other Format, ANALYZE, LONI Pipeline, Web Environment, English, Beta, Java, JavaScript, Developers, End Users, Atlas Data, Database, LONI Software License http://www.nitrc.org/projects/mcp/ iwaterpolo@gmail.com Attribution Non-Commercial Yes Marcus Kaiser, mail@mkaiser.de NITRC Marcus Kaiser Network nodes can be described by node-motifs--a combination of local network features. Certain node-motifs such as highly connected nodes or hubs have been shown to be important components of networks. Costa et al. 2009 have presented a technique to detect and specify more complex compound motifs which are characterised by multiple features in combination. We described improvements to that method and showed how its parameters can be determined automatically Echtermeyer et al. 2011. SIMONO is our implementation of the enhanced workflow which can be controlled via a graphical user interface or through the command-line for batch processing. Documentation is available at httpwww.biological-networks.orgpsinomo You can also directly download the MatlabOctave code following the link below. References L. D. F. Costa F. A. Rodrigues C. C. Hilgetag and M. Kaiser Europhys. Lett. 87 1 2009 C. Echtermeyer L. Da Fontoura Costa F. A. Rodrigues M. Kaiser PLoS ONE 6 9 2011 2012-1-30 2011 Release SINOMO SIngular NOde MOtifs Attribution Non-Commercial http://www.nitrc.org/projects/sinomo/ mail@mkaiser.de BSD License Yes Valerio Luccio, valerio.luccio@nyu.edu NITRC FreeBSD,Linux C Valerio Luccio Convert DICOM images to NIfTI format. dinifti FreeBSD, Linux, DICOM, NIfTI-1, ANALYZE, Console Text Based, English, ProductionStable, C, Format Conversion, BSD License, End Users http://www.nitrc.org/projects/dinifti/ valerio.luccio@nyu.edu Yes Karl Helmer, helmer@nmr.mgh.harvard.edu NITRC OS Independent Karl Helmer BIRN is a geographically distributed virtual community of shared resources to advance the diagnosis and treatment of disease. Its emphasis is on enabling the sharing of biomedical data through a suite of software capabilities. It currently consists of expertise in Data Movement Data Security Mediation Across Data Sources Knowledge Engineering Workflows and Genetics. The main BIRN site is at the Information Sciences Institute at USC with collborators at the University of Chicago the Massachusetts General Hospital University of California Irvine and University of California Los Angeles. Biomedical Informatics Research Network Knowledge Environment, Data Resource, Web Resource, ProductionStable, MR, Web Environment, Developers, End Users, English, OS Independent http://www.nitrc.org/projects/birn/ helmer@nmr.mgh.harvard.edu CeCill v2 Yes Denis Rivière, denis.riviere.gm@gmail.com NITRC MacOS,Linux,Windows C,Python Denis Rivière Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images meshes regions of interest fibers textures color palettes referential changes etc. A user can interact in 3D and in real time with the objects of an Anatomist scene change point of view select objects addsupress objects change colors draw regions of interests do manual registration etc. Anatomist Linux, MacOS, Windows, NIfTI-1, ANALYZE, DICOM, MINC, Other Format, X11 Applications, Win32 MS Windows, English, French, Mature, C, Python, Visualization, CeCill v2, End Users, Developers http://www.nitrc.org/projects/anatomist/ denis.riviere.gm@gmail.com GNU General Public License GPL Yes James Brinkley, brinkley@u.washington.edu NITRC James Brinkley MindSeer is a cross-platform application for 3D brain visualization. It is written in JavaJava3D and runs in both standalone and client-server mode. Click on the MindSeer Project Page for downloads tutorials source code demos and a publication. MindSeer GNU General Public License GPL http://www.nitrc.org/projects/mindseer/ brinkley@u.washington.edu NVM License Yes Andrew Worth, nitrc@neuromorphometrics.com NITRC MacOS,Linux,Windows Yes C Andrew Worth NVM is an open-source software tool for locating and measuring neuroanatomy in structural volumetric image data. It is used to draw regions of interest for subsequent fMRI analysis. 2007-9-30 Beta 1.93 NVM Win32 MS Windows, Morphology, Volumetric Analysis, Anatomic, Volumetric Analysis, Visualization, ANALYZE, bshortbfloat, COR, DICOM, Other Format, Beta, End Users, NVM License, X11 Applications, Linux, C, English, NIfTI-1, MacOS, Windows http://www.nitrc.org/projects/nvm/ nitrc@neuromorphometrics.com GNU General Public License GPL Yes , NITRC PHP The NeuroLex is being constructed to help improve the way that neuroscientists communicate about their data so that information systems like the NIF can find data more easily and provide more powerful means of integrating data that occur across distributed resources. One of the big roadblocks to data integration in neuroscience is the inconsistent use of terminology in databases and other resources like the literature. When we use the same terms to mean different things we cannot easily ask questions that span across multiple resources. For example if three databases have information about what genes are expressed in cortex but they all use different definitions of cerebral cortex then we cannot compare them easily. 2009-5-17 Beta Neurolex database dump NeuroLex Atlas Application, Other KE, Web Service, Beta, Domain Independent, Web Environment, GNU General Public License GPL, PHP http://www.nitrc.org/projects/incf_neurolex-w/ GNU General Public License GPL Yes Matthew Brett, matthew.brett@gmail.com NITRC OS Independent Yes MATLAB Matthew Brett MarsBaR MARSeille Boîte À Région dIntérêt is a toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition combination of regions of interest with simple algebra extraction of data for regions with and without SPM preprocessing scaling filtering and statistical analyses of ROI data using the SPM statistics machinery. MarsBaR region of interest toolbox OS Independent, NIfTI-1, ANALYZE, GNU General Public License GPL, Other Environment, English, ProductionStable, MATLAB, Linear, Developers, End Users http://www.nitrc.org/projects/marsbar/ matthew.brett@gmail.com GNU General Public License GPL Yes Bing Jian, bing.jian@gmail.com NITRC OS Independent Python Bing Jian This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data. It is a subset of the code internally used in the CVGMI lab at the University of Florida. Three different reconstruction methods are currently included in this program namely Mixture of Wisharts MOW Diffusion Orientation Transform DOT and Q-ball Imaging QBI. This program is mainly developed and maintained by Bing Jian as part of his Ph.D. research supervised by Prof. Baba Vemuri. Please note that the source code of this program is hosted at Google Code see the amp;quot;Source Codeamp;quot; link on the left. Multi-fiber Reconstruction from DW-MRI Console Text Based, English, Algorithm or Reusable Library, Diffusion MR Fiber Tracking, Python, Developers, OS Independent, GNU General Public License GPL http://www.nitrc.org/projects/diffusion-mri/ bing.jian@gmail.com Public Domain Yes Andrew Worth, nitrc@neuromorphometrics.com NITRC OS Independent Yes PHP Andrew Worth The Internet Brain Segmentation Repository IBSR provides manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the evaluation and development of segmentation methods. 2005-12-31 Beta 1.0 IBSR Data, Database, Knowledge Environment, Websites, Web Service, Quality Metrics, Test Data, Beta, MR, Web Environment, End Users, Public Domain, English, OS Independent, PHP http://www.nitrc.org/projects/ibsr/ nitrc@neuromorphometrics.com GNU Lesser General Public License LGPL Yes Aaron Carass, aaron_carass+nitrc@jhu.edu NITRC MacOS,POSIXUNIX-like,Microsoft Java Aaron Carass This repository stores plugins tutorial code and examples demonstrating MRI manipulation within the MIPAV plugin environment. This project is separate from JIST so that we can provide WRITE access to any interested party without overly exposing the infrastructure to unplanned modification. Please contact the administrators if you would like to join this project - open use is encouraged. 2009-9-24 Beta Binary Release all platforms JIST Resources for Algorithm Development bshortbfloat, COR, DICOM, GIfTI, MGHMGZ, MINC, MINC2, NIfTI-1, Nrrd, Microsoft, No InputOutput Daemon, Win32 MS Windows, X11 Applications, Java, English, Beta, Developers, End Users, LONI Pipeline, GNU Lesser General Public License LGPL, AFNI BRIK, ANALYZE, MacOS, POSIXUNIX-like, Other Format, Application, Platform or Development Environment, Other Software Resource http://www.nitrc.org/projects/jhumipavplugins/ aaron_carass+nitrc@jhu.edu MGH CSRL License Yes Joseph Mandeville, jbm@nmr.mgh.harvard.edu NITRC MacOS,Linux Yes C Joseph Mandeville Download jip-overview.pdf to see if these tools interest you. The JIP Toolkit was developed primarily for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables highly portable open-source c code and image resources that enable 1 Automated registration based upon mutual information affine non-linear warps with flexible control and visualization of each step; 2 visualization of 4-dimensional data using either mosaic or tri-planar display of the zslice dimension and integration of a general linear model for graphical display of time series analysis; 3 A simple and flexible 1st-order GLM for time series analysis plus a 2nd-order GLM analysis following the Worsley 2002 scheme and 4 MRI templates to place your rodent and non-human primate data into standardized spaces. 2011-1-16 Beta v2.1 2011-1-16 Beta v2.1 2011-1-16 Beta v2.1 2011-1-05 Beta v2.0 2011-1-05 Beta v2.0 2011-1-05 Beta v2.0 2011-1-05 Beta v2.0 2011-1-05 Beta v2.0 JIP fMRI Analysis Toolkit X11 Applications, Console Text Based, English, Beta, C, NIfTI-1, Other Format, End Users, Developers, Linux, MacOS, Atlas Application, Image-to-Image, Affine Warp, Nonlinear Warp, Resampling, Atlas Data, Time Domain Analysis, Image Display, MGH CSRL License http://www.nitrc.org/projects/jip/ jbm@nmr.mgh.harvard.edu BSD License Yes Mahshid Farzinfar, mahshid.lightmoon@gmail.com NITRC Linux,Windows XP Yes C Mahshid Farzinfar DTIPrep performs a amp;quot;Study-specific Protocolamp;quot; based automatic pipeline for DWIDTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes imagediffusion information check paddingCropping of data slice-wise interlace-wise and gradient-wise intensity and motion check head motion and Eddy current artifact correction and DTI computing. 2011-12-14 Pre-Alpha DTIPrep1.1.3 2011-12-09 Pre-Alpha DTIPrep_1.1.3_darwin_10.7 2011-11-03 Pre-Alpha DTIPrep1.1.2 2011-8-09 Pre-Alpha DTIPrep1.1.1 2011-8-09 Pre-Alpha DTIPrep1.1 2011-1-27 Pre-Alpha v1.0 2010-2-24 Pre-Alpha DTIPrepWorld Darwin_10.6 with Qt 4.6.1 2010-2-24 Pre-Alpha DTIPrepWorld Darwin10.5.8 Release with QT 4.6.1 DWIDTI Quality Control Tool DTIPrep Win32 MS Windows, X11 Applications, English, Pre-Alpha, Application, C, Nrrd, BSD License, End Users, Windows XP, Linux http://www.nitrc.org/projects/dtiprep/ mahshid.lightmoon@gmail.com BSD License Yes Michael Waskom, mwaskom@stanford.edu NITRC Michael Waskom PySurfer is a Python based program for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data. PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets. PySurfer MR, EEGMEGECoG, BSD License http://www.nitrc.org/projects/pysurfer/ mwaskom@stanford.edu Yes Aaron Carass, aaron_carass+nitrc@jhu.edu NITRC Aaron Carass Java Image Science Toolkit JIST is an extension to the MIPAV Medical Image Processing Analysis and Visualization plug-in framework that allows the user to design and execute pipelines which are multi-stage processing tasks. JIST was formerly known as the MedIC Automated Pipeline Scheduler MAPS. This is the exploratory development tree. New features and designs are tested here before general release into the JIST project. Access to the source code is freely given. However registration is required so that we can notify users of critical changes. For unrestricted access to the stable release see the JIST project. httpwww.nitrc.orgprojectsjist 2009-9-24 Binary Release all platforms 2009-4-17 Alpha 0.6 2009-3-27 Alpha 0.5 2009-2-23 Alpha 0.4 2009-2-09 Alpha 0.3 2009-2-03 Build Scripts 2009-1-12 Alpha 0.2 2008-12-01 Alpha 0.1 Maps4Mipav Exploratory JIST http://www.nitrc.org/projects/maps4mipav/ aaron_carass+nitrc@jhu.edu GNU General Public License GPL Yes Francois Tadel, francois.tadel@gmail.com NITRC OS Independent Yes Java,MATLAB Francois Tadel Brainstorm is a free Matlab application dedicated to MEG and EEG data visualization processing and cortical source estimation. Its rich and intuitive graphic interface does not require any programming knowledge or experience with Matlab. MEGEEG visualization and processing - Support for most of the common file formats for MEG EEG and MRI - Basic pre-processing frequency filtering resampling epoching baseline removal averaging etc. - Visualization of recordings time series 2D3D topographies - MRIEEGMEG co-registration - Database and powerful database explorer Source estimation - Forward modeling spherical models overlapping spheres BEM - Inverse modeling minimum norm beamformers - Visualization of sources cortex surface MRI volume Post-processing - Definition of clusters of electrodes - Regions of interests at cortical level - Group analysis registration of individual brains on a template - Statistical tests t-test permutations 2009-9-24 Beta Brainstorm3 daily update Brainstorm End Users, Developers, GNU General Public License GPL, OS Independent, MATLAB, Java, ANALYZE, NIfTI-1, MGHMGZ, Other Format, EEG Modeling, MEG Modeling, Visualization, Temporal Transformation, Time Domain Analysis, Database Application, Beta, EEGMEGECoG http://www.nitrc.org/projects/bst/ francois.tadel@gmail.com FNIR COBI Suite Yes Davood Tashayyod, davood@fnirdevices.com NITRC Davood Tashayyod fNIR Imager 1100 is a new generation portable functional near-infrared fNIR imaging research tool capable of monitoring brain’s hemodynamics and thereby the cognitive state of the subject in natural environments. Neuroimaging Solution for Natural Environments • fNIR is the only stand-alone and field-deployable technology able to determine localized brain activity. • fNIR can be readily integrated with other physiological and neurobehavioral measures that assess human brain activity including eye tracking pupil reflex respiration and electrodermal activity. fNIR can also complement other techniques. • Studies have shown a positive correlation between a participants performance and fNIR responses as a function of task load. • It has also been shown that fNIR can effectively monitor attention and working memory in real-life situations. fNIR Devices Physiological Recording, FNIR COBI Suite http://www.nitrc.org/projects/fnirdevices/ davood@fnirdevices.com Commercial License Yes Marcus Johnson, marcus@sr-research.com NITRC Marcus Johnson SR Research makers of the world leading EyeLink High-Speed eye tracker line have been developing advanced eye tracking technologies and serving world class support to our research user base since 1992. The EyeLink line provides eye tracking capabilities for behavioral labs as well as for MRI MEG and EEG environments. SR Research EyeLink Eye Trackers Response Monitoring, Eye Tracking, Commercial License http://www.nitrc.org/projects/srresearch/ marcus@sr-research.com E-Prime Extensions for fMRI Yes Psychology Software Tools, gretchen.archer@pstnet.com NITRC Windows Vista,Windows XP Psychology Software Tools E-Prime® Extensions for fMRI EEfMRI software is designed to optimize E-Prime® experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime® experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime®. E-Prime Extensions for fMRI Win32 MS Windows, English, ProductionStable, E-Prime Extensions for fMRI, End Users, Windows Vista, Windows XP, Experimental Control http://www.nitrc.org/projects/eefmri/ gretchen.archer@pstnet.com MITX Consortium License Yes Michael Hanke, michael.hanke@gmail.com NITRC OS Independent Python Michael Hanke The PyNIfTI module is a Python interface to the NIfTI IO libraries. Using PyNIfTI one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays. PyNIfTI ProductionStable, ANALYZE, NIfTI-1, Python, Developers, End Users, OS Independent, Algorithm or Reusable Library, MITX Consortium License http://www.nitrc.org/projects/pynifti/ michael.hanke@gmail.com BSD License Yes John Sullivan, sullivan@wpi.edu NITRC John Sullivan The MIVA software package Medical Image Visualization and Analysis is a powerful graphical interface that displays segments aligns manipulates and blends image pixel and geometry real-world coordinates data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive ROI and VOI tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator. Medical Image Visualization and Analysis BSD License http://www.nitrc.org/projects/miva/ sullivan@wpi.edu BSD License,BIRN License Yes Jinran Chen, jinranc@uci.edu NITRC Linux,Windows Yes Java,JavaScript Jinran Chen The Human Imaging Database HID is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. 2010-9-22 ProductionStable 2.2 2010-9-22 ProductionStable 2.2 2008-10-20 ProductionStable HID 1.6.3 2008-6-27 ProductionStable HID Graphical User Interface 1.6.2 2008-6-27 ProductionStable HID Oracle amp;amp; PostgreSQL Schemas 2008-6-27 ProductionStable Clinical Assessment Layout Manager CALM 1.6.2 2008-6-27 ProductionStable Clinical Assessment Layout Manager CALM Forms Repository Human Imaging Database HID Data, Database, Database Application, Workflow, Other, Other Web Resource, Other Software Resource, ProductionStable, CT, MR, PETSPECT, Web Environment, Developers, End Users, BSD License, BIRN License, English, Windows, Linux, Java, JavaScript, Other Format http://www.nitrc.org/projects/hid/ jinranc@uci.edu GNU General Public License GPL Yes Paul Yushkevich, pauly2@grasp.upenn.edu NITRC Yes Paul Yushkevich A software package described in the upcoming NeuroImage paper amp;quot;Nearly Automatic Segmentation of Hippocampal Subfields in In Vivo Focal T2-Weighted MRIamp;quot; by Yushkevich et al. httptinyurl.com2e5zwen 2010-6-30 Current Release Segmentation of Hippocampus Subfields GNU General Public License GPL http://www.nitrc.org/projects/ashs/ pauly2@grasp.upenn.edu GNU General Public License GPL Yes Karsten Tabelow, tabelow@wias-berlin.de NITRC MacOS,POSIXUNIX-like,Microsoft Yes Fortran,R Karsten Tabelow The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures. 2011-9-16 ProductionStable dti_0.9-6.2 for Windows 2011-9-16 ProductionStable dti 0.9-6.2 2010-10-12 ProductionStable dti 0.9-2.1 for Windows 2010-10-12 ProductionStable dti 0.9-2.1 2009-4-23 ProductionStable dti 0.8-0 for Windows 2009-4-23 ProductionStable dti 0.8-0 2009-2-13 ProductionStable dti 0.6-0 for Windows 2009-2-13 ProductionStable dti 0.6-0 R-package for adaptive DWI analysis MacOS, Microsoft, POSIXUNIX-like, AFNI BRIK, ANALYZE, NIfTI-1, DICOM, Console Text Based, English, ProductionStable, Fortran, R, GNU General Public License GPL, End Users http://www.nitrc.org/projects/rdti/ tabelow@wias-berlin.de BIRN License Yes Syam Gadde, gadde@biac.duke.edu NITRC MacOS,Linux,Other UNIX-like,Windows Yes C,Perl,C,shbash Syam Gadde A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulationconversion event-related analysis QA tools and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts. 2012-1-30 ProductionStable 1.9.11 2011-12-21 ProductionStable 1.9.10 2011-4-21 ProductionStable 1.9.9.5 2011-2-24 ProductionStable 1.9.9.4 2011-2-24 ProductionStable 1.9.9.3 2011-1-18 ProductionStable 1.9.9.2 2011-1-04 ProductionStable 1.9.9.1 2010-12-20 ProductionStable 1.9.9 2010-11-08 ProductionStable 1.9.8.9 2010-11-08 ProductionStable 1.9.8.8 2010-10-29 ProductionStable 1.9.8.7 2010-8-26 ProductionStable 1.9.8.6 2010-7-12 ProductionStable 1.9.8.5 2010-7-09 ProductionStable 1.9.8.4 2010-3-17 ProductionStable 1.9.8.3 2010-3-09 ProductionStable 1.9.8.2 2010-3-03 ProductionStable 1.9.8.1 2010-3-02 ProductionStable 1.9.8 2010-2-09 ProductionStable 1.9.7.3 2010-1-13 ProductionStable 1.9.7.2 2010-1-05 ProductionStable 1.9.7.1 2009-12-23 ProductionStable 1.9.7 2009-12-21 ProductionStable 1.9.6 2009-11-17 ProductionStable 1.9.5 2009-11-09 ProductionStable 1.9.4 2009-10-15 ProductionStable 1.9.3 2009-8-10 ProductionStable 1.9.2 2009-7-08 ProductionStable 1.9.1 2009-4-28 ProductionStable 1.9.0 2009-4-20 ProductionStable 1.8.65 2008-10-01 ProductionStable 1.8.64 2008-7-29 ProductionStable 1.8.63 BXHXCEDE Tools Format Conversion, Quantification, Statistical Operation, ProductionStable, MR, Console Text Based, Developers, End Users, BIRN License, English, Linux, Windows, MacOS, Other UNIX-like, C, C, Perl, shbash, ANALYZE, DICOM, MGHMGZ, MINC, NIfTI-1, Other Format http://www.nitrc.org/projects/bxh_xcede_tools/ gadde@biac.duke.edu BSD License Yes Clement Vachet, cvachet@unc.edu NITRC OS Independent Other Programming Language,C Clement Vachet DTI-Reg is an open-source C application that performs pair-wise DTI registration using scalar FA map to drive the registration. Individual steps of the pair-wise registration pipeline are performed via external applications - some of them being 3D Slicer modules. Starting with two input DTI images scalar FA maps are generated via dtiprocess. Registration is then performed between these FA maps via BRAINSFitBRAINSDemonWarp or ANTS -Advanced Normalization Tools- which provide different registration schemes rigid affine BSpline diffeomorphic logDemons. The final deformation is then applied to the source DTI image via ResampleDTI. 2011-11-23 Beta DTI-Reg_1.1.1 2011-11-21 Beta DTI-Reg_1.1 2011-11-16 Beta DTI-Reg_1.0 DTI-Reg BSD License, English, OS Independent, C, Other Programming Language, ANALYZE, Nrrd, Other Format, Workflow, Resampling, Registration, Beta, X11 Applications, Developers, End Users http://www.nitrc.org/projects/dtireg/ cvachet@unc.edu GNU General Public License GPL Yes Karsten Tabelow, tabelow@wias-berlin.de NITRC MacOS,POSIXUNIX-like,Microsoft Yes Fortran,R Karsten Tabelow The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution. 2011-9-16 ProductionStable fmri_1.4-5 for Windows 2011-9-16 ProductionStable fmri_1.4-5 2010-10-12 ProductionStable fmri 1.4-1 for Windows 2010-10-12 ProductionStable fmri 1.4-1 2009-4-23 ProductionStable fmri 1.3 for Windows 2009-4-23 ProductionStable fmri 1.3 2009-2-13 ProductionStable fmri 1.2-6 for Windows 2009-2-13 ProductionStable fmri 1.2-6 R-package for adaptive fMRI analysis AFNI BRIK, ANALYZE, NIfTI-1, DICOM, Console Text Based, End Users, POSIXUNIX-like, MacOS, Microsoft, English, ProductionStable, Fortran, R, GNU General Public License GPL http://www.nitrc.org/projects/rfmri/ tabelow@wias-berlin.de OtherProprietary License Yes , NITRC API and demo application for the ABA Mouse Brain data. Data available via the API includes download high resolution images expression data from a 3D volume 3D coordinates of the Allen Reference Atlas and searching genes with similar gene expression profiles using NeuroBlast. Allen Brain Atlas API OtherProprietary License, ProductionStable, Atlas Application http://www.nitrc.org/projects/incf_allen-brai/ Yes Bhaskar Kishore, bhaskar@jhu.edu NITRC Bhaskar Kishore NeuroWeb provides infrastructure for data aggregation processing and management in multi-dimensional medical imaging research i.e. MRI CT PET. NeuroWeb is designed for rapid deployment on a smallmoderate scale with limited hardware. NeuroWeb - NeuroImaging Database CT, MR, PETSPECT http://www.nitrc.org/projects/neuroweb/ bhaskar@jhu.edu Mozilla Public License Yes Fabienne Lathuiliere, Fabienne.Lathuiliere@elekta.com NITRC Fabienne Lathuiliere TAPIR Tools for Advanced Parameterized Image Registration is a set of command line tools allowing 2D and 3D image registration mainly for medical imaging although also relevant to other image registration problems. TAPIR Mozilla Public License http://www.nitrc.org/projects/tapir/ Fabienne.Lathuiliere@elekta.com MITX Consortium License Yes Mark Pearrow, mjp@mit.edu NITRC OS Independent Yes Python,MATLAB Mark Pearrow RapidArt provides software for detecting artifacts and performing individual region-of-interest ROI based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed consistent and reliable results. 2009-2-09 Alpha matlabart-0.1 RapidArt English, Alpha, NIfTI-1, Python, MATLAB, End Users, OS Independent, Algorithm or Reusable Library, MITX Consortium License http://www.nitrc.org/projects/rapidart/ mjp@mit.edu Yes Luis Ibanez, luis.ibanez@kitware.com NITRC Luis Ibanez The goal of the project is to provide an open source implementation of a non-rigid groupwise registration method. This project is implemented by Serdar K Balci serdar at csail.mit.edu and supervised by Polina Golland William M. Wells All metrics are implementing in a multi-threaded fashion. The algorithm will run faster on computers with multiple CPUs. Non-rigid groupwise registration method http://www.nitrc.org/projects/groupwisereg/ luis.ibanez@kitware.com MITX Consortium License Yes Yaroslav Halchenko, yoh@onerussian.com NITRC OS Independent Yes Python,C Yaroslav Halchenko PyMVPA is a Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification regression feature selection data import and export. While it is not limited to the neuroimaging domain it is eminently suited for such datasets. PyMVPA is truly free software in every respect and additionally requires nothing but free-software to run. 2011-3-04 Beta 0.6 PyMVPA Multivariate Analysis, Console Text Based, Nonlinear, Linear, Principal Component Analysis, Algorithm or Reusable Library, MITX Consortium License, X11 Applications, English, Beta, Python, C, ANALYZE, NIfTI-1, Other Format, Developers, End Users, OS Independent, Modeling, Temporal Transformation, Workflow, Independent Component Analysis, Frequency Domain http://www.nitrc.org/projects/pymvpa/ yoh@onerussian.com 3D Slicer License Yes Guorong Wu, grwu@med.unc.edu NITRC Guorong Wu HAMMER is an acronym for Hierarchical Attribute Matching Mechanism for Elastic Registration Dinggang Shen Christos Davatzikos HAMMER Hierarchical Attribute Matching Mechanism for Elastic Registration IEEE Trans. on Medical Imaging 21111421-1439 Nov 2002 - an elastic registration algorithm for medical images matching morphological signatures of images in a hierarchical multi-scale regime. White matter lesion WML segmentation is a novel multi-spectral WML segmentation protocol via incorporating information from T1-w T2-w PD-w and FLAIR MR brain images. Zhiqiang Lao Dinggang Shen Dengfeng Liu Abbas F Jawad Elias R Melhem Lenore J Launer Nick R Bryan Christos Davatzikos Computer-Assisted Segmentation of White Matter Lesions in 3D MR images Using Pattern Recognition Academic Radiology 153300-313 March 2008. 2011-11-18 Complete package of HAMMER V_1.0 2011-11-14 WMLSeg_Manual 2011-11-11 Development document of HAMMER 2011-11-11 Tutorial for HAMMER in 3D Slicer 2011-2-11 WMLSeg_SourceCode 2010-7-09 WMLSeg_Slicer_Tutorial 2010-7-09 WMLSeg_TEST_DATA 2010-7-09 HAMMER_TEST_DATA 2010-7-09 HAMMER_ITK_VERSION Hammer And WML Modules for 3D Slicer 3D Slicer License http://www.nitrc.org/projects/hammerwml/ grwu@med.unc.edu CIGAL License Yes Syam Gadde, gadde@biac.duke.edu NITRC Syam Gadde CIGAL is a program that provides accurate real-time stimulus control behavioral and physiological recording and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings e.g. screen color and a list of stimulus events which can include images animated movies sound files text stimuli video graphics or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL’s real-time programming capabilities. Output files can be automatically created in a variety of output formats e.g. FSL 3-column files XML Events files CSV trial tables. 2011-10-17 CIGALVSync downloader CIGAL CIGAL License http://www.nitrc.org/projects/cigal/ gadde@biac.duke.edu SBIA License Yes Bilwaj Gaonkar, Bilwaj.Gaonkar@uphs.upenn.edu NITRC Bilwaj Gaonkar Brain lesions appear in different brain diseases as well as in normal aging; they can be due to small vessel disease infarcts MS or other reasons. MRI is used as surrogate imaging marker as MRI signal changes reflect certain aspects of brain pathology.Computer algorithms have started to complement expert-readings of MRI as they may improve throughput and consistency in addition to providing more accurate quantitative measures of lesion type and volume. Computerized segmentation methods can also offer more precise measurements of longitudinal change of a lesion with disease progression or treatment response. The brain lesion segmentation tool uses image analysis and machine learning techniques Support Vector Machines. Image intensities from multiple MR acquisition protocols after coregistration are used to form a voxel-wise attribute vector which is used to perform the segmentation. Primary Contact Christos Davatzikos Contributors Zhiqiang Lao Dinggang Shen Eva ZacharakiNick Bryan 2008-12-29 WMLS1.2 Brain lesion segmentation tool using SVM SBIA License http://www.nitrc.org/projects/wmls/ Bilwaj.Gaonkar@uphs.upenn.edu Yes Psychology Software Tools, gretchen.archer@pstnet.com NITRC Windows Vista,Windows XP Other Programming Language Psychology Software Tools VR Worlds 2 is designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs. Create complex environments with meaningful content using VR Worlds 2’s user-friendly drag-and-drop interface. Include triggers to launch simple or intricate events such as a conversation between characters or a customizable rating scale. VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments including ResidentialUrban Area Hotel Lobby Medical Office Grocery Store VR Worlds 2 Win32 MS Windows, English, ProductionStable, Other Programming Language, Other Format, End Users, Developers, Windows Vista, Windows XP, Experimental Control http://www.nitrc.org/projects/vr2/ gretchen.archer@pstnet.com BSD License Yes Eun Young Kim, eunyoung-kim@uiowa.edu NITRC OS Independent,MacOS,POSIXUNIX-like,Windows Yes C Eun Young Kim NOTE All active development of BRAINSConstellationDetector is now being stored in a Git repository at github.com. Please go to httpsgithub.comBRAINSiaBRAINSStandAlone A program for registering images with with mutual information based metric. Several registration options are given for 36 91216 parameter i.e. translate rigid scale scaleskew full affine based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3 2008-7-25 ProductionStable BinaryRelease 2008-3-14 ProductionStable SlicerIntegrationRelease BRAINSFit POSIXUNIX-like, NIfTI-1, DICOM, ANALYZE, Other Format, Console Text Based, Intermodal, Intersubject, Affine Warp, Linear Warp, English, ProductionStable, End Users, Developers, Other Audience, BSD License, OS Independent, Windows, C, MacOS http://www.nitrc.org/projects/multimodereg/ eunyoung-kim@uiowa.edu LONISVE Terms of Use Yes David Shattuck, shattuck@loni.ucla.edu NITRC OS Independent Yes David Shattuck The Segmentation Validation Engine SVE provides an automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes skull-strip them with the algorithm of their choice and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server and the measures are viewable by visitors to the site. Details on the methodology can be found in the following paper Shattuck DW Prasad G Mirza M Narr KL and Toga AW in press Online Resource for Validation of Brain Segmentation Algorithms NeuroImage e-pub available online Nov. 25 2008 doi10.1016j.neuroimage.2008.10.066. 2008-11-29 ProductionStable SVE Segmentation Validation Engine OS Independent, ANALYZE, DICE Coefficient, Tanomoto Coefficient, LONISVE Terms of Use, NIfTI-1, Web Environment, English, ProductionStable, End Users, Developers, Web Service, Quality Metrics http://www.nitrc.org/projects/sve/ shattuck@loni.ucla.edu NYUMC FireVoxel-BrainMask Software License Agreement Yes Henry Rusinek, hr18@nyu.edu NITRC Windows XP Yes C Henry Rusinek Segmentation of the brain from three-dimensional MR images is a crucial pre-processing step in morphological and volumetric brain studies. BrainMask implements a fully automatic brain segmentation algorithm that uses advanced amp;quot;thresholding with morphologyamp;quot; and 3D edge detection algorithms. BrainMask demonstrates high segmentation accuracy. For a representative 26 datasets the segmentation error averaged 3.4% ± 1.3% Mikheev A et al. J Magn Reson Imag 2761235-41;2008. BrainMask includes NNN - a tool based on the algorithm developed by John Sled for correcting the intensity non-uniformity in MR data Sled JG et al. IEEE Trans Med Imag 17187-97;1998. BrainMask also includes a versatile DICOM wiewer and allows to selectively load and organize DICOM images into 3D and 4D datasets. 2009-10-15 ProductionStable build 62A 2009-5-27 ProductionStable build 57F BrainMask Volume Processing Tool Windows XP, NYUMC FireVoxel-BrainMask Software License Agreement, End Users, DICOM, ANALYZE, bshortbfloat, Other Format, Win32 MS Windows, English, ProductionStable, Mature, C, Volume Measurement, Region of Interest, Volumetric Analysis, Image Display, Constrained Region Growing http://www.nitrc.org/projects/brainmask/ hr18@nyu.edu Attribution Yes David Kennedy, dave@dnkc.net NITRC Yes David Kennedy The Child and Adolescent NeuroDevelopment Initiative CANDI at UMass Medical School is making available a series of structural brain images as well as their anatomic segmentations demographic and behavioral data and a set of related morphometric resources. 2011-12-04 Beta SchitzBull_Atlas_V1.0 2011-7-08 Beta ImgSeg_V1.1 2010-7-27 Beta SS_1.0 2010-7-27 Beta BPDwithPsy_1.0 2010-7-07 Beta BPDwithoutPsy_1.0 2010-7-01 Beta HC_1.0 CANDI Neuroimaging Access Point Data, Knowledge Environment, Web Resource, Atlas Data, Volumetric Analysis, Segmentation, Beta, MR, Web Environment, End Users, Attribution, English, NIfTI-1 http://www.nitrc.org/projects/candi_share/ dave@dnkc.net BSD License Yes Michael Hanke, michael.hanke@gmail.com NITRC Yes Michael Hanke NiBabel is a Python package for reading and writing a variety of medical and neuroimaging file formats. This includes ANALYZE plain SPM99 SPM2 NIfTI1 as well as MINC. NiBabel is the successor of PyNIfTI. NIPY File IO BSD License http://www.nitrc.org/projects/nibabel/ michael.hanke@gmail.com Attribution Yes , NITRC Yes Here you can download image volumes representing the canonical Waxholm Space WHS mouse brain. These images include T1- T2- and T2-Weighted MR volumes generated at the Duke Center for In-Vivo Microscopy Nissl-stained optical histology acquired at Drexel and a label volume describing 37 structures. All volumes are represented at 21.5μ isotropic resolution. 2009-9-14 Beta Label Volume 2009-9-14 Beta Nissl-stained Optical Histology Atlas 2009-9-14 Beta T2-Weighted Atlas 2009-9-14 Beta T2-Weighted Atlas 2009-9-12 Beta T1-Weighted Atlas Waxholm Space Atlas Attribution, Beta, Atlas Application http://www.nitrc.org/projects/incf_waxholm-sp/ MagPro Medical Device License Yes Kerry Rome, kr@magventure.com NITRC Kerry Rome MagPro is a complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology neurology cognitive neuroscience rehabilitation and psychiatry. MagPro Magnetic Stimulator TMS Microsoft Word Document, Stimulus Presentation, Response Monitoring, MagPro Medical Device License http://www.nitrc.org/projects/magpro/ kr@magventure.com GNU General Public License GPL Yes Erik Türke, tuerke@cbs.mpg.de NITRC Erik Türke Lipsia is a software tool for processing functional magnetic resonance imaging fMRI data. It was developed over the course of several years at the Max-Planck-Institute for Human Cognitive and Brain Sciences in Leipzig Germany. Lipsia contains software tools for all aspects of fMRI data processing registration and normalization preprocessing exploratory processing statistical evaluation region of interest analysis timecourse analysis visualization rendering converters to various data formats It was developed in CC on Linux PCs. Lipsia provides extremely fast implementations. A standard analysis sequence from the raw data to a statistical parametric map generally takes less than 10 minutes per test subject. Lipsia GNU General Public License GPL http://www.nitrc.org/projects/lipsia/ tuerke@cbs.mpg.de 3D Slicer License Yes Carlos S. Mendoza, carlos.sanchez.mendoza@gmail.com NITRC Carlos S. Mendoza The modules in the framework support different tasks in the segmentation realization in 3DSlicer. A module called Level-set label map evolver was developed which takes an initial label image and a feature image as input and performs a Geodesic Active Contours evolution on the label image according to the feature image and to a different terms in the level-set equation. The evolution takes place for a customizable number of iterations. The output is a label image that can be used to produce a model. Other modules were developed to accompany the main module as can be seen in httpwww.slicer.orgslicerWikiindex.phpSlicer3ModuleLevel-Set_Segmentation_Framework-Documentation 2008-12-10 devel 2008-12-10 devel 2008-12-10 devel 2008-12-10 devel Level-set Segmentation for Slicer3 3D Slicer License http://www.nitrc.org/projects/levelsetslicer3/ carlos.sanchez.mendoza@gmail.com MGH CSRL License Yes Matti Hamalainen, msh@nmr.mgh.harvard.edu NITRC MacOS,Linux Yes MATLAB,C Matti Hamalainen The MNE software has been developed to compute cortically-constrained L2 minimum-norm current estimates and associated dynamic statistical parametric maps from MEG and EEG data optionally constrained by fMRI. This software includes MEG and EEG preprocessing tools interactive and batch-mode modules for the forward and inverse calculations as well as various data conditioning and data conversion utilities. This is a subproject of the Center for Functional Neuroimaging Techniques httpwww.nitrc.orgprojectscfnt 2008-10-21 Beta 2.5.2 MNE - Minimum Norm Current Estimates Forward - Inverse, Time Domain Analysis, Temporal Transformation, Beta, EEGMEGECoG, X11 Applications, End Users, MGH CSRL License, English, Linux, MacOS, C, MATLAB, Other Format, MGHMGZ http://www.nitrc.org/projects/mne/ msh@nmr.mgh.harvard.edu MINC Licence BSDish Yes Andrew Janke, a.janke@gmail.com NITRC Yes Andrew Janke nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data the method can be applied at an early stage in an automated data analysis before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization N3 the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction. 2009-5-08 N3-1-11-0 N3 - MINC B0 nonuniformity correction MINC Licence BSDish http://www.nitrc.org/projects/nu_correct/ a.janke@gmail.com BIRN License Yes Seth Ruffins, sruffins@loni.ucla.edu NITRC Yes Seth Ruffins The Mouse BIRN Testbed is helping scientists study neurodegenerative diseases by marshaling multi-modal data from the mouse as an animal model to investigate neurological disorders. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. Mouse BIRN MR, BIRN License http://www.nitrc.org/projects/mousebirn/ sruffins@loni.ucla.edu GNU General Public License GPL Yes Rob Ellis, robjellis@gmail.com NITRC Rob Ellis amp;quot;imcalcamp;quot; is an image calculator with batch functionality for SPM5SPM8. Options 1 binarize non-zero voxels; 2 binarize each image to a unique threshold; 3 binarize each image to a unique threshold then sum; 4 binarize non-zero voxels then sum; 5 binarize non-zero voxels sum rebinarize; 6 pairwise operation add sub mult div ... etc.; 7 flip sign of all non-zero voxels; 8 flip image along x-axis; 9 mask images to a template; 10 T-to-Z transform; 11 cap positivenegative values. For a screenshot visit httptools.robjellis.net 2012-1-31 imcalc_2012.01.29 imcalc SPM batch image calulator Statistical Operation, GNU General Public License GPL http://www.nitrc.org/projects/imcalc/ robjellis@gmail.com BSD License Yes Kevin Archie, karchie@npg.wustl.edu NITRC Java Kevin Archie DicomBrowser is a platform-independent desktop tool for inspecting DICOM header fields editing DICOM header fields viewing DICOM images and transferring DICOM files to a DICOM receiver. DicomBrowser includes scriptable header editing to support various de-identification protocols. Dicomrowser is written in Java and uses ImageJ for image viewing and the dcm4che toolkit for much of its DICOM implementation. For more information httpnrg.wustl.edusoftwaredicom-browser 2012-1-06 1.5.0 2009-7-13 1.4 Java Web Start DicomBrowser Other Software Resource, End Users, System Administrators, BSD License, Java, DICOM http://www.nitrc.org/projects/dicom_browser/ karchie@npg.wustl.edu Freeware Yes Xu Cui, cuixiaofei@gmail.com NITRC OS Independent,Linux,Windows XP MATLAB Xu Cui xjView is a viewing program for SPM2 and SPM5. p-value slider displays multiple images at a time and can be used to build ROI masks. For a given region you can find the anatomical name and search the selected region in online database wiki google scholar and pubmed. 2008-12-05 Mature xjview4 xjView a viewing tool for SPM Windows XP, Linux, OS Independent, ANALYZE, NIfTI-1, Other Environment, English, Mature, End Users, MATLAB, Image Display, Freeware http://www.nitrc.org/projects/xjview/ cuixiaofei@gmail.com GNU Lesser General Public License LGPL Yes Jonathan Farrell, jonfarrell@jhu.edu NITRC MacOS,POSIXUNIX-like,Microsoft Java,MATLAB Jonathan Farrell The DW-MRI Random Walk Simulator provides a simple interface to simulate Brownian motion in arbitrary complex environments. The analysis routines enable visualization of these models with DTI q-space and higher order diffusion weighted MRI.. 2009-3-17 Beta Compiled Bundle DW-MRI Random Walk Simulator Other Environment, Java, MATLAB, English, Beta, End Users, Developers, GNU Lesser General Public License LGPL, Random Walk, Monte Carlo, Simulation, Other Software Resource, MacOS, Microsoft, POSIXUNIX-like http://www.nitrc.org/projects/randomwalks/ jonfarrell@jhu.edu iBrain™ Licence Yes David Abbott, iBrain@brain.org.au NITRC MacOS,POSIXUNIX-like,Windows Other Programming Language David Abbott iBrain™ is an easy-to-use processing and visualisation platform designed to explore functional fMRI and other neuroimaging data. iBrain can be used stand-alone or in conjunction with other analysis packages e.g. SPM8. 2011-9-05 Mature Version 5.4c iBrain™ Region of Interest, Volumetric Analysis, Resampling, Linear, Motion Analysis, Correlation, Visualization, Algorithm or Reusable Library, Position, Frequency Domain, Intensity Operations, Quality Metrics, iBrain™ Licence, Volumetric Analysis, X11 Applications, Win32 MS Windows, Other Environment, English, Mature, ANALYZE, DICOM, MINC, NIfTI-1, Other Format, Other Programming Language, End Users, POSIXUNIX-like, MacOS, Windows, Format Conversion http://www.nitrc.org/projects/ibrain/ iBrain@brain.org.au Attribution Non-Commercial Yes Paul Mazaika, mazaika@stanford.edu NITRC OS Independent Yes MATLAB Paul Mazaika ArtRepair is a toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects. The toolbox includes special algorithms for motion adjustment data repair and noise filtering and methods to find outlier subjects in group studies. Visualization tools are included for quality checking the data including a movie format for viewing all data and all contrast estimates on every voxel of every subject. Methods are included to quantify results into percent signal change. ArtRepair for robust fMRI Image Display, Quality Metrics, Attribution Non-Commercial, End Users, OS Independent, NIfTI-1, ANALYZE, X11 Applications, English, Beta, MATLAB, Algorithm or Reusable Library, Motion Analysis, Artifact Removal http://www.nitrc.org/projects/art_repair/ mazaika@stanford.edu GNU General Public License GPL Yes Mary Raven, m_raven@lifesci.ucsb.edu NITRC OS Independent Yes MATLAB Mary Raven Spatial Analysis 3D is a user-friendly graphical user interface GUI that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns. The analyses use files containing sets of X Y Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X Y Z coordinates for program exploration and modeling purposes. Spatial Analysis 3D ProductionStable, MATLAB, Simulation, Statistical Operation, Position, GNU General Public License GPL, End Users, OS Independent, English http://www.nitrc.org/projects/sa3d/ m_raven@lifesci.ucsb.edu Web Application - Free to use Yes Marc Rousseau, marc.rousseau@mcgill.ca NITRC OS Independent Other Programming Language,Ruby,JavaScript Marc Rousseau BrainBrowser httpsbrainbrowser.cbrain.mcgill.ca is a web-enabled brain surface viewer that allows the user to explore in real time a 3D brain map expressed on a base surface. BrainBrowser has two modes of operation exploring either a pre-calculated database of structural correlation maps or working with user-defined data. In this mode the user may choose to explore the correlation structure for cortical thickness cortical area or cortical volume or any other pre-calculated metric. In the second mode the user is prompted for the local filenames of the statistical map and the base surface. BrainBrowser can also be used to manipulate 3D fibre pathways derived from DTI using the same simple file format .obj as for surface data. BrainBrowser on Youtube httpwww.youtube.comwatchv=HlRTUYUf1Ew NOTE BrainBrowser requires a WebGL-enabled browser such as Google Chrome to support its 3D graphics capability. BrainBrowser Web Environment, English, Beta, Ruby, JavaScript, Other Programming Language, End Users, OS Independent, Web Application - Free to use, Three Dimensional Display, Surface Rendering, Volume Rendering, Two Dimensional Display, Data, Web Resource, MINC2, NIfTI-1, Other Format http://www.nitrc.org/projects/brainbrowser/ marc.rousseau@mcgill.ca MITX Consortium License Yes Darcy Mason, darcymason@gmail.com NITRC OS Independent Yes Python Darcy Mason pydicom is a pure python package for working with DICOM files. It was made for inspecting and modifying DICOM data in an easy amp;quot;pythonicamp;quot; way. The modifications can be written again to a new file. As a pure python package it should run anywhere python runs without any other requirements. Pydicom DICOM, Console Text Based, Other Environment, English, ProductionStable, Python, Developers, OS Independent, Algorithm or Reusable Library, MITX Consortium License http://www.nitrc.org/projects/pydicom/ darcymason@gmail.com MGH CSRL License Yes Rick Hoge, r.hoge@umontreal.ca NITRC MacOS Yes Objective C Rick Hoge NeuroLens is an integrated environment for the analysis and visualization of functional neuroimages. 2008-3-10 ProductionStable 1.7.3 NeuroLens English, ProductionStable, End Users, MGH CSRL License, Objective C, MacOS, AFNI BRIK, ANALYZE, COR, DICOM, MGHMGZ, MINC, Other Format, Other Environment, Three Dimensional Display, Surface Rendering, Image-to-Image, Linear, Temporal Convolution - Deconvolution, Multivariate Analysis http://www.nitrc.org/projects/nldo/ r.hoge@umontreal.ca Freeware Yes Gary Boas, gboas@nmr.mgh.harvard.edu NITRC Windows NT2000,MacOS,Linux,Other UNIX-like Yes C Gary Boas Optseq is a tool for automatically scheduling events for rapid-presentation event-related RPER fMRI experiments the schedule is the order and timing of events. Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation expectation and set because the subject does not know when the next stimulus will appear or which stimulus type it will be. RPER is also more efficient than fixed-interval event related FIER because more stimuli can be presented within a given scanning interval at the cost of assuming that the overlap in the hemodynamic responses will be linear. In SPM parlance RPER is referred to as stochastic design. This is a subproject of the Center for Functional Neuroimaging Techniques httpwww.nitrc.orgprojectscfnt 2008-10-20 ProductionStable 2.0 Optseq - fMRI Event Scheduler Experimental Control, ProductionStable, MR, Console Text Based, End Users, Freeware, English, Linux, Other UNIX-like, MacOS, Windows NT2000, C http://www.nitrc.org/projects/optseq/ gboas@nmr.mgh.harvard.edu MINC Licence BSDish Yes Andrew Janke, a.janke@gmail.com NITRC OS Independent Yes Perl,Fortran,C,shbash Andrew Janke MINC is primarily a file format and a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. 2009-6-12 ProductionStable 2.0.18 2008-10-22 ProductionStable 2.0.16 2006-11-29 ProductionStable 1.5.1 2006-11-12 ProductionStable 1.5 2006-11-12 ProductionStable 2.0.12 2006-6-28 ProductionStable 2.0.11 2006-4-18 ProductionStable 2.0.10 2005-7-18 ProductionStable 2.0.09 2005-7-18 ProductionStable 2.0 2005-6-01 ProductionStable 1.4 2005-1-27 ProductionStable 2.0.08 2004-6-06 ProductionStable 2.0.07 2004-4-29 ProductionStable 2.0.06 MINC - Medical Image NetCDF MINC, MINC2, Other Environment, English, ProductionStable, C, Fortran, Perl, shbash, Developers, OS Independent, Algorithm or Reusable Library, File Format, MINC Licence BSDish http://www.nitrc.org/projects/minc/ a.janke@gmail.com GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov MultiTracer httpwww.loni.ucla.eduSoftwareMultiTracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. MultiTracer is distributed by the Laboratory of Neuro Imaging httpwww.LONI.ucla.eduSoftwareMultiTracer at UCLA. MultiTracer GNU General Public License GPL http://www.nitrc.org/projects/multitracer/ iwaterpolo@gmail.com Yes Shawn Mikula, brainmaps@gmail.com NITRC Shawn Mikula BrainMaps.org is an interactive multiresolution next-generation brain atlas that is based on over 20 million megapixels of sub-micron resolution annotated scanned images of serial sections of both primate and non-primate brains. BrainMaps.org http://www.nitrc.org/projects/brainmaps/ brainmaps@gmail.com BrainMap License Yes Mick Fox, foxm@uthscsa.edu NITRC OS Independent Yes Java Mick Fox The Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach atlas. 2008-10-10 Mature Talairach Client 2.4.2 2007-10-03 Mature Talairach Client 2.4 Talairach Daemon Database Application, Atlas Application, Other Format, OS Independent, Java, English, Mature, End Users, BrainMap License http://www.nitrc.org/projects/tal-daemon/ foxm@uthscsa.edu OASIS,GNU General Public License GPL Yes Matthew Kempton, matthew.kempton@kcl.ac.uk NITRC Matthew Kempton The Brain Segmentation Testing Protocol Neuroimage 2011 httpdx.doi.org10.1016j.neuroimage.2011.06.080 is a freely available collection of MRI images for testing segmentation algorithms. The 312 MRI datasets may be downloaded to assess the accuracy reproducibility and sensitivity of MRI segmentation software. The accuracyvalidation dataset includes images from infants adults and patients with Alzheimer’s disease and the reproducibility dataset includes 9 subjects who have been scanned with 8 different sequences at 1.0T and 3.0T. 2011-12-15 BSTP v1 Brain Segmentation Testing Protocol Data, Segmentation, OASIS, GNU General Public License GPL, ANALYZE, NIfTI-1, Test Data http://www.nitrc.org/projects/bstp/ matthew.kempton@kcl.ac.uk GNU General Public License GPL Yes Ping Gu, ping@brainvis.wustl.edu NITRC Linux Java,C Ping Gu SumsDB is a repository of neuroimaging data surfaces amp;amp; volumes; structural amp;amp; functional data mainly from humans and macaques but also mouse rat and great apes. WebCaret is an online visualization tool for viewing SumsDB datasets. Visit the ToolResource Home Page for more information. SumsDB Database Web Environment, AFNI BRIK, ANALYZE, NIfTI-1, Other Format, Database Application, Surface Analysis, C, Java, Linux, Database, Atlas Application, Surface Rendering, Registration, Volume Rendering, English, ProductionStable, End Users, GNU General Public License GPL http://www.nitrc.org/projects/sumsdb/ ping@brainvis.wustl.edu Yes Ben Rogers, ben-rogers@uiowa.edu NITRC Ben Rogers UploadGUI is a Java tool that takes an unorganized collection of DICOM scans sorts and categorizes them according to user-customizable rules gathers metadata about the scans and saves out this information to help facilitate data uploads. Batch pr DICOM_UploadGUI http://www.nitrc.org/projects/dicomuploadgui/ ben-rogers@uiowa.edu GNU General Public License GPL Yes Christian Kothe, christiankothe@gmail.com NITRC Christian Kothe BCILAB is a MATLAB toolbox for Brain-Computer Interface BCI research. It facilitates the design and development of new methods for cognitive state estimation and their use in both offline data analysis and real-time applications. BCILAB includes an easily extensible collection of currently over 100 methods from the literature covering signal processing machine learning and BCI-specific methods. Aside from supporting advanced BCI research a special aim of BCILAB is to facilitate the adoption of machine learning and advanced statistical modeling for functional neuroimaging purposes in tandem with the EEGLAB platform. 2012-1-06 1.0-beta BCILAB GNU General Public License GPL http://www.nitrc.org/projects/bcilab/ christiankothe@gmail.com IIT Human Brain Template License Yes Konstantinos Arfanakis, arfanakis@iit.edu NITRC Yes Konstantinos Arfanakis The IIT2 diffusion tensor template of the human brain was developed using artifact-free Turboprop-DTI data collected on 67 subjects. The template is in ICBM-152 space allowing use of ICBM resources. Advantages of the IIT2 template a constructed based on a large number of subjects with a limited age-range b no artifacts c even small white matter structures are visible d high image sharpness e low noise levels f DTI information that is representative of single-subject data g excellent matching to ICBM-152 space. The following information is provided in NIfTI format and 1mm isotropic resolution Mean DW and b=0 maps. Mean and median tensors. FA trace eigenvalues eigenvectors of mean and median tensors. Standard deviation of mean and median FA and trace cone of uncertainty and total variance of mean and median tensors. When using the IIT2 template please cite Zhang S Peng H Dawe RJ Arfanakis K. Enhanced ICBM diffusion tensor template of the human brain. Neuroimage 2011;54974–984. 2010-12-20 READ_ME_IIT2 2010-12-20 IIT2median 2010-12-20 IIT2mean IIT2 DTI Human Brain Template Atlas Data, IIT Human Brain Template License http://www.nitrc.org/projects/iit2/ arfanakis@iit.edu Available by Purchase Only Yes Mark Horsfield, m.horsfield@xinapse.com NITRC MacOS,Linux,SunOSSolaris,Microsoft Yes Java Mark Horsfield Jim is a medical image display package that allows easy viewing and analysis of Magnetic Resonance x-ray CT and other types of medical image. Jim is an up-to-the-minute design with a familiar user-interface. 2011-3-07 ProductionStable 6.0 Jim Other Environment, Win32 MS Windows, Gnome, KDE, End Users, Developers, Available by Purchase Only, English, MacOS, Microsoft, Linux, SunOSSolaris, Java, ANALYZE, DICOM, NIfTI-1, Other Format, VRML, Algorithm or Reusable Library, Application, ProductionStable, CT, MR, Optical Imaging, PETSPECT, Domain Independent http://www.nitrc.org/projects/jim/ m.horsfield@xinapse.com MITX Consortium License Yes Kristen Zygmunt, krismz@sci.utah.edu NITRC MacOS,Linux,Windows Yes C Kristen Zygmunt Seg3D is a free volume processing sgementing tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering. Seg3D X11 Applications, Win32 MS Windows, ANALYZE, Three Dimensional Display, Volume Rendering, DICOM, Nrrd, English, ProductionStable, Segmentation, End Users, MITX Consortium License, Linux, Other Format, C, MacOS, Windows http://www.nitrc.org/projects/seg3d/ krismz@sci.utah.edu Yes Gleb Bezgin, g.bezgin@science.ru.nl NITRC Yes Gleb Bezgin CoCoMac-Paxinos3D viewer represents an interactive interface of macaque stereotaxic atlas with a connectivity database allowing integrated data analysis and mapping between 3D structures with database vocabularies. 2008-8-09 CP3D_v2.2.1 CoCoMac-Paxinos3D viewer http://www.nitrc.org/projects/cp3d/ g.bezgin@science.ru.nl Yes Danny Younes, dyounes@uci.edu NITRC Danny Younes The XML-Based Clinical Experiment Data Exchange Schema provides an extensive metadata hierarchy for describing and documenting research and clinical studies. XCEDE was originally designed in the context of neuroimaging studies and complements the BIRN-HID XCEDE Schema Domain Independent, CT, EEGMEGECoG, MR, PETSPECT http://www.nitrc.org/projects/qa_procedure/ dyounes@uci.edu GNU General Public License GPL Yes Thies Jochimsen, thies@jochimsen.de NITRC OS Independent Yes C Thies Jochimsen ODIN is a C software framework to develop simulate and run magnetic resonance sequences on different platforms. ODIN OS Independent, X11 Applications, Console Text Based, C, English, ProductionStable, Developers, GNU General Public License GPL, ANALYZE, DICOM, NIfTI-1, Simulation, Image Display, Image Reconstruction http://www.nitrc.org/projects/od1n/ thies@jochimsen.de GNU General Public License GPL Yes Zeynep Akalin Acar, zakalin@gmail.com NITRC Zeynep Akalin Acar Neuroelectromagnetic Forward Head Modeling Toolbox NFT httpsccn.ucsd.edunft is a MATLAB Toolbox for generating realistic head models from available data MRI andor electrode locations for computing numerical solutions for the forward problem of electromagnetic source imaging and for single dipole source localization. The NFT includes tools for segmenting scalp skull cerebrospinal fluid CSF and brain tissues from T1-weighted magnetic resonance MR images. The Boundary Element Method BEM and Finite Element Method FEM are used for the numerical solution of the forward problem. When a subject MR image is not available a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB or from the MATLAB command line. The toolbox is freely available under the GNU Public License for noncommercial use and open source development. NFT Neuroelectromag Forward Modeling GNU General Public License GPL http://www.nitrc.org/projects/nft/ zakalin@gmail.com Yes Paul Yushkevich, pauly2@grasp.upenn.edu NITRC Paul Yushkevich The continuous medial representation cm-rep is a set of deformable modeling algorithms for shape analysis and structure-specific normalization. Applications of cm-reps include structure-specific fMRI analysis DTI analysis and structural brain mor cmrep http://www.nitrc.org/projects/cmrep/ pauly2@grasp.upenn.edu GNU Lesser General Public License LGPL Yes I Dinov, iwaterpolo@gmail.com NITRC OS Independent Yes Java I Dinov iTools is an infrastructure for managing of diverse computational biology resources - data software tools and web-services. The iTools design implementation and meta-data content reflect the broad NCBC needs and expertise www.NCBCs.org. iTools is distributed by the Laboratory of Neuro Imaging httpwww.loni.ucla.eduSoftwareiTools at UCLA ITools Resourceome Web Environment, Other Environment, English, Beta, End Users, Developers, Other Audience, LONI Pipeline, GNU Lesser General Public License LGPL, Other Format, Java, OS Independent, Web Resource, Other Information Resource, Data Resource, Experiment Control, Ontology, Model http://www.nitrc.org/projects/itools/ iwaterpolo@gmail.com Yes Daniel Margulies, daniel.margulies@gmail.com NITRC Daniel Margulies The Neuro Bureau is neuro-collaboration in action. More specifically the Neuro Bureau is a neuroscience collaboratory that supports open neuroscience. To join the Neuro Bureau use the amp;quot;join the teamamp;quot; link in the yellow box to the right. For more information please contact theneurobureaugmail.com Preprocessed imaging data can be downloaded using the Downloads link on the left for more information on the preprocessed data use the MediaWiki link on the left. Brain-Art Competition 2011 is now over. All of the submissions and the winners are posted at the Brain-Art Gallery. neurobureau.projects.nitrc.orgBrainArtGallery 2011-10-10 Beijing-Enhanced 2011-5-31 1.0 2011-5-19 1.0 2011-4-16 1.0 The Neuro Bureau Community, Other Information Resource, MR http://www.nitrc.org/projects/neurobureau/ daniel.margulies@gmail.com 3D Slicer License,BSD License Yes Daniel Haehn, haehn@bwh.harvard.edu NITRC MacOS,POSIXUNIX-like,Windows Yes Python Daniel Haehn This project provides a series of modules which enable functions of the Vascular Modeling Toolkit httpwww.vmtk.org in 3D Slicer httpwww.slicer.org. The functionality includes vessel enhancement filtering level set segmentation centerline computation network extraction and branch splitting. Installation notes and documentation are available at the official project page httpwww.vmtk.orgMainVmtkIn3DSlicer VMTK in 3D Slicer Alpha, End Users, Developers, Python, Segmentation, Visualization, Modeling, BSD License, 3D Slicer License, MacOS, POSIXUNIX-like, Windows, DICOM, Nrrd, Other Format, Win32 MS Windows, X11 Applications, English http://www.nitrc.org/projects/slicervmtklvlst/ haehn@bwh.harvard.edu BSD License Yes Babak Ardekani, ardekani@nki.rfmh.org NITRC Linux Yes C Babak Ardekani ART `acpcdetect program for automatic detection of the AC and PC landmarks and the mid-sagittal plane on 3D structural MRI scans. ART `brainwash program for automatic multi-atlas skull-stripping of 3D structural MRI scans. ART `3dwarper program of non-linear inter-subject registration of 3D structural MRI scans. Software art2 for linear rigid-body intra-subject inter-modality MRI-PET image registration. 2011-9-22 Alpha Linux x86_64 binary 2011.09.22 2011-9-22 Alpha Linux x86_64 binary 2011.09.22 2011-9-22 Alpha Linux x86_64 binary 2011.09.22 2011-7-29 Alpha 2011-07-29 Linux binary 2011-6-10 Alpha acpcdetect 2011-06-10 Linux binary 2011-2-23 Alpha acpcdetect 2011-02-23 Linux binary 2011-2-16 Alpha acpcdetect 2011-02-16 Linux binary 2010-8-04 Alpha Revised acpcdetect Linux binary 2010-8-04 Alpha Revised 3dwarper Linux binary 2009-3-12 Alpha Linux Mac G5 amp;amp; Intel binaries Automatic Registration Toolbox Artifact Removal, Nearest Neighbor, Spline Interpolation, Tri-linear, Image Display, Affine Warp, Nonlinear Warp, Image-to-Template, Intermodal, Intersubject, Intramodal, Intrasubject, Alpha, MR, PETSPECT, Console Text Based, Developers, End Users, BSD License, English, Linux, C, ANALYZE, NIfTI-1 http://www.nitrc.org/projects/art/ ardekani@nki.rfmh.org GNU General Public License GPL Yes Shun Xu, xushun@gmail.com NITRC Yes Shun Xu MeshValmet is a tool that measures surface to surface distance between two triangle meshes using user-specied uniform sampling. Thus users can choose finer sampling level to calculate errors to gain more accuracy in the amp;quot;error spaceamp;quot; or sparser sampling to gain speed and get an approximate feeling of error distribution between boundaries. Besides its pleasant visualization using the VTK library MeshValmet also provides useful histogram and statistical information based on the sample errors such as mean and median distance root mean square distance mean square distance mean absolute distance Hausdor distance 95 percentile 68 percentile etc. MeshValmet is based on the work of Nicolas Aspert etc. MESH Measuring Errors between Surfaces using the Hausdor distance in the proceedings of the IEEE Int. Conf. on Multimedia and Expo 2002 ICME vol. I pp. 705-708. The calculation of the Dices Coefficient is calculated by Joshua Stough using the concept of a Riemannian sum. 2011-2-11 v3.0 MeshValmet Validation Metric for Meshes GNU General Public License GPL http://www.nitrc.org/projects/meshvalmet/ xushun@gmail.com GNU General Public License GPL Yes Jonas Larsson, jonas.larsson@rhul.ac.uk NITRC Jonas Larsson cbiNifti An IO library for MatlabOctave Matlab and Octave library for reading and writing Nifti-1 files. cbiNifti is intended to be a small self-contained library that makes minimal assumptions about what Nifti files should look like and allow users easy access to the raw data. cbiNifti handles compressed file formats for reading and writing using Unix pipes for compression and decompression. More information and code examples at httpwww.pc.rhul.ac.ukstaffJ.Larssonsoftware.html cbiNifti MatlabOctave Nifti library GNU General Public License GPL http://www.nitrc.org/projects/cbinifti/ jonas.larsson@rhul.ac.uk Commercial License Yes Maarten Van de Velde, mvelde@ant-neuro.com NITRC Maarten Van de Velde EEProbe is a complete software package for the study of event-related brain activity with high-resolution EEGMEG. This package has been designed to suit the high standards of neuroscience research. The software has been developed originally at the Max Planck Institute for Cognitive Neuroscience in Leipzig Germany and is available for other institutions through ANT Neuro B.V. The Netherlands enhanced with the EEProbe Databrowser. ERP investigations both in psychophysiology research and clinical applications require a multitude of processing steps. Analysis of large data sets is made efficient through advanced scripting possibilities. All different aspects of data handling are efficiently available in the EEProbe Databrowser. Alternatively external data can be imported from a multitude of formats. Processing in EEProbe makes use of open file formats see LIBEEP and is designed to integrate with ASA for advanced source analysis. EEProbe is available for Linux and Mac OS X. www.ant-neuro.com EEProbe Commercial License http://www.nitrc.org/projects/eeprobe/ mvelde@ant-neuro.com Yes Jinran Chen, jinranc@uci.edu NITRC Linux Yes C,TclTk,PLSQL,Python,cshtcsh,JavaScript Jinran Chen The FBIRN Federated Informatics Research Environment FIRE includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection storage sharing and management tracking and analysis of large fMRI datasets. 2011-10-26 Beta Ver 1.1 2010-11-10 Beta 2.2 2010-11-10 Beta 2.2 2009-7-28 Beta Function BIRN Stability Phantom QA Procedures 2.0 2009-7-21 Beta SPM XML Toolbox Manual 2009-7-21 Beta SPM XML Toolbox 2008-10-22 Beta Upload GUI 1.0 2008-7-09 Beta Data Upload Scripts 1.0 2008-6-27 Beta Human Imaging Database HID System 1.6.3 2008-6-16 Beta FBIRN Image Processing Scripts FIPS based in FSL 2008-6-16 Beta XML-Based Clinical Experiment Data Exchange Schema XCEDE 2.0 2008-6-16 Beta Phase II Auditory Oddball Task EPRIME Phase II 1.0 2008-6-16 Beta Phase II Reaction Time Task EPRIME Phase II 1.0 2008-6-16 Beta Phase II Sensory Motor Task EPRIME Phase II 1.0 2008-6-16 Beta Phase II Breath Hold Task EPRIME Phase II 1.0 2008-6-16 Beta Phase II Audio Setup Task EPRIME Phase II 1.0 2008-6-16 Beta Phase II Program amp;amp; Dataset Description 2008-6-16 Beta Phase I Program amp;amp; Dataset Description 2008-6-16 Beta Phase I Functional Imaging Paradigms EPrime Phase I 1.0 2008-6-16 Beta Multi-site Functional Imaging Recommendations Best Practices 2008-6-16 Beta Function BIRN Stability Phantom QA Procedures 1.0 Functional Imaging BIRN English, Linux, cshtcsh, Python, C, JavaScript, PLSQL, TclTk, NIfTI-1, DICOM, ANALYZE, Data, Quality Metrics, Statistical Operation, Workflow, Visualization, Database, Other Data Resource, Ontology, Web Service, Database Application, Beta, MR, Developers, End Users http://www.nitrc.org/projects/fbirn/ jinranc@uci.edu Attribution Yes Andrew Worth, nitrc@neuromorphometrics.com NITRC Yes Andrew Worth This NITRC Resource was created to host descriptions of protocols definitions and amp;quot;rules of thumbamp;quot; for the reliable identification and localization of neuroanatomical regions of interest and discussions of best practices in brain labeling. The main focuses of this resource are the amp;quot;MediaWikiamp;quot; and amp;quot;Forumsamp;quot; in the tool bar on the left. Neuroanatomical Labeling Methods Knowledge Environment, Planning, MR, Other Audience, Attribution, English http://www.nitrc.org/projects/neurolabels/ nitrc@neuromorphometrics.com BSD License,BIRN License Yes Danny Younes, dyounes@uci.edu NITRC MacOS,Linux cshtcsh Danny Younes FBIRN Imaging Processing Scripts FIPS is a FSL package for the comprehensive management of large-scale multi-site fMRI projects including data storage retrieval calibration analysis multi-modal integration and quality control. 2008-6-27 FIPS Tutorials 2008-6-27 FBIRN Image Processing Scripts Based on FSL FBIRN Image Processing Scripts FIPS Database Application, Statistical Operation, MR, Web Environment, Developers, End Users, BSD License, BIRN License, English, Linux, MacOS, cshtcsh, DICOM, ANALYZE http://www.nitrc.org/projects/fips/ dyounes@uci.edu Freeware Yes Alfonso Nieto-Castanon, alfnie@gmail.com NITRC MacOS,Linux,Windows Yes MATLAB Alfonso Nieto-Castanon Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing but adaptable for FSL as well. 2011-7-19 Beta art-2011-07 2011-6-21 Beta art-2011-06 2010-1-26 Beta art-2010-01 2009-12-10 Beta art-2009-12 2009-10-09 Beta art-2009-10 2009-3-05 Beta art-2009-03 Artifact Detection Tools ART ANALYZE, MATLAB, Windows, Linux, MacOS, Artifact Removal, Quality Metrics, Registration, Motion Analysis, English, Beta, End Users, Freeware, X11 Applications http://www.nitrc.org/projects/artifact_detect/ alfnie@gmail.com Yes Giorgio Ascoli, ascoli@gmu.edu NITRC OS Independent Yes Giorgio Ascoli Neuroinformatics publishes original articles and reviews with an emphasis on data structure and software tools related to analysis modeling integration and sharing in all areas of neuroscience research. Coverage extends to theory and methodology including discussions on ontologies modeling approaches database design and meta-analyses; descriptions of developed databases and software tools and of the methods for their distribution; relevant experimental results such as reports accompanied by the release of massive data sets; computational simulations of models integrating and organizing complex data; and neuroengineering approaches including hardware robotics and information theory studies. Neuroinformatics also publishes independent amp;quot;tests and evaluationsamp;quot; of available neuroscience databases and software tools and fosters a commitment to the principles of tool and data sharing. Neuroinformatics - The Journal Journal, ProductionStable, Clinical Neuroinformatics, Computational Neuroscience, EEGMEGECoG, MR, Web Environment, Other Environment, Developers, End Users, English, OS Independent, Other Format http://www.nitrc.org/projects/nein/ ascoli@gmu.edu BRAINS License Yes Mark Scully, mark-scully@uiowa.edu NITRC Mark Scully NOTE All new development is being managed in a github repository. Please visit httpsgithub.comBRAINSiaBRAINSStandAlone Automatically creates a mask based on the foreground of an anatomical scan volume. BRAINSROIAuto BRAINS License http://www.nitrc.org/projects/brainsroiauto/ mark-scully@uiowa.edu GNU Lesser General Public License LGPL Yes Rick Giuly, rgiuly@gmail.com NITRC Rick Giuly The goal of the Cytoseg project is to produce tools for automatic segmentation of of 3D electron microscopy specifically neuropil. The project is written in Python and uses the pythonxy platform which includes scipy and ITK image processing tools. Cytoseg GNU Lesser General Public License LGPL http://www.nitrc.org/projects/cytoseg/ rgiuly@gmail.com BSDMIT-Style Open Source License Yes Michael Esparza, michael.a.esparza@vanderbilt.edu NITRC Michael Esparza This site provides access to the VUIIS Image and Data Analysis Cores data processing tools written for MATLAB. These tools are written for ease of use from within MATLAB. Unless stated otherwise each of the tools is capable of processing 2D3D images matrices. vuTools BSDMIT-Style Open Source License http://www.nitrc.org/projects/vutools/ michael.a.esparza@vanderbilt.edu GNU Lesser General Public License LGPL Yes Bennett Landman, bennett.landman@vanderbilt.edu NITRC Java,MATLAB Bennett Landman Project to provide long-term hosting and release for small tools related to medical image analysis. Source repository contains highly experimental code intended for collaborative development. However any interested parties are welcome to browsereuse code. Stableevolved projects will be moved to independent projects. 2009-7-07 Beta IDT Toolbox 1.0 Landman NeuroImaging Tools English, Beta, MATLAB, Java, Statistical Operation, End Users, Developers, GNU Lesser General Public License LGPL http://www.nitrc.org/projects/landman/ bennett.landman@vanderbilt.edu 3D Slicer License Yes Antonio Tristán-Vega, atriveg@bwh.harvard.edu NITRC Antonio Tristán-Vega This module uses the output of the amp;quot;Finsler tractographyamp;quot; to actually trace the estimated fiber bundles from a set of target regions to the seeding regions used to compute the Finsler distance map. The map of optimal arrival directions is integrated with a second order Runge-Kutta method starting at the target regions and until the seeding region is reached or some other stopping criterion is met. Note that you should have amp;quot;Finsler Tractography based on HARDIamp;quot; installed and working in order to be able to use the present module see the documentation therein for more details on the Finsler Tractography method. This software can be compiled either as a 3D-Slicer CLI module or a stand-alone program you need ITK and VTK. In the latter case the fibers are written to disk. NOTE This software is currently provided as a sub-project in the Finsler-tractography module httpwww.nitrc.orgprojectsfinslertract Fiber-tracking based on Finsler distance Diffusion MR Fiber Tracking, 3D Slicer License http://www.nitrc.org/projects/finslerbacktr/ atriveg@bwh.harvard.edu Yes Syam Gadde, gadde@biac.duke.edu NITRC Syam Gadde XML-Based Clinical Experiment Data Exchange Schema XCEDEprovides an extensive metadata hierarchy for describing and documenting research and clinical studies. XCEDE Schema http://www.nitrc.org/projects/xcede/ gadde@biac.duke.edu Attribution Yes Timothy Herron, tjherron@ebire.org NITRC Windows NT2000,Linux,Windows 95982000,Windows XP Yes MATLAB Timothy Herron VAMCA Visualization And Meta-analysis on Cortical Anatomy is a stand-alone open source human cortical meta-analysis and visualization toolbox for MatLab. It projects stereotaxic coordinates to a mean cortical surface by using an anatomical database of 60 young adults to provide multiple mappings of normalized cortical surfaces into MNI space. VAMCA performs the following analyses 1 Multi-Fiducial Projection Mapping Map stereotaxic 3D coordinates to the normalized cortical location for each of 60 database subjects. 2 Computing Centroid Locations for groups of foci both on a mean cortical surface and in MNI space. 3 Comparing Two Groups of Foci for differences in location surface or 3D of their group centroids and computing the groups overlap extent using permutation tests. 4 Detecting Significant Densities of Foci or Density Differences of Two Groups within anatomical ROIs on a mean cortical surface by using Monte Carlo analyses. Coordinate weights allow fixed or random effects type analyses. 2011-7-31 ProductionStable July_2011_Cumulative_Update 2011-6-29 ProductionStable June_2011_Cumulative_Update 2011-4-18 ProductionStable VAMCA_cumulative_update_April_2011 2010-8-24 ProductionStable August 2010 Update 2009-6-24 ProductionStable 2009-06-24 VAMCA Cortical Meta-analysis Toolbox Console Text Based, English, ProductionStable, MATLAB, End Users, Windows 95982000, Windows XP, Linux, Windows NT2000, Database Application, Visualization, Attribution http://www.nitrc.org/projects/vamca/ tjherron@ebire.org Yes Donald Kalar, donkalar@ucla.edu NITRC Donald Kalar PubBrain is a literature search and visualization tool that allows end users to enter any PubMed query and see that query rendered as a heatmap illustrating which regions of interest are most commonly mentioned within the search results. PubBrain Database http://www.nitrc.org/projects/pubbrain/ donkalar@ucla.edu Attribution Non-Commercial Yes Erik Beall, ebeall@gmail.com NITRC MacOS,Linux MATLAB,shbash Erik Beall Do you have 3Dtime EPI data BOLD or perfusion but no usable physio signals for pulse and respiration Are you concerned about the effect of physio noise on your data but dont know what to do but regress data-derived signals that mix unknown functional signal with possible physio noise signal This is for you. This distribution includes a tool Physiologic EStimation by Temporal ICA or PESTICA to detect physiologic signals _from the data itself_ These signals are equivalent to a parallel monitored pulse signal and a respiratory chest-bellows signal. Are you concerned about the number of regressors youre incorporating once you add 5th order RETROICOR 20 more regressors The other half of PESTICA is an adaptive physiologic noise removal tool Impulse Response Function or IRF-RETROICOR that zooms in on noise with only 6 regressors getting all the noise that 5th order RETROICOR gets. These tools will allow you to correct your data for physiologic noise with what you currently have. 2011-6-06 Beta NYU_TRT_classic_all_sessions 2011-5-25 Beta PaloAlto_FCP_classic 2011-2-16 Beta pestica v1.2 additions 2010-11-19 Beta pestica v1.2 for AFNI users recommended 2010-6-28 Beta pestica-AFNI example 1 PESTICA fMRI Physio DetectionCorrection English, Beta, MATLAB, shbash, ANALYZE, End Users, Linux, MacOS, Physiological Recording, Algorithm or Reusable Library, Independent Component Analysis, Multivariate Analysis, Workflow, Attribution Non-Commercial, Console Text Based http://www.nitrc.org/projects/pestica/ ebeall@gmail.com Yes Hester Breman, breman@brainvoyager.com NITRC Yes Java,MATLAB,C Hester Breman The Neuroimaging Informatics Technology Initiative NIfTI and NIfTI Data Format Working Group creator and maintainer of the NIfTI-1 data format. 2011-11-08 ProductionStable Structural 2010-7-19 ProductionStable nifticlib-2.0.0 2008-8-06 ProductionStable nifticonverter for BrainVoyager QX 2007-9-30 ProductionStable 0.20070930.1 2006-4-05 ProductionStable niftimatlib-1.0 2006-3-20 ProductionStable niftijlib-0.2 NIfTI Algorithm or Reusable Library, Other Information Resource, ProductionStable, CT, MR, PETSPECT, Developers, English, C, Java, MATLAB, NIfTI-1 http://www.nitrc.org/projects/nifti/ breman@brainvoyager.com HI-SPEED Software Packets License Yes Cheng Guan Koay, cgkoay@uwalumni.com NITRC OS Independent Java Cheng Guan Koay HI-SPEED Software Packets contain 1 unconstrained and constrained nonlinear least squares diffusion tensor estimation techniques 2 2-dimensional and 3-dimensional analytical Shepp-Logan magnetic resonance imaging phantoms in both the Fourier and image domains 3 techniques for reporting the underlying signal-to-noise ratio in magnetic resonance MR images 4 Probabilistic Identification and EStimation of NOise PIESNO---a technique for identifying noise-only pixels and estimating the underlying noise standard deviation in MR images and 5 a signal-transformational technique for breaking the noise floor in MR images. Many more computational tools will be shared with users and developers as they become available. Download info httpsites.google.comsitehispeedpackets 2009-6-16 ProductionStable ISMRM 2009 Workshop Poster 2009-6-16 ProductionStable Download Info HI-SPEED Software Packets OS Independent, English, ProductionStable, Java, Algorithm or Reusable Library, Image Reconstruction, Statistical Operation, Tensor Metric, Developers, End Users, HI-SPEED Software Packets License http://www.nitrc.org/projects/hispeed/ cgkoay@uwalumni.com Yes Vision Zheng, zheng.vision@gmail.com NITRC Vision Zheng NICE-SIGN is a nice sign of bias field correction nonuniformity in medical images. This tool is fast and efficient. Technical details can be found at httpzheng.vision.googlepages.combiasCorrection_miccai09_Zheng.pdf NICE-SIGN http://www.nitrc.org/projects/nicesign/ zheng.vision@gmail.com Commercial NordicNeuroLab Yes Vlad Borimsky, vlad@nordicneurolab.com NITRC Windows Vista,Windows XP Vlad Borimsky With over a decade of experience NordicNeuroLab NNL provides products and solutions that define the field of functional MR imaging. We understand the growing need for reliable and innovative tools in this growing field. As a result we closely collaborate with research and clinical teams from both academic and medical centers MR system manufacturers and third party vendors to develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. From state of the art post-processing and visualization software for BOLD DiffusionDTI and PerfusionDCE imaging to fMRI hardware for audio and visual stimulation eye tracking and patient response collection NNLs products are used around the world by researchers and clinicians alike. Ultimately we are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. NordicNeuroLab English, ProductionStable, End Users, Windows XP, Windows Vista, Eye Tracking, Stimulus Presentation, Perfusion, Scanner, Diffusion MR Fiber Tracking, ANALYZE, ASCII, DICOM, NIfTI-1, Commercial NordicNeuroLab http://www.nitrc.org/projects/nnl/ vlad@nordicneurolab.com Freeware Yes Stephen Frey, stephen@bic.mni.mcgill.ca NITRC Stephen Frey We present unbiased standard macaque monkey magnetic resonance imaging template brain volumes that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual nonhuman primates and studies. MNI Macaque Atlases English, Atlas Application, MINC, MINC2, NIfTI-1, Freeware http://www.nitrc.org/projects/mniatlas/ stephen@bic.mni.mcgill.ca Yes Evan Fletcher, evanfletcher@gmail.com NITRC Linux Yes C,cshtcsh Evan Fletcher Suite of tools for brain image analysis. Image manipulation 2D visualization linear alignment BBSI template-based bias correction skullstrip. GUI Image analysis tools. Now modified to readwrite single file nifti .nii format. Other packages to be added. 2009-7-16 ProductionStable IDeA Lab Suite IDeA Lab brain image processing suite NIfTI-1, Linux, ANALYZE, Other Format, Console Text Based, X11 Applications, English, ProductionStable, C, cshtcsh, Two Dimensional Display, Intermodal, Intersubject, Tri-linear, Image-to-Template, Spline Interpolation, Nonlinear Warp, Volume Measurement, End Users http://www.nitrc.org/projects/idea_lab/ evanfletcher@gmail.com Apache License 2.0 Yes Luis Ibanez, luis.ibanez@kitware.com NITRC OS Independent Yes Java,C,TclTk,Python Luis Ibanez The ITK toolkit is based on generic programming with a data pipeline architecture supports for multi-threads and it is tested Nightly in multiple platforms including Linux Windows Sun and Mac. Insight Toolkit Other Environment, Console Text Based, Mature, C, Java, Python, TclTk, Developers, OS Independent, Algorithm or Reusable Library, ANALYZE, DICOM, MINC2, NIfTI-1, Nrrd, Philips PARREC, bshortbfloat, Apache License 2.0 http://www.nitrc.org/projects/insighttoolkit/ luis.ibanez@kitware.com Freeware Yes Felix Carbonell, felix.carbonell@mail.mcgill.ca NITRC OS Independent Yes MATLAB Felix Carbonell A Matlab toolbox for the statistical analysis of fMRI data. fMRIstat ANALYZE, MINC, NIfTI-1, MATLAB, OS Independent, Principal Component Analysis, Linear, Modeling, English, Mature, End Users, Freeware, Console Text Based, AFNI BRIK http://www.nitrc.org/projects/fmristat/ felix.carbonell@mail.mcgill.ca GNU General Public License GPL Yes Mira Raman, mraman@stanford.edu NITRC MacOS,Windows Yes Java Mira Raman BrainImageJava is a multiplatform highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers. BrainImageJava can o Delineate ROIs in slices along X Y or Z axes with 3D feedback in the other axes. o Create and display triangular mesh surfaces from MRI volumes. o Draw Surfaces-of-Interest SOIs in 3D and edit them in a planar display. o Set Talairach grid on a volume export an ACPC stack and measure the values within each grid unit. 2009-8-28 Beta BIJ-SampleFiles-08_2009 2009-8-28 Beta BIJ-1.0.0-Mac 2009-8-28 Beta BIJ-1.0.0-Win BrainImageJava English, Beta, Java, Volumetric Analysis, Artifact Removal, Three Dimensional Display, Rendering, Platform or Development Environment, GNU General Public License GPL, Anatomic, ANALYZE, Other Format, End Users, Developers, MacOS, Windows, Data, Mesh Generation, Volume Measurement, Other Environment http://www.nitrc.org/projects/bij/ mraman@stanford.edu Creative Commons License Yes Linda Lanyon, lindal@incf.org NITRC Linda Lanyon Neuroscience data particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology are associated with a rich set of descriptive information often called metadata. For data archive storage sharing and re-use metadata are of equal importance to primary data as they define the methods and conditions of data acquisition such as device characteristics studyexperiment protocol and parameters behavioral paradigms and subjectpatient information and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications. The overall scope of this program is to develop generic standards and tools to facilitate the recording sharing and reporting of metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. INCF Neuroimaging Data Sharing Community, Beta, MR, Web Environment, Developers, Creative Commons License, English, NiPyPe, LONI Pipeline http://www.nitrc.org/projects/incf_nidstf/ lindal@incf.org GNU General Public License GPL Yes Vince Calhoun, vcalhoun@unm.edu NITRC MacOS,Linux,Windows Yes MATLAB Vince Calhoun FIT is a MATLAB toolbox which uses Independent Component Analysis ICA to extract the shared information across modalities like fMRI EEG sMRI and SNP data. Fusion ICA Toolbox FIT End Users, GNU General Public License GPL, Win32 MS Windows, Gnome, KDE, NIfTI-1, ANALYZE, MacOS, Windows, Linux, Algorithm or Reusable Library, Independent Component Analysis, Principal Component Analysis, MATLAB, English, Mature http://www.nitrc.org/projects/fit/ vcalhoun@unm.edu Textpresso License Yes Hans-Michael Muller, mueller@caltech.edu NITRC MacOS,Linux Perl,shbash Hans-Michael Muller Textpresso is a text-mining system for scientific literature. Textpressos two major elements are 1 access to full text so that entire articles can be searched and 2 introduction of categories of biological concepts and classes that relate two objects e.g. association regulation etc. or describe one e.g. methods etc. A search engine enables the user to search for one or a combination of these categories andor keywords within an entire literature. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 17 different literatures among them Neuroscience and can readily be extended to other corpora of text. Textpresso can be used online httpwww.textpresso.org but also installed locally via a downloadable software package httpwww.textpresso.orgdownloads.html Textpresso - literature search engine Bibliographic Resource, Web Environment, English, ProductionStable, MacOS, PDF - Portable Document Format, Knowledge Environment, Websites, Web Service, Database Application, Textpresso License, End Users, Perl, shbash, Linux http://www.nitrc.org/projects/textpresso-2-0/ mueller@caltech.edu BSD License Yes Randall Frank, randall-frank@computer.org NITRC Yes Randall Frank Brainvox is an interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data Damasio and Frank 1991; Frank Damasio and Grabowski 1997. 2009-12-14 Brainvox 3.14 OS X Tiger 2009-12-14 Brainvox 3.14 OpenSuse 10.2 Brainvox BSD License http://www.nitrc.org/projects/brainvox/ randall-frank@computer.org Yes Xin Li, xli16@jhmi.edu NITRC Microsoft Yes C Xin Li MRI and DTI imaging software tool. 2008-5-27 ProductionStable MRI Studio Suite MRI Studio Win32 MS Windows, ANALYZE, C, Microsoft, Diffusion MR Fiber Tracking, ProductionStable, End Users http://www.nitrc.org/projects/mri_studio/ xli16@jhmi.edu GNU Lesser General Public License LGPL Yes Xue Yang, xue.yang@Vanderbilt.Edu NITRC Xue Yang Biological parametric mapping has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities both for regressors and regressands along with scalar valued observations. Current statistical methods in the imaging community assume that the regressors are non-random. For more realistic multi-parametric assessment e.g. voxel-wise modeling distributional consideration of all observations is appropriate. Herein we present two unified regression and inference approaches Model II regression and regression calibration for use in massively univariate inference with imaging data. These methods use the design matrix paradigm and account for both random and non-random imaging regressors. 2011-10-26 BPM_Random Regressors BPM Accounting for Random Regressors GNU Lesser General Public License LGPL http://www.nitrc.org/projects/bpm_ran_reg/ xue.yang@Vanderbilt.Edu 3D Slicer License Yes Marcel Prastawa, prastawa@sci.utah.edu NITRC Marcel Prastawa A multichannel capable tool for probabilistic inhomogeneity correction implemented as both a standalone command line tool and a Slicer3 module. ProbabilisticBiasCorrection 3D Slicer License http://www.nitrc.org/projects/probbiascor/ prastawa@sci.utah.edu 3D Slicer License Yes Mark Scully, mark-scully@uiowa.edu NITRC Mark Scully The purpose of this Slicer3 module is to provide a capability for performing white matter lesion classification and summary. 2009-6-25 2.2.2 2009-6-25 2.2.1 2009-6-25 2.20 2009-1-07 2.02 2009-1-06 2.01 2009-1-06 2.0 2008-11-19 1.01 2008-11-16 1.0 3DSlicerLupusLesionModule 3D Slicer License http://www.nitrc.org/projects/lupuslesion/ mark-scully@uiowa.edu OtherProprietary License Yes Evan McCreedy, mccreedy@mail.nih.gov NITRC Other OS,MacOS,Linux,Other UNIX-like,Windows Yes Java Evan McCreedy The MIPAV Medical Image Processing Analysis and Visualization application enables quantitative analysis and visualization of medical images of numerous modalities such as PET MRI CT or microscopy. 2008-11-17 Mature MIPAV Stable and Nightly Releases MIPAV Algorithm or Reusable Library, Colocalization, Mesh Generation, Simulation, Volumetric Analysis, Segmentation, Surface Rendering, Registration, Resampling, Spatial Convolution - Deconvolution, Volume Rendering, Diffusion MR Fiber Tracking, Frequency Domain, Animation, Image Display, Mature, CT, MR, PETSPECT, X11 Applications, Console Text Based, Win32 MS Windows, Developers, Other Audience, End Users, OtherProprietary License, English, Linux, Other UNIX-like, Other OS, MacOS, Windows, Java, AFNI BRIK, ANALYZE, bshortbfloat, COR, DICOM, MGHMGZ, MINC, MINC2, NIfTI-1, Nrrd, Other Format http://www.nitrc.org/projects/mipav/ mccreedy@mail.nih.gov Yes Mark Scully, mark-scully@uiowa.edu NITRC Mark Scully Implement the methods defined in httpwww5.informatik.uni-erlangen.deForschungPublikationen2006Jaeger06-ANM.pdf as and ITK filter. VectorValuedHistogramNormalizer http://www.nitrc.org/projects/vvhistomatch/ mark-scully@uiowa.edu GNU General Public License GPL Yes Bin Chen, bc15@duke.edu NITRC Microsoft Yes C,C Bin Chen Software tool excecutable and source code in C and C to correct distortions in diffusion MR images that are generated by main magnetic field inhomogeneities and eddy current induced fields generated from the direction-dependent diffusion encoding 2008-4-24 Beta dtic B0 and eddy current correction for DTI Other Software Resource, C, C, English, Beta, End Users, Developers, GNU General Public License GPL, Win32 MS Windows, ANALYZE, Microsoft http://www.nitrc.org/projects/dtic/ bc15@duke.edu 3D Slicer License Yes Antonio Tristán-Vega, atriveg@bwh.harvard.edu NITRC MacOS,Linux,Other UNIX-like,Microsoft C Antonio Tristán-Vega This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points the paths are estimated as the shortest path taking into account a local directional dependent cost. The output provided is the connectivity map from each voxel in the volume to the seeding points plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built these directions can be traced back to actually compute the fiber bundles VTK required. The software can be built as either a stand-alone or a CLI plugin for 3D Slicer. Finsler tractography module for Slicer Nrrd, 3D Slicer License, Console Text Based, Other Environment, English, Mature, C, End Users, MacOS, Microsoft, Linux, Other UNIX-like, Diffusion MR Fiber Tracking http://www.nitrc.org/projects/finslertract/ atriveg@bwh.harvard.edu BSD License Yes Clementine Ouziel, clementine.ouziel@gmail.com NITRC MacOS,Linux,Windows Yes C Clementine Ouziel AutoSeg is a novel C based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction rigid registration to a common coordinate image tissue segmentation skull-stripping intensity rescaling atlas-based registration subcortical segmentation and lobar parcellation regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes. 2011-11-11 Mature AutoSeg_2.6 2011-10-28 Mature AutoSeg_2.5 2011-8-09 Mature AutoSeg_2.4.1 2011-8-02 Mature AutoSeg_2.4 2011-8-02 Mature AutoSeg_2.3.1 2011-8-02 Mature AutoSeg_2.3 2011-8-02 Mature UNC Primate Brain Atlas 2011-6-23 Mature AutoSeg_2.2 2011-6-16 Mature Adult and pediatric human brain atlases 2011-6-15 Mature AutoSeg_2.1 2011-3-04 Mature AutoSeg_2.0 AutoSeg Image-to-Template, Spline Interpolation, Nonlinear Warp, Developers, End Users, Linux, MacOS, Windows, BSD License, Win32 MS Windows, English, Mature, ANALYZE, Nrrd, Other Format, C, Workflow, Volumetric Analysis, Labeling, Expectation Minimization, Image-to-Image, X11 Applications http://www.nitrc.org/projects/autoseg/ clementine.ouziel@gmail.com Yes , NITRC Experimental data can be imported in Atlas3D and warped to atlas space using linear registration with the possibility to scale rotate and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images. Atlas3D Beta, Visualization http://www.nitrc.org/projects/incf_atlas3d/ 3D Slicer License Yes Antonio Tristán-Vega, atriveg@bwh.harvard.edu NITRC MacOS,Linux,Other UNIX-like,Microsoft Yes C Antonio Tristán-Vega This is a fast and robust implementation of the popular Nonlocal Means for MRI-Rician denoising. It works by computing the non-local weights based on distances in a features space comprising the local mean value and gradients of the image. It can reach an acceleration factor of 20x over the original implementation with an improved performance for medium-low SNR images. We use a bias correction step for Rician noise based on the well-known Conventional Approach. This software can be compiled either as a Slicer module or a stand-alone httpwww.nitrc.orgsnapshots.phpgroup_id=518 Key words nonlocal non-local means NLM C ITK Fast Nonlocal Means for MRI denoising 3D Slicer License, Other Format, MINC, Filtering, Quality Metrics, Intensity Non-uniformity Correction, NIfTI-1, ANALYZE, Nrrd, Other Environment, English, Mature, C, End Users, MacOS, Microsoft, Linux, Other UNIX-like, Artifact Removal, Console Text Based http://www.nitrc.org/projects/unlmeans/ atriveg@bwh.harvard.edu Personal License Yes Jamaan Alghamdi, j.alghamdi@liv.ac.uk NITRC Jamaan Alghamdi The main aim of this blog is presenting some scripts that can be used to facilitate and automate processing and analysis of brain data. In addition it could be helpful explaining non clear stages and steps of brain data processing using some software. Neuroimaging Made Easy Blog Personal License http://www.nitrc.org/projects/easy_neuroimage/ j.alghamdi@liv.ac.uk Yes Daniel Handwerker, handwerkerd@mail.nih.gov NITRC Daniel Handwerker The methodology and applications of task independent fluctuation measures including connectivity maps of fMRI resting state scans research using EEGMEGPET etc methods to remove non-neural fluctuations and applications to clinical populations. 2008-4-17 Pre-Alpha SFIM Processing Script Files Task Independent Fluctuations Discussion Web Environment, English, Pre-Alpha, Developers, End Users, Other Audience, Community, Web Resource, Model, Other Software Resource http://www.nitrc.org/projects/fluctuations/ handwerkerd@mail.nih.gov Artistic License Yes Peter Kochunov, pkochunov@mprc.umaryland.edu NITRC MacOS,Linux,Windows Yes C Peter Kochunov An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness 3D gyrification index sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa 2011-6-24 ProductionStable Reprint of a manuscript 2011-6-24 ProductionStable Version 4.1 plugins Mac 2011-6-24 ProductionStable Version 4.1 plugins Linux 2011-6-24 ProductionStable Version 4.1 plugins 2011-6-24 ProductionStable Source code for 4.1 version 2011-5-02 ProductionStable Version 4.02 plugins Linux x32 2011-5-02 ProductionStable Version 4.02 plugins Mac OS10.X 2011-5-02 ProductionStable Version 4.02 plugins Windows 2011-5-02 ProductionStable Eclipse Workspace with Source Code for 4.02 version 2010-8-25 ProductionStable Linux OS 2010 version of Plugin Including Gyral Span 2010-8-25 ProductionStable Mac OS 2010 Version of Plugins including Gyral Span 2010-8-25 ProductionStable MS Windows 2010 Version including Gyral Span 2010-8-25 ProductionStable Eclipse Workspace 2008-9-29 ProductionStable brainvisa_ext_3.1_all_plugins_single_package BrainVisa Morphology extensions Image Display, Artistic License, End Users, MacOS, Windows, NIfTI-1, ANALYZE, Other Format, X11 Applications, English, ProductionStable, C, Morphology, Shape Analysis, Linux http://www.nitrc.org/projects/brainvisa_ext/ pkochunov@mprc.umaryland.edu Freeware Yes Guorong Wu, grwu@med.unc.edu NITRC Linux,Windows Yes C Guorong Wu GLIRT Groupwise and Longitudinal Image Registration Toolbox provides solutions for both groupwise registration and longitudinal registration which are the necessary steps for many brain-related applications. Specifically groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore in this software package we have included two of our recently-developed groupwise registration algorithms 1 Improved unbiased groupwise registration guided with the sharp group-mean image and 2 Hierarchical feature-based groupwise registration with implicit template Groupwise-HAMMER for short. On the other hand we also included our recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject but also align all longitudinal image sequences of all subjects to the common space simultaneously. This software package was developed in the IDEA group at UNC-Chapel Hill httpbric.unc.eduideagroup . 2011-10-31 Pre-Alpha 1.0.10 2011-7-26 Pre-Alpha 1.0.9 2011-7-25 Pre-Alpha 1.0.8 2011-6-21 Pre-Alpha GLIRT 1.0.7 2011-4-08 Pre-Alpha GLIRT -1.0.6 2011-4-06 Pre-Alpha GLIRT_1.0.5 2011-4-03 Pre-Alpha GLIRT doc GLIRT ANALYZE, Freeware, Intersubject, Motion Analysis, X11 Applications, English, Pre-Alpha, C, Windows, Linux, Win32 MS Windows http://www.nitrc.org/projects/glirt/ grwu@med.unc.edu LONI Software License Yes Scott Neu, neu@loni.ucla.edu NITRC OS Independent Yes Java Scott Neu The LONI Debabeler manages the conversion of imaging data from one file format and convention to another. It consists of a GUI to visually program the translations and a data translation engine to read sort and translate the input files. 2009-11-02 Mature 2.10 2008-1-02 Mature 2.8 2007-5-30 Mature 2.7 LONI Debabeler Platform or Development Environment, ANALYZE, DICOM, MINC, NIfTI-1, OS Independent, Java, English, Mature, End Users, LONI Software License, X11 Applications, Win32 MS Windows, Other Environment, Workflow, Other Software Resource http://www.nitrc.org/projects/debabeler/ neu@loni.ucla.edu Commercial License ASA Software Yes Maarten Van de Velde, mvelde@ant-neuro.com NITRC Maarten Van de Velde ASA is a highly flexible EEGERP and MEG analysis package with a variety of source reconstruction signal analysis and MRI processing features. ASA combines functional brain imaging with the visualization and incorporation of morphological information obtained from MRI or CT. ASA is a highly interactive and flexible software tool that can be applied to neuro-physiological and clinical brain research. ASA gives a realistic impression of your experimental configuration together with topographical mapping of EEG and MEG and the results of your analysis. ASA is developed for and by people dedicated to brain research. The concept of flexibility and openness covers even most complex analysis demands. The ASA environment is particularly attractive for those that wish to develop their own methods in third party packages like Matlab and use ASA for pre-processing and visualization purposes. ASA - Advanced Source Analysis EEGMEGECoG, Commercial License ASA Software http://www.nitrc.org/projects/asa/ mvelde@ant-neuro.com Freeware Yes Felix Carbonell, felix.carbonell@mail.mcgill.ca NITRC OS Independent Yes MATLAB Felix Carbonell SurfStat is a Matlab toolbox for the statistical analysis of univariate and multivariate surface data using linear mixed effects models and random field theory. SurfStat Console Text Based, AFNI BRIK, ANALYZE, MINC, NIfTI-1, MATLAB, OS Independent, Modeling, Linear, English, ProductionStable, End Users, Freeware http://www.nitrc.org/projects/surfstat/ felix.carbonell@mail.mcgill.ca LONI Software License,BIRN License Yes Queenie Ng, queenie.ng@loni.ucla.edu NITRC OS Independent Java Queenie Ng The BrainGraph Editor 1.0 Beta is a JAVA application designed to create taxonomies or hierarchies in order to classify and organize information. BrainGraph Editor 1.0 Beta Other Information Resource, Ontology, Visualization, Beta, Domain Independent, Win32 MS Windows, Gnome, KDE, Other Environment, End Users, BIRN License, LONI Software License, English, OS Independent, Java, Other Format http://www.nitrc.org/projects/braingrpheditor/ queenie.ng@loni.ucla.edu Yes Maria de la iglesia-Vayá, maigva@itaca.upv.es NITRC Yes Maria de la iglesia-Vayá Spanish Resting State Network SRSN; Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de España y centros nacionales e internacionales. Spanish Resting State Network Spanish, Planning, PDF - Portable Document Format, Microsoft Word Document, NIfTI-1, End Users, Data http://www.nitrc.org/projects/srsn/ maigva@itaca.upv.es Yes Jeanette Mumford, mumford@ucla.edu NITRC Jeanette Mumford FSL extensions is a reference for modifications extensions and utilities for the FMRIB Software Library FSL. FSL extensions http://www.nitrc.org/projects/fsl_extensions/ mumford@ucla.edu Yes ADRIANA CARNELLI, adriana.carneli@frontiersin.org NITRC OS Independent ADRIANA CARNELLI If you are seeking journals addressing functional and structural neuroimaging topics this is the right place to start. Journals Journal, Beta, Domain Independent, Web Environment, End Users, English, OS Independent http://www.nitrc.org/projects/journals/ adriana.carneli@frontiersin.org BIRN License Yes Karl Helmer, helmer@nmr.mgh.harvard.edu NITRC Linux Yes Python,C Karl Helmer The Brain Morphometry testbed of the BIRN provides a tool to correct gradient non-linearity distortions in MR structural images. This correction improves test-retest reproducibility crucial for multi-site studies. 2009-7-01 Beta 2.01 2009-2-26 Beta 2.0 2007-12-31 Beta V1.0 Gradient Non-linearity Unwarping Tool Artifact Removal, Beta, MR, Console Text Based, End Users, BIRN License, English, Linux, Python, C, DICOM, NIfTI-1 http://www.nitrc.org/projects/grad_unwarp/ helmer@nmr.mgh.harvard.edu Public Domain Yes Chad Cumba, chad.cumba@mail.utexas.edu NITRC MATLAB Chad Cumba A common question investigators ask statisticians when working on grants is how to calculate power. FMRIpower is an easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data. 2011-6-15 Beta FRMIPower-v1.1 FMRIpower End Users, Public Domain, ANALYZE, NIfTI-1, Beta, Linear, Other Software Resource, MATLAB http://www.nitrc.org/projects/fmripower/ chad.cumba@mail.utexas.edu Yes Ali Gholipour, bag032000@utdallas.edu NITRC MacOS,Linux,Windows XP Yes C Ali Gholipour NPTK provides non-rigid registrationdistortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI. 2011-2-10 Beta V.2.0 fast field map distortion correction 2009-5-28 Beta 1.8 2009-3-09 Beta 1.8 beta 2008-1-03 Beta 1.7 NPTK Linux, MacOS, Windows XP, NIfTI-1, C, Intermodal, Artifact Removal, Nonlinear Warp, End Users, ANALYZE, X11 Applications, English, Beta http://www.nitrc.org/projects/nptk/ bag032000@utdallas.edu GNU General Public License GPL Yes Chao-Gan YAN, ycg.yan@gmail.com NITRC Chao-Gan YAN Data Processing Assistant for Resting-State fMRI DPARSF is a convenient plug-in software based on SPM and REST. You just need to arrange your DICOM files and click a few buttons to set parameters DPARSF will then give all the preprocessed slice timing realign normalize smooth data FC ReHo ALFF and fALFF results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. You can use DPARSF to extract AAL or ROI time courses or extract Gray Matter Volume of AAL regions command line only efficiently if you want to perform small-world analysis. Please download it and find more information from httpwww.restfmri.netforumDPARSF DPARSF GNU General Public License GPL http://www.nitrc.org/projects/dparsf/ ycg.yan@gmail.com SBIA License Yes christos davatzikos, christos@rad.upenn.edu NITRC Yes christos davatzikos The HAMMER package performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps in order to examine regional volumetrics effects of disease or correlations with clinical measurements. 2007-11-27 hammer1_0_linux 2007-11-27 hammer1_0_windows HAMMER Deformable Registration SBIA License http://www.nitrc.org/projects/hammer/ christos@rad.upenn.edu GNU General Public License GPL Yes Christophe Lenglet, clenglet@umn.edu NITRC Yes Christophe Lenglet This is a Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images introduced in Aganj et al MRM 2011. 2011-7-18 1.0 Wavelet-based Image Fusion GNU General Public License GPL http://www.nitrc.org/projects/wlfusion/ clenglet@umn.edu BSD License Yes Vincent Magnotta, vincent-magnotta@uiowa.edu NITRC Vincent Magnotta This program provides a tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language. BRAINSSurfaceStats BSD License http://www.nitrc.org/projects/surfacestat/ vincent-magnotta@uiowa.edu GNU General Public License GPL Yes Cinly Ooi, co224@cam.ac.uk NITRC MacOS,Linux Yes Java,C,Unix Shell Cinly Ooi Software respository containing pipelines of chained modules and GUI for batch processing. Current pipelines include fMRI analysis statistical testing based on randomisation methods and fractal spectral analysis. Pipelines are continually being added. 2007-9-10 ProductionStable Main CamBA SourceForge Package Link CamBA NIfTI-1, Other Environment, Image-to-Template, Spectral Analysis, Time Domain Analysis, X11 Applications, Web Environment, Algorithm or Reusable Library, Regression, Affine Warp, Wavelet Transformation, Linux, MacOS, C, Java, Unix Shell, English, GNU General Public License GPL, ProductionStable, End Users, Developers http://www.nitrc.org/projects/camba/ co224@cam.ac.uk GNU General Public License GPL Yes Brain Mapping Unit, co224@cam.ac.uk NITRC MacOS,Linux,Other UNIX-like Yes Brain Mapping Unit Characterisation of small-world networks constructed from wavelet analysis of resting fMRI. This package is currently available as an R library. Futrure development will take place within the CamBA software repository 2007-9-10 Mature Brainwaver CRAN Link Brainwaver MacOS, Algorithm or Reusable Library, Application, End Users, Developers, Mature, GNU General Public License GPL, English, Other Environment, Linux, Other UNIX-like http://www.nitrc.org/projects/brainwaver/ co224@cam.ac.uk GNU General Public License GPL Yes Jon Schindler, jschindl@brainvis.wustl.edu NITRC Jon Schindler CIFTI Connectivity Informatics Technology Initiative standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties. Use the MEDIAWIKI entry in the menu on the left for more information about the CIFTI file formats. Access the CIFTI discussion forum using the Forums entry in the menu on the left. Subscribe to the discussion forum and you will be informed about issues involving the CIFTI file formats via email. 2011-6-16 1.0.1 CIFTI Connectivity File Format GNU General Public License GPL http://www.nitrc.org/projects/cifti/ jschindl@brainvis.wustl.edu Yes Greg Book, gbook@gbook.org NITRC Greg Book MIview is an OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM AnalyzeNifti and raster images and can write AnalyzeNifti and raster images. 2011-3-23 MIView 0.7.39 2008-7-08 MIView 0.6.344 MIView http://www.nitrc.org/projects/miview/ gbook@gbook.org Freeware Yes Quoc Nguyen, qnguyen@physics.ucsd.edu NITRC Windows NT2000,Windows 95982000 Pascal Quoc Nguyen MPScope is a comprehensive software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan the analysis program MPView and several software utilities MPScope bshortbfloat, Other Format, End Users, Developers, Windows NT2000, Windows 95982000, ProductionStable, Freeware, Experiment Control, Scanner, Pascal, Win32 MS Windows, English http://www.nitrc.org/projects/mpscope/ qnguyen@physics.ucsd.edu Yes Mark Scully, mark-scully@uiowa.edu NITRC Mark Scully BRAINSTracer - a graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3 and integrates the Slicer3 theme. 2008-9-27 Beta-0.9.0 BRAINSTracer http://www.nitrc.org/projects/brainstracer/ mark-scully@uiowa.edu Yes Christian Haselgrove, ch@neuromorphometrics.com NITRC Yes Christian Haselgrove This project is meant for planning the NITRC Grantee meetings. The meetings introduce NITRC participants to one another promote discussion of common interests and identify opportunities for collaboration and interoperability. Plans for the 2009 Grantee Meeting are underway. Click on the MediaWiki link in gray menu on left to learn more. Grantees Meeting for NITRC Other KE, ProductionStable, Domain Independent, Developers, End Users, English http://www.nitrc.org/projects/nihgrantees/ ch@neuromorphometrics.com Yes Vincent Magnotta, vincent-magnotta@uiowa.edu NITRC Vincent Magnotta This project contains tools appropriate for the registration of diffusion tensor images to an average coordinate system. The tools include image registration methods and algorithms for the correct alignment of the diffusion tensor when applying the resulting transformation. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated using the module discovery capabilities of Slicer3. Diffusion Warp http://www.nitrc.org/projects/diffusionwarp/ vincent-magnotta@uiowa.edu GNU General Public License GPL Yes Jennifer Elam, elam@wustl.edu NITRC MacOS,Linux,Windows Yes C Jennifer Elam Caret is free open source software used to visualize and analyze the structural and functional characteristics of cerebral and cerebellar cortex in humans nonhuman primates and rodents. Visit the ToolResource Home Page for more information. 2007-8-23 ProductionStable 5.5 and others Caret Animation, C, MacOS, Linux, Windows, Atlas Application, Shape Analysis, Segmentation, Intersubject, Image-to-Template, Gaussian Curvature, Mean Curvature, AFNI BRIK, ANALYZE, ProductionStable, End Users, GNU General Public License GPL, MINC, NIfTI-1, Other Format, Three Dimensional Display, Two Dimensional Display, Surface Rendering, Mesh Generation, Quantitative Shape Analysis, English, Other Environment http://www.nitrc.org/projects/caret/ elam@wustl.edu GNU General Public License GPL Yes J-Donald Tournier, d.tournier@brain.org.au NITRC Linux Yes C J-Donald Tournier MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres using constrained spherical deconvolution CSD and probabilistic streamlines. 2010-8-25 ProductionStable 0.2.9 2010-8-23 ProductionStable 0.2.9 2010-4-14 ProductionStable 0.2.8 2010-4-13 ProductionStable 0.2.8 2010-3-18 ProductionStable 0.2.7 2009-8-25 ProductionStable 0.2.7 2009-3-18 ProductionStable 0.2.6 2008-9-02 ProductionStable 0.2.5 2008-8-03 ProductionStable 0.2.4 2008-7-08 ProductionStable 0.2.3 2008-7-03 ProductionStable 0.2.2 MRtrix X11 Applications, NIfTI-1, ANALYZE, bshortbfloat, Other Format, Diffusion MR Fiber Tracking, Image Display, Linux, C, English, ProductionStable, End Users, Developers, GNU General Public License GPL, DICOM http://www.nitrc.org/projects/mrtrix/ d.tournier@brain.org.au Non-Commercial Software License Agreement Yes Angelos Barmpoutis, abarmpou@cise.ufl.edu NITRC Angelos Barmpoutis FanDTasia is a Java applet tool for DT-MRI processing. It opens dw-mri datasets from users computer and performs very efficient tensor field estimation using parallel threaded processing on users browser. No installation is required. It runs on any operating system that supports Java Windows Mac Linux.... The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in users local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking DTI-based which is also shown using 3d graphics on the users browser. 2011-2-07 fanDTasia - Version 0.01.090125 fanDTasia Java Applet DT-MRI Processing Non-Commercial Software License Agreement http://www.nitrc.org/projects/fandtasia/ abarmpou@cise.ufl.edu BSD License Yes Matthew Brett, matthew.brett@gmail.com NITRC Yes Matthew Brett DiPy is a python package for analyzing diffusion data. NIPY Diffusion Imaging Analysis BSD License http://www.nitrc.org/projects/dipy/ matthew.brett@gmail.com GNU General Public License GPL Yes Sylvain Gouttard, gouttard@sci.utah.edu NITRC Linux C Sylvain Gouttard Two Slicer3 modules removing rician noise in diffusion tensor MRI 2010-5-20 Beta dtiricianrem Beta7 2007-12-13 Beta dtiricianrem Beta6 2007-10-25 Beta dtiricianrem Beta5 2007-10-23 Beta dtiricianrem Beta4 2007-10-22 Beta dtiricianrem Beta3 2007-10-22 Beta dtiricianrem Beta2 2007-10-22 Beta dtiricianrem Beta Slicer3 Module Rician noise filter Linux, C, English, GNU General Public License GPL, Beta, Developers, Console Text Based, Other Environment, Application, Other Format http://www.nitrc.org/projects/dtiricianrem/ gouttard@sci.utah.edu BSD License Yes Tri Ngo, tringo@gmail.com NITRC OS Independent,Linux C Tri Ngo Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images. This project provides tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography System End Users, Linux, C, Developers, English, BSD License, ProductionStable, Console Text Based, Other Environment, Application, Algorithm or Reusable Library, Other Format, OS Independent http://www.nitrc.org/projects/stfilter/ tringo@gmail.com SBIA License Yes Bilwaj Gaonkar, Bilwaj.Gaonkar@uphs.upenn.edu NITRC Bilwaj Gaonkar COMPARE Generic classification tool for 3D images 2011-2-28 COMPARE COMPARE SBIA License http://www.nitrc.org/projects/compare/ Bilwaj.Gaonkar@uphs.upenn.edu Columbia University Non-Commercial Software License Agreement Yes Qi Zhao, qz2106@columbia.edu NITRC Windows C Qi Zhao 3D Interactive Chemical Shift Imaging 3DiCSI is a user-friendly and comprehensive software program for multi-dimensional CSI data visualization spectral processing localization quantification and multi-variate analysis. 2007-12-21 ProductionStable 1.9.9 3D Interactive Chemical Shift Imaging Win32 MS Windows, Quantification, Spatial Transformation, Visualization, Statistical Operation, Temporal Transformation, DICOM, Other Format, Windows, C, English, ProductionStable, End Users, Columbia University Non-Commercial Software License Agreement http://www.nitrc.org/projects/threedicsi/ qz2106@columbia.edu GNU General Public License GPL Yes David Abbott, iBrain@brain.org.au NITRC OS Independent MATLAB David Abbott The iBrain Laterality Toolbox contains Matlab scripts that implement an objective threshold-independent assessment of whether the balance of activity between two regions of interest is typical or atypical based on statistical comparison between an individual and a group of controls. The toolbox displays laterality index LI plots as a function of an adaptive threshold and provides statistical assessment of the plots to determine lateralisation. The method is described in the following paper Abbott DF Waites AB Lillywhite LM Jackson GD. fMRI assessment of language lateralization An objective approach. Neuroimage 5041446-1455 2010. This toolbox is compatible with SPM2 SPM5 and SPM8. The data on which the toolbox operates need not have been generated by SPM. 2010-3-23 ProductionStable Version 1.0 iBrain™ Laterality Toolbox NIfTI-1, Win32 MS Windows, Other Environment, English, ProductionStable, MATLAB, ANALYZE, DICOM, MINC, End Users, Developers, OS Independent, Algorithm or Reusable Library, Quantification, Linear, Visualization, Other Software Resource, GNU General Public License GPL, X11 Applications http://www.nitrc.org/projects/ibrainli/ iBrain@brain.org.au LONI Software License Yes Scott Neu, neu@loni.ucla.edu NITRC OS Independent Yes Java Scott Neu The LONI Inspector is an application for examining medical image files. The Inspector focuses on reading displaying searching comparing and exporting amp;quot;metadataamp;quot; e.g. patient name the model of scanner. 2008-10-07 ProductionStable 2.0.1 2007-6-21 ProductionStable 2.0 LONI Inspector ProductionStable, End Users, Developers, LONI Software License, Java, English, Win32 MS Windows, X11 Applications, Other Environment, Workflow, Platform or Development Environment, Other Software Resource, ANALYZE, DICOM, MINC, NIfTI-1, OS Independent http://www.nitrc.org/projects/inspector/ neu@loni.ucla.edu Attribution Share Alike Yes Torsten Rohlfing, torsten@synapse.sri.com NITRC OS Independent Yes Torsten Rohlfing SRI24 is an MRI-based atlas of normal adult human brain anatomy generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1 T2 and PD weighted structural MRI tissue probability maps GM WM CSF maximum-likelihood tissue segmentation DTI-based measures FA MD longitudinal and transversal diffusivity and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze NIFTI and Nrrd format. We are also providing an experimental packaging for use with SPM8. As per the CC-BY-SA license please cite the following paper in publications using the SRI24 atlas T. Rohlfing N. M. Zahr E. V. Sullivan and A. Pfefferbaum “The SRI24 multichannel atlas of normal adult human brain structure” Human Brain Mapping vol. 31 no. 5 pp. 798-819 2010. DOI 10.1002hbm.20906 Free article on PMC httpwww.ncbi.nlm.nih.govpmcarticlesPMC2915788 2011-10-05 ProductionStable 1.02 2011-10-05 ProductionStable 1.02 2010-9-24 ProductionStable 0.00 SRI24 Atlas Normal Adult Brain Anatomy Data, Model, ProductionStable, End Users, Attribution Share Alike, OS Independent, ANALYZE, NIfTI-1, Nrrd http://www.nitrc.org/projects/sri24/ torsten@synapse.sri.com BrainMap License Yes Mick Fox, foxm@uthscsa.edu NITRC OS Independent Yes Java Mick Fox BrainMap is a community database of published functional neuroimaging studies mainly PET and fMRI. BrainMap contains both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates. 2011-8-30 ProductionStable Scribe 2.0 2011-8-30 ProductionStable Sleuth 2.0 2011-8-30 ProductionStable GingerALE 2.1 2009-8-20 ProductionStable GingerALE 2.0 2009-8-20 ProductionStable Sleuth 1.2 2008-10-10 ProductionStable Scribe 1.1.1 2007-10-01 ProductionStable Sleuth 1.1 2007-10-01 ProductionStable Scribe 1.1 2007-10-01 ProductionStable GingerALE 1.1 2007-4-01 ProductionStable Sleuth 1.0 2007-4-01 ProductionStable Scribe 1.0 2007-4-01 ProductionStable GingerALE 1.0 BrainMap Database Modeling, Visualization, Ontology, Websites, Database, ProductionStable, MR, PETSPECT, End Users, BrainMap License, English, OS Independent, Java, NIfTI-1 http://www.nitrc.org/projects/brainmap/ foxm@uthscsa.edu GNU General Public License GPL,OtherProprietary License Yes Robert Oostenveld, r.oostenveld@fcdonders.ru.nl NITRC OS Independent Yes MATLAB,C Robert Oostenveld FieldTrip is a Matlab software toolbox for MEG and EEG analysis that is being developed at the Centre for Cognitive Neuroimaging of the Donders Institute for Brain Cognition and Behaviour in Nijmegen The Netherlands together with collaborating institutes. The software includes algorithms for simple and advanced analysis of MEG and EEG data such as time-frequency analysis source reconstruction using dipoles distributed sources and beamformers and non-parametric statistical testing. It supports the data formats of all major MEG systems CTF Neuromag BTi and of the most popular EEG systems and new formats can be added easily. FieldTrip contains high-level functions that you can use to construct your own analysis protocols in Matlab. Furthermore it easily allows developers to incorporate low-level algorithms for new EEGMEG analysis methods. FieldTrip EEG Modeling, MEG Modeling, Fourier Time-domain Analysis, Algorithm or Reusable Library, Workflow, Spectral Analysis, Visualization, Multivariate Analysis, Registration, Independent Component Analysis, Mature, EEGMEGECoG, Console Text Based, End Users, Developers, GNU General Public License GPL, OtherProprietary License, English, OS Independent, MATLAB, C, MINC2, Other Format, AFNI BRIK, ANALYZE, DICOM, NIfTI-1, MINC http://www.nitrc.org/projects/fieldtrip/ r.oostenveld@fcdonders.ru.nl Public Domain Yes Christian Haselgrove, ch@neuromorphometrics.com NITRC OS Independent Yes PHP Christian Haselgrove The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community. IATR Database, Knowledge Environment, Software, Websites, Web Service, ProductionStable, Domain Independent, Web Environment, End Users, Developers, Public Domain, English, OS Independent, PHP http://www.nitrc.org/projects/iatr/ ch@neuromorphometrics.com Yes Monika Torres, torres@cedrus.com NITRC Yes Monika Torres The Lumina LP-400 is a reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields. Lumina LP- 400 Response System English, Mature, Response Monitoring http://www.nitrc.org/projects/lumina/ torres@cedrus.com Freeware Yes Daniel Glen, glend@mail.nih.gov NITRC MacOS,Linux Yes Python,C Daniel Glen AFNI is a set of C programs for processing analyzing and displaying FMRI data. It runs on UnixX11Motif systems including SGI Solaris Linux and Mac OS X. It is available free for research purposes. AFNI Volumetric Analysis, Region of Interest, Registration, C, Python, MacOS, Mature, End Users, Developers, Linux, Nonlinear, Freeware, Temporal Convolution - Deconvolution, Haemodynamic Response, Image Display, Rendering, Resampling, Tensor Metric, DICOM, AFNI BRIK, NIfTI-1, GIfTI, MINC, ANALYZE, X11 Applications, English, Surface Analysis, Response Monitoring http://www.nitrc.org/projects/afni/ glend@mail.nih.gov Commerical LicenseNIRx Yes Christoph Schmitz, cschmitz@nirx.net NITRC Christoph Schmitz NIRx Medical Technologies LLC. is a leader in providing integrated solutions for NIRS neuroimaging. We provide custom technology solutions to the investigative community for a wide range of NIRS imaging applications. While many of our systems are in the field of neuroscience infants to adults they are also used for investigation of breast cancer peripheral vascular disease and the study of small animals. NIRx NIRS Neuroimaging Tomography, NIRSFNIR, Commerical LicenseNIRx http://www.nitrc.org/projects/nirx/ cschmitz@nirx.net GNU General Public License GPL Yes Cinly Ooi, co224@cam.ac.uk NITRC OS Independent Java Cinly Ooi A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBAs and Brainwavers User interface. 2007-9-10 ProductionStable BrainFX SourceForge Link BrainFX NIfTI-1, Other Environment, OS Independent, Workflow, Platform or Development Environment, Developers, ProductionStable, GNU General Public License GPL, English, Java http://www.nitrc.org/projects/brainfx/ co224@cam.ac.uk GNU General Public License GPL Yes Gary Hui Zhang, garyhuizhang@gmail.com NITRC MacOS,Linux Yes C,shbash Gary Hui Zhang DTI-TK is a spatial normalization amp;amp; atlas construction toolkit designed from ground up to support the manipulation of diffusion-tensor images DTI with special cares taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter WM tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. The key features include - NIfTI support for scalar vector and DTI volumes - tool chains for manipulating DTI volumes resampling smoothing warping registration amp;amp; visualization - pipelines for WM morphometry spatial normalization amp;amp; atlas construction for population-based studies - built-in cluster-computing support - Interoperability with other major DTI tools AFNI Camino DTIStudio amp;amp; FSL 2012-1-09 ProductionStable 2.3 2012-1-09 ProductionStable 2.3 2011-6-06 ProductionStable 2.0.0 2011-5-31 ProductionStable 1.8.4 2011-2-16 ProductionStable 2.1 2009-6-21 ProductionStable web DTI-TK Console Text Based, X11 Applications, English, ProductionStable, NIfTI-1, ANALYZE, C, shbash, End Users, MacOS, Linux, Atlas Application, Intersubject, Image-to-Template, Visualization, GNU General Public License GPL http://www.nitrc.org/projects/dtitk/ garyhuizhang@gmail.com GNU General Public License GPL Yes Eugene DUff, eduff@pcomm.hfi.unimelb.edu.au NITRC MacOS,Linux Yes MATLAB Eugene DUff REX is a stand-alone MATLAB-based toolkit for the rapid and flexible exploration of ROI response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial. 2008-8-24 Alpha alpha0.5 2008-5-04 Alpha example_dataset 2008-5-03 Alpha alpha REX End Users, GNU General Public License GPL, Other Environment, NIfTI-1, ANALYZE, Visualization, Workflow, MATLAB, English, Alpha, Linux, MacOS, Time Domain Analysis http://www.nitrc.org/projects/rex/ eduff@pcomm.hfi.unimelb.edu.au Freeware Yes Chuyang Ye, Chuyang.Ye@yahoo.com NITRC Chuyang Ye Diffusion-Oirented Tract Segmentation DOTS is a fast scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation DOTS directly estimates the tract probabilities bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. 2011-2-28 Release 1B 2011-1-28 DOTS Release 1A DOTS Freeware http://www.nitrc.org/projects/dots/ Chuyang.Ye@yahoo.com LONI Software License Yes Scott Neu, neu@loni.ucla.edu NITRC OS Independent Yes Java Scott Neu The LONI de-identification Debablet is an application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner. 2005-10-13 ProductionStable 1.0 LONI De-identification Debablet Console Text Based, Win32 MS Windows, X11 Applications, Other Environment, Workflow, Platform or Development Environment, Other Software Resource, ANALYZE, DICOM, MINC, NIfTI-1, OS Independent, Java, English, ProductionStable, End Users, LONI Software License http://www.nitrc.org/projects/did/ neu@loni.ucla.edu Personal License Yes Donald McLaren, mclaren.donald@gmail.com NITRC Donald McLaren An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST. The automated toolbox can do the following a1 produce identical results to the current implementation in SPM a2 use the current implementation of PPI in SPM but using the regional mean instead of the eigenvariate a3 uses a generalized form that allows a PPI for each task to be in the same model using either the regional mean of eigenvariate b creates the model using the output of one of the a options and the first level design c estimates the model results directory d computes the contrasts specified 2012-1-22 PPPI_v2012_1_22 A Generalized Form of PPI Personal License http://www.nitrc.org/projects/gppi/ mclaren.donald@gmail.com GNU General Public License GPL Yes Arno Klein, arno@binarybottle.com NITRC OS Independent Yes MATLAB Arno Klein Mindboggle automates anatomical labeling of human brain MR data. Note the code here was part of a doctoral dissertation from 2005 is written in Matlab and has FSL 3.2 as a dependency. A new version is under development and will be completed in 2012. More information may be obtained from httpwww.mindboggle.info 2005-10-01 Beta 0.5 2005-10-01 Beta 0.5 Mindboggle automated brain labeling Console Text Based, OS Independent, Beta, GNU General Public License GPL, English, End Users, Developers, Anatomic, Atlas Application, ANALYZE, MATLAB http://www.nitrc.org/projects/mindboggle/ arno@binarybottle.com Attribution Yes Michael Milham, milham01@med.nyu.edu NITRC OS Independent Yes Michael Milham The NYU CSC TestRetest resource includes EPI-images of 25 participants gathered during rest as well as anonymized anatomical images of the same participants. The resting-state fMRI images were collected on several occasions 1. the first resting-state scan in a scan session 2. 5-11 months after the first resting-state scan 3. about 30 amp;lt; 45 minutes after 2. Each scan occasion is released as a new version release of the resource. Make sure to check all releases to get all files. Data use is unrestricted but users should reference our original publications and NITRC see Documentations. Caution Participants here are part of the NewYork_a contribution to the 1000 Functional Connectomes Project. DO NOT combine datasets. Acquisition was funded by Stavros S. Niarchos Foundation the Leon Lowenstein Foundation NARSAD The Mental Health Research Association grants to F.Xavier Castellanos; and Linda and Richard Schaps Jill and Bob Smith and the Taubman Foundation gifts to F.Xavier Castellanos. 2009-9-01 NYU_TRT_session1 2009-9-01 NYU_TRT_session2 2009-9-01 NYU_TRT_session3 NYU CSC TestRetest Data, Test Data, MR, End Users, Other Audience, Attribution, OS Independent, NIfTI-1 http://www.nitrc.org/projects/nyu_trt/ milham01@med.nyu.edu BSD License Yes Terry Lorber, tgl@rideside.net NITRC Windows NT2000,Windows Vista,MacOS,Linux Yes C Terry Lorber Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. 2008-11-24 Alpha 0.0.2 2008-10-29 Alpha 0.0.1 2008-10-21 Alpha 0.0.1 Slicer3 Example Modules Win32 MS Windows, X11 Applications, Alpha, Developers, Platform or Development Environment, Application, DICOM, NIfTI-1, ANALYZE, MacOS, Windows NT2000, Windows Vista, Linux, C, English, BSD License, Console Text Based http://www.nitrc.org/projects/slicer3examples/ tgl@rideside.net Freeware Yes Rainer Goebel, rainergoebel@mac.com NITRC MacOS,Windows C Rainer Goebel The free BrainVoyager Brain Tutor teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging MRI scans. Besides having fun with the rotatable 3D models the program contains information about the major lobes gyri sulci and Brodmann areas of the cerebral cortex. 2010-11-10 ProductionStable BrainVoyager Brain Tutor 2.5 2010-9-24 ProductionStable BrainVoyager Brain Tutor HD for iPad 2009-1-14 ProductionStable Brain Tutor 3D for iPhone BrainVoyager Brain Tutor MacOS, Windows, Other Format, Win32 MS Windows, Other Environment, English, ProductionStable, End Users, C, Application, Information Resource, Freeware http://www.nitrc.org/projects/bvbraintutor/ rainergoebel@mac.com GNU General Public License GPL Yes , NITRC Microsoft MATLAB MEG Localization using FOCUSS and MR-FOCUSS MEG Tools Image Reconstruction, Alpha, EEGMEGECoG, X11 Applications, Win32 MS Windows, End Users, GNU General Public License GPL, English, Microsoft, MATLAB, Other Format http://www.nitrc.org/projects/meg-tools/ BSD License Yes Karen Pease, karen-pease@uiowa.edu NITRC MacOS,Linux,Microsoft C Karen Pease This suite of tools will generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature. BRAINSCortex Morphology, BSD License, MacOS, Linux, Microsoft, ANALYZE, NIfTI-1, Nrrd, Console Text Based, English, Alpha, End Users, C http://www.nitrc.org/projects/brainscortex/ karen-pease@uiowa.edu BSD License Yes Stephan Gerhard, connectome@unidesign.ch NITRC Python Stephan Gerhard The Connectome File Format CFF is a container format for multi-modal neuroimaging data. It comprises connectome objects of type CMetadata CNetwork CVolume CSurface CTrack CScript CData CTimeseries CImagestack. The Python library cfflib provides readwrite functionality. Connectome File Format CFF Python, End Users, BSD License, File Format, GIfTI, NIfTI-1, PDF - Portable Document Format, Other Format http://www.nitrc.org/projects/cff/ connectome@unidesign.ch Personal License Yes Donald McLaren, mclaren.donald@gmail.com NITRC Donald McLaren peak_nii Statistical image clustering peak detection and data extraction. The Peak_nii toolbox was developed to allow the user to have flexibility of clustering their data. Based on your threshold it will cluster your data and find the peaks within each cluster. Additionally it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters along with several other extraction options with a single command. peak_nii Personal License http://www.nitrc.org/projects/peak_nii/ mclaren.donald@gmail.com Freeware Yes Todd Woodward, toddswoodward@gmail.com NITRC MacOS,Linux,Windows Yes MATLAB Todd Woodward Constrained Principal Component Analysis CPCA combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time using all other scans as baseline. CPCA provides allows 1 determination of multiple functional networks involved in a task 2 estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points 3 quantification of the degree of interaction between these multiple functional networks and 4 a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format as well as writing images in analyze format for all components rotated and unrotated. 2012-1-30 Beta fMRI_CPCA GUI 2011-12-02 Beta fMRI-CPCA Example Data 2011-7-07 Beta fMRI-CPCA Installation amp;amp; Use 2011-7-07 Beta fMRI-CPCA Literature fMRI-CPCA English, Beta, ANALYZE, NIfTI-1, MATLAB, End Users, Linux, Windows, MacOS, Principal Component Analysis, Regression, Freeware http://www.nitrc.org/projects/fmricpca/ toddswoodward@gmail.com GNU General Public License GPL Yes Kristian Kvilekval, kris@cs.ucsb.edu NITRC Kristian Kvilekval Bisque Bio-Image Semantic Query User Environment is a scalable web-based system for biological image analysis management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops. Bisque GNU General Public License GPL http://www.nitrc.org/projects/bisque/ kris@cs.ucsb.edu 3D Slicer License Yes Dominik Meier, meier@bwh.harvard.edu NITRC MacOS,Linux,Windows Yes C,TclTk,Python Dominik Meier An extensible cross-platform totally open research platform for image computing. 2011-3-03 ProductionStable 3.6.3 2010-6-10 ProductionStable Slicer 3.6 2009-6-11 ProductionStable Slicer 3.4 2008-8-21 ProductionStable Slicer 3.2 2007-9-23 ProductionStable 3 2.6 and others 3D Slicer C, TclTk, DICOM, NIfTI-1, MGHMGZ, Nrrd, Other Format, ANALYZE, bshortbfloat, Morphology, Volume Measurement, Image-to-Image, Resampling, Warping, Tensor Metric, Tractography, Visualization, Platform or Development Environment, ProductionStable, CT, MR, PETSPECT, Win32 MS Windows, X11 Applications, End Users, Developers, 3D Slicer License, English, MacOS, Windows, Linux, Python http://www.nitrc.org/projects/slicer/ meier@bwh.harvard.edu GNU General Public License GPL Yes Michael T Rubens, michael@gazzaleylab.ucsf.edu NITRC Michael T Rubens This script will take any .img file and correct it based on a cluster extent cluster definition and voxelwise threshold. The threshold entered will be applied to positive and negative values separately and separate pos and neg corrected images will be output. This script requires a license for the matlab image processing toolbox. 2011-3-08 1.1 Cluster Extent Correction GNU General Public License GPL http://www.nitrc.org/projects/cluster_correct/ michael@gazzaleylab.ucsf.edu 3D Slicer License Yes Jean-Baptiste BERGER, jibberger@gmail.com NITRC Linux Yes C Jean-Baptiste BERGER This is a command line tool which allows the user to study the behavior of water diffusion using DTI data along the length of the white matter fiber-tracts. Various tract-oriented scalar diffusion measures obtained from DTI brain images are treated as a continuous function of white matter fibers arc-length. To analyze the trend along a given fiber tract a command line tool performs kernel regression on this data. The idea is to try out different noise models and maximum likelihood estimates within kernel windows along the tract such that they best represent the data and are robust to noise and Partial Volume effect. The package contains several command line based modules and an GUI based tool called DTIAtlasFiberAnalyzer to access most functions. The features available in the tool currently its use and input output formats and other relevant details are provided in the first draft of the documentation. httpwww.na-mic.orgWikiindex.phpProjectsdtistatisticsfibers. 2011-12-07 dti_tract_stat_1.2 2011-7-28 dti_tract_stat_1.1 2010-9-28 dti_tract_stat version 2 2010-9-20 dti_tract_stat version 1 DTI Fiber Tract Statistics English, C, Developers, End Users, Linux, Regression, 3D Slicer License http://www.nitrc.org/projects/dti_tract_stat/ jibberger@gmail.com GNU Lesser General Public License LGPL Yes Zhoubing Xu, doraemon3719@gmail.com NITRC Zhoubing Xu This collection of tools is maintained by the Medical-image Analysis and Statistical Interpretation MASI group at Vanderbilt University. The purpose of this tool is to provide a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote weighted voting and regionally weighted voting. Additionally multiple statistical fusion methods will be included notably STAPLE Spatial STAPLE STAPLER and COLLATE. In addition to the fusion algorithms code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided. 2011-11-02 masi-fusion-v1.1 2011-11-02 masi-fusion-v1 MASI Label Fusion GNU Lesser General Public License LGPL http://www.nitrc.org/projects/masi-fusion/ doraemon3719@gmail.com GNU General Public License GPL Yes Michael T Rubens, michael@gazzaleylab.ucsf.edu NITRC Michael T Rubens This matlab script and associated files will take resultant statistical images and essentially output everything you could ever want to know. It can work off of images that were previously corrected for multiple comparisons but it can actually do the correction itself. This is because the cluster_correct script is incorporated within. It will iterate through atlases borrowed from other software to tell you the location of significant results. It outputs an extremely detailed report as well as a summary table for quick investigation. In addition it will output statistics for each surviving cluster and the image as a whole.Feedback would be much appreciated. 2011-3-10 1.1 Cluster reporter GNU General Public License GPL http://www.nitrc.org/projects/cluster_report/ michael@gazzaleylab.ucsf.edu GNU General Public License GPL Yes Ariana Anderson, ariana82@ucla.edu NITRC Ariana Anderson We demonstrate and provide R code that can classify between groups of fMRI scans based on functional network connectivity differences requiring only 4 lines of code to be altered. In addition we include a detailed article explaining the methods behind and motivations of this tool. This code can also be altered to perform connectivity analysis and classification using ROI based methods by reading in distance arrays previously created. We run ICA on fMRI data to establish functional networks measure the functional connectivity between these networks using the temporal cross-correlations between independent component to create a distance matrix and indicating the networking. Connectivity properties are used as a feature matrix for an SVM classifier. Collectively this project provides and explains both methods and code to perform functional network connectivity and fMRI SVM classification. 2011-3-15 version1 fMRI Classification in R GNU General Public License GPL http://www.nitrc.org/projects/fmriclassify/ ariana82@ucla.edu Paradigm License Yes Bruno Tagliaferri, bruno@prsemail.com NITRC Microsoft Python Bruno Tagliaferri Flexible and millisecond accurate experimental control for cognitive neuroscience psychology and linguistics research. Build your experiments using Paradigms simple drag and drop interface. Presents text images sounds movies self-paced reading trials and rating scales. An integrated Python scripting API is available to ensure total flexibility and control. Joystick and microphone response are available. Supports button boxes from PST Cedrus and custom built response boxes. Paradigm can detect fMRI triggers through serial and parallel ports. Includes sample experiments that implement many of the most popular experiment designs. 2011-7-13 ProductionStable Paradigm v1.0.3 Paradigm Win32 MS Windows, ProductionStable, Python, Experimental Control, Eye Tracking, Microsoft, Paradigm License, EEG, Scanner http://www.nitrc.org/projects/paradigm/ bruno@prsemail.com GNU General Public License GPL Yes Tim Mullen, mullen.tim@gmail.com NITRC Yes Tim Mullen The Source Information Flow Toolbox SIFT is an GUI-enabled EEGLAB plugin for modeling and visualizing dynamical interactions between electrophysiological signals EEG ECoG MEG etc preferably after transforming signals into the source domain. The toolbox consists of four modules 1 Data Preprocessing 2 Model Fitting and Connectivity Estimation 3 Statistical Analysis 4 Visualization with a fifth Group Analysis module in development. Module 2 currently includes several adaptive multivariate autoregressive modeling AMVAR algorithms including segmentation AMVAR and Kalman filtering. This subsequently allows the user to validate the model and estimate in the time-frequency domain a wide range of multivariate Granger-causal and coherence measures published to date. Module 3 includes routines for parametric and non-parametric significance testing. Module 4 contains routines for interactive visualization of dynamical interactions across time frequency and anatomical source location. 2011-12-16 SIFT_R085a Source Information Flow Toolbox EEGMEGECoG, GNU General Public License GPL http://www.nitrc.org/projects/sift/ mullen.tim@gmail.com BSD License Yes Valerie Cardenas NIcolson, valerie.cardenas-nicolson@ucsf.edu NITRC Linux,Windows XP Yes Java,C,C Valerie Cardenas NIcolson valmap is a command line voxel-wise statistical analysis program for images. Images can be gray matter density jacobian images etc. The linear model is implemented i.e. designs that can be modeled as Y=AB where Y is a vector or matrix of dependent variables B is a vector or matrix of parameters to be estimated and A is a design matrix. Why use valmap 1. Do not need a Matlab license to run. 2. Can incorporate a spatially varying independent variable e.g. you have a perfusion map as your dependent variable and you want to co-vary for gray matter at each voxel so use a gray matter map as an independent variable. 3. Can use spatially invariant independent variables e.g. you can have a cognitive test score as the dependent variable and use jacobian maps as the independent variable. 4. Can have multiple dependent variables and do multivariate analyses e.g. want to know the overall effect of disease on perfusion and structure so use perfusion maps and jacobian maps as dependent variables. 2011-3-31 ProductionStable valmap 2.0 2009-11-12 ProductionStable valmap-1.0 ValMap simple statistical mapping tool Win32 MS Windows, English, ProductionStable, BSD License, Morphology, Linear, C, C, Java, ANALYZE, NIfTI-1, End Users, Windows XP, Linux, Console Text Based http://www.nitrc.org/projects/valmap/ valerie.cardenas-nicolson@ucsf.edu GNU Lesser General Public License LGPL Yes Yogesh Rathi, yogesh@bwh.harvard.edu NITRC POSIXUNIX-like,Windows C Yogesh Rathi We present a framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1- 2- or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape the second and third eigenvalue are assumed to be identical and the other one uses a full tensor representation. The project is written in C. It could be used both as a Slicer3 module and as a standalone commandline application. 2011-11-18 Alpha ukf-1.1-alpha 2011-7-25 Alpha ukf-1.0-alpha Tractography with Unscented Kalman Filte GNU Lesser General Public License LGPL, Diffusion MR Fiber Tracking, Console Text Based, Win32 MS Windows, X11 Applications, English, Alpha, C, End Users, Developers, Windows, POSIXUNIX-like, Other Format, Nrrd http://www.nitrc.org/projects/ukftractography/ yogesh@bwh.harvard.edu Yes Pierre FILLARD, Pierre.Fillard@gmail.com NITRC Pierre FILLARD MedINRIA allows to process and analyze a wide range of magnetic resonance MR images including anatomical MRI functional MRI fMRI and diffusion tensor MRI DT-MRI. MedINRIA is intended to be used by anyone curious about medical images MedINRIA http://www.nitrc.org/projects/medinria/ Pierre.Fillard@gmail.com 3D Slicer License Yes Marcel Prastawa, prastawa@sci.utah.edu NITRC Linux,Windows Yes C Marcel Prastawa ABC Atlas Based Classification is a comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration filtering segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput. 2011-10-20 Beta UNC Primate Brain Atlas 2011-10-20 Beta UNC Human Brain Atlas 2010-11-22 Beta v1.4 2010-10-04 Beta v1.3 2010-9-16 Beta v1.2 2010-1-21 Beta v1.1 2010-1-05 Beta v1.0.1 2009-12-04 Beta ICBMSPM Adult Atlas ABC Atlas Based Classification Linux, Segmentation, Windows, Beta, 3D Slicer License, C http://www.nitrc.org/projects/abc/ prastawa@sci.utah.edu LONI Software License Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The FFT Java library httpwww.loni.ucla.eduSoftwareFFT is used for the execution of discrete Fourier transforms in 1-D 2-D and 3-D through the implementation of Fast Fourier Transform FFT algorithms. FFT toolbox is distributed by the Laboratory of Neuro Imaging httpwww.loni.ucla.eduSoftwareFFT at UCLA. Fast Fourier Transform FFT JavaLibrary LONI Software License http://www.nitrc.org/projects/fft/ iwaterpolo@gmail.com Apache License 2.0 Yes Rupert Brooks, rupert.brooks@gmail.com NITRC TclTk Rupert Brooks Draw3D is a 3D rendering tool written entirely in VTK-TCL script. It is intended for fast command line rendering and visual inspection of datasets commonly found in medical imaging. It also allows the generation of images for reports or videos. As it is based on pure VTK it can render whatever VTK can render and runs wherever VTK can run. Meshinator is a simpler tool that uses VTKs isosurface functions to generate meshes from volumetric data. Please see the wiki for documentation 2011-3-29 Beta 1.0 Draw3D and Meshinator Beta, TclTk, Visualization, Apache License 2.0 http://www.nitrc.org/projects/draw3d/ rupert.brooks@gmail.com LONI Software License Yes I Dinov, iwaterpolo@gmail.com NITRC Windows NT2000,MacOS,Linux,SunOSSolaris Yes Java I Dinov The LONI Pipeline is a free workflow application primarily aimed at neuroimaging researchers but is useful for many other fields of science. The Pipeline Client runs on your PCMacLinux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools e.g. FSL AIR FreeSurfer AFNI etc. The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Visit httppipeline.loni.ucla.edu for more info. The Pipeline is distributed by the Laboratory of Neuro Imaging httpwww.loni.ucla.eduSoftwarePipeline at UCLA. 2011-11-22 ProductionStable Pipeline V.5.3.1 2011-5-18 ProductionStable Pipeline V5.2.1 2010-9-16 ProductionStable V.5.1 2010-5-24 ProductionStable Pipeline V5.0.1 2010-4-01 ProductionStable Pipeline V5.0 2010-3-03 ProductionStable Pipeline V4.5.2 2010-1-19 ProductionStable Pipeline V4.5.1 2009-12-15 ProductionStable Pipeline V4.5 2009-9-20 ProductionStable Pipeline V4.4. 2009-7-14 ProductionStable Pipeline V4.3.3 2009-6-23 ProductionStable Pipeline V4.3.2 2009-5-03 ProductionStable Pipeline V4.3.1 2009-4-27 ProductionStable Pipeline V4.3 2009-1-26 ProductionStable Pipeline V4.2 2007-12-17 ProductionStable 4.0 RC2 build 1247 2007-8-27 ProductionStable v4.0 Beta LONI Pipeline Environment DICOM, Other Environment, Workflow, ANALYZE, MINC, MINC2, NIfTI-1, End Users, bshortbfloat, AFNI BRIK, MGHMGZ, Other Format, Windows NT2000, MacOS, LONI Software License, Linux, SunOSSolaris, Java, English, ProductionStable, Developers http://www.nitrc.org/projects/pipeline/ iwaterpolo@gmail.com Creative Commons License Yes Karen Pease, karen-pease@uiowa.edu NITRC C Karen Pease NOTE All active development of BRAINSConstellationDetector is now being stored in a Git repository at github.com. Please go to httpsgithub.comBRAINSiaBRAINSStandAlone This program will find the mid-sagittal plane the AC PC and mpj points in an image and create an ACPC aligned data set with the AC point at the center of the voxel lattice la beled at the origin of the image physical space. This work is an extention of the algorithms originally described by Dr. Babak A. Ardekani Alvin H. Bachman Model-based automatic detection of the anterior and posterior commissures on MRI scans N euroImage Volume 46 Issue 3 1 July 2009 Pages 677-682 ISSN 1053-8119 DOI 10.1016j.neuroimage.2009.02.030. httpwww.sciencedirect.comsciencearticleB6WNP-4VRP25C-428207b962a38aa83c822c6379bc43fe4c BRAINSConstellationDetector NIfTI-1, ANALYZE, Creative Commons License, Fiducial, DICOM, Nrrd, English, ProductionStable, C, End Users http://www.nitrc.org/projects/brainscdetector/ karen-pease@uiowa.edu Yes Hongjun Jia, jiahj@email.unc.edu NITRC Windows NT2000,Windows Vista,Linux,Windows 95982000,Windows XP Yes Other Programming Language,C,C Hongjun Jia This software package implements ABSORB Atlas Building by Self-Organized Registration and Bundling – an algorithm for effective groupwise registration which has been published as Hongjun Jia Guorong Wu Qian Wang Dinggang Shen amp;quot;ABSORB Atlas Building by Self-Organized Registration and Bundlingamp;quot; NeuroImage Vol. 51 No. 3 1 July 2010 pp. 1057-1070. The package is available free to the public for the academic research purpose at httpbric.unc.eduideagroupfree-softwares . The required input is a set of 3D MR intensity images in Analyze format with paired .hdr and .img files with a text file .txt listing all header file .hdr names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP 32-bit and Linux 64-bit kernel version 2.6.18-194.el5. This software was developed in IDEA group in UNC-Chapel Hill. For more information please visit our lab at httpbric.unc.eduideagroup . 2010-10-29 Alpha Webpage about ABSORB 2010-9-01 Alpha ABSORB_manual_20100901 2010-7-29 Alpha ABSORB_software_win32_20100729 2010-7-29 Alpha ABSORB_software_linux64_20100729 2010-7-29 Alpha ABSORB_testdata 2010-7-29 Alpha ABSORB_manual ABSORB for groupwise registration Windows 95982000, Win32 MS Windows, X11 Applications, Other Environment, English, Alpha, Beta, ProductionStable, ANALYZE, Microsoft Word Document, PDF - Portable Document Format, C, C, Other Programming Language, End Users, Developers, Other Audience, System Administrators, Windows XP, Windows Vista, Windows NT2000, Linux, Algorithm or Reusable Library, Nonlinear Warp, Affine Warp, Image-to-Template, Intermodal, Intrasubject, Intersubject http://www.nitrc.org/projects/absorb/ jiahj@email.unc.edu Creative Commons License Yes Joshua Vogelstein, jv.work@jhu.edu NITRC Joshua Vogelstein The Open Connectome Project OCP openconnectomeproject.org provides access to high resolution neuroanatomical images that can be used to explore connectomes. We also provide programmatic access to this data for human and machine annotation with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access so collectively we can begin to unravel connectomes. Open Connectome Project Creative Commons License http://www.nitrc.org/projects/ocp/ jv.work@jhu.edu Attribution Non-Commercial Yes sharad sikka, ssikka25@gmail.com NITRC OS Independent Yes sharad sikka ATTENTION The 1000 Functional Connectomes Project has a new home page at NITRC. Please visit us at httpfcon_1000.projects.nitrc.org or simply click on DOWNLOAD NOW below to be redirected. 2010-10-01 ProductionStable fcon_1000.projects.nitrc.org 2010-3-10 ProductionStable fcon_1000_scripts_ver1.1 2010-3-03 ProductionStable fcon_1000_scripts_ver1.1-beta 2009-12-11 ProductionStable Baltimore Pekar J.J.Mostofsky S.H.; n = 23 8M15F; ages 20-40; TR = 2.5; slices = 47; timepoints = 123 2009-12-11 ProductionStable Bangor Colcombe S.; n = 20 20M0F; ages 19-38; TR = 2; slices = 34; timepoints = 265 2009-12-11 ProductionStable Beijing_Zang Zang Y.F.; n = 198 76M122F; ages 18-26; TR = 2; slices = 33; timepoints = 225 2009-12-11 ProductionStable Berlin_Margulies Margulies D.; n = 26 13M13F; ages 23-44; TR = 2.3; slices = 34; timepoints = 195 2009-12-11 ProductionStable Cambridge_Buckner Buckner R.L.; n = 198 75M123F; ages 18-30; TR = 3; slices = 47; timepoints = 119 2009-12-11 ProductionStable Cambridge_Whitfield-Gabrieli Whitfield-Gabrieli S.; n = 39 18M20F1; ages 20-32; TR = 2; slices = 36; timepoints = 145 2009-12-11 ProductionStable Cleveland Lowe M.J.; n = 31 11M20F; ages 24-60; TR = 2.8; slices = 31; timepoints = 127 2009-12-11 ProductionStable Dallas Rypma B.; n = 24 12M12F; ages 20-71; TR = 2; slices = 36; timepoints = 115 2009-12-10 ProductionStable Durham_Madden Madden D.J.; n = 42 na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable ICBM Evans A.C.; n = 86 41M45F; ages 19-85; TR = 2; slices = 23; timepoints = 128 2009-12-10 ProductionStable Leiden Rombouts S.A.R.B. 2009-12-10 ProductionStable Leipzig Villringer A.; n = 37 16M21F; ages 20-42; TR = 2.3; slices = 34; timepoints = 195 2009-12-10 ProductionStable Milwaukee Li S.J. 2009-12-10 ProductionStable Munchen Sorg C.Riedl V.; n = 16 10M6F; ages 63-73; TR = 3; slices = 33; timepoints = 72 2009-12-10 ProductionStable Newark Biswal B.; n = 19 9M10F; ages 21-39; TR = 2; slices = 32; timepoints = 135 2009-12-10 ProductionStable New Haven Hampson M. 2009-12-10 ProductionStable New York Milham M.P.Castellanos F.X. 2009-12-10 ProductionStable New York Test-Retest Reliability Milham M.P.Castellanos F.X.; n = 25 10M15F; ages 22-49; TR = 2; slices = 39; timepoints = 197 2009-12-10 ProductionStable Ontario Williamson P.; n = 11 na; ages na; TR = 3; slices = 29; timepoints = 105 2009-12-10 ProductionStable Orangeburg Hoptman M.; n = 20 15M5F; ages 20-55; TR = 2; slices = 22; timepoints = 165 2009-12-10 ProductionStable Oulu Kiviniemi V.J.Veijiola J.; n = 103 37M66F; ages 20-23; TR = 1.8; slices = 28; timepoints = 245 2009-12-10 ProductionStable Oxford Smith S.M.Mackay C.; n = 22 12M10F; ages 20-35; TR = 2; slices = 34; timepoints = 175 2009-12-10 ProductionStable Palo Alto Greicius M.; n = 17 2M15F; ages 22-46; TR = 2; slices = 29; timepoints = 235 2009-12-10 ProductionStable Pittsburgh Siegle G.; n = 17 10M7F; ages 25-54; TR = 1.5; slices = 29; timepoints = 275 2009-12-10 ProductionStable Queensland McMahon K.; n = 19 11M8F; ages 20-34; TR = 2.1; slices = 36; timepoints = 190 2009-12-10 ProductionStable Saint Louis Schlaggar B.Petersen S.; n = 31 14M17F; ages 21-29; TR = 2.5; slices = 32; timepoints = 127 2009-12-10 ProductionStable Taipei Lin C.P. 2009-12-10 ProductionStable Atlanta Mayberg H.S.; n = 28 13M15F; ages 22-57; TR = 2; slices = 20; timepoints = 205 2009-12-10 ProductionStable Ann Arbor Monk C.S.Seidler R.D.Peltier S.J. 2009-12-10 ProductionStable Berlin_Schmidt Schmidt S.; n = 11 na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Nanjing Teng G.J.Zhang H.Y.; n = 22 4M12F6; ages 60-80; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Durham_Wang Wang L.; n = na na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Hvidovre Dogonowski A.M.Madsen K.; n = na na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Magdeburg Walter M.; n = na na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Portland Fair D.Nagel B.; n = na na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Vienna Windischberger C.; n = na na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Beijing_Weng Weng X.C.; n = na na; ages na; TR = na; slices = na; timepoints = na 2009-12-10 ProductionStable Bethesda Ernst M.; n = na na; ages na; TR = na; slices = na; timepoints = na 1000 Functional Connectomes Project English, OS Independent, NIfTI-1, Data, ProductionStable, MR, End Users, Attribution Non-Commercial http://www.nitrc.org/projects/fcon_1000/ ssikka25@gmail.com Free For Non-Commercial Use Only Yes roberto d. pascual-marqui, pascualm@key.uzh.ch NITRC roberto d. pascual-marqui LORETA low resolution brain electromagnetic tomography is a technique for functional imaging of the human brain. It computes the three dimensional distribution of electric neuronal activity throughout cortical grey matter from non-invasive measurements of scalp electric potential differences EEG electroencephalogram with high time resolution in the millisecond range. The non-invasive intracranial time series are used for studying functional dynamic connectivity. The current software implementation is limited to EEG although LORETA is defined for EEG and MEG magnetoencephalogram. The standardized and exact versions of LORETA produce images with zero localization error. Low Resolution Electromag TomogrAphy EEGMEGECoG, Free For Non-Commercial Use Only http://www.nitrc.org/projects/loreta/ pascualm@key.uzh.ch Yes Michael T Rubens, michael@gazzaleylab.ucsf.edu NITRC Michael T Rubens Input either normalized amp;quot;MNIamp;quot; coordinates from a 3D image or input amp;quot;real worldamp;quot; XYZ matrix coordinates and this code will convert coordinates of one type to the other. 2011-10-26 version2 2011-4-08 1.0 Convert MNI coordinates to or from XYZ http://www.nitrc.org/projects/mni2orfromxyz/ michael@gazzaleylab.ucsf.edu 3D Slicer License Yes Ryan Eckbo, reckbo@bwh.harvard.edu NITRC Ryan Eckbo This package is a set of three slicer modules which together are able to compute a DWI Atlas given a set of DWIs. The modules included are 1 A Groupwise Registration module -amp;gt; computes a deformation field for each DWI using for example FA maps as input 2 Warp DWI module -amp;gt; used to warp each DWI using the deformation from 1 3 DWI Averager -amp;gt; used to average the set of warped DWIs producing the final DWI Atlas Create DWI Atlas 3D Slicer License http://www.nitrc.org/projects/createdwiatlas/ reckbo@bwh.harvard.edu BSD License Yes Nitin Bangera, nitinb2@gmail.com NITRC Linux,Windows MATLAB Nitin Bangera POLGUI is an interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 on both linux and windows platforms 1. polgui_ver1_r14 works with 1 receiver stylus pen 2. polgui_ver2_r14 works with 2 receivers including the pen 3. polgui_ver3_r14 works with 3 receiversincluding the pen 4. polgui_ver4_r14 works with 4 receivers including the pen 5. polgui_ver5_r14 Generic version which works with 1234 receivers WARNING Ver 5 might be buggy; not fully tested Requirements MATLAB R14 LinuxWindows 2008-11-04 Beta 1.0-5.0 POLGUI- Matlab GUI for Polhemus Fastrak Windows, Linux, X11 Applications, Win32 MS Windows, English, Beta, MATLAB, Other Software Resource, End Users, BSD License http://www.nitrc.org/projects/polgui/ nitinb2@gmail.com GNU General Public License GPL Yes Stephan Gerhard, connectome@unidesign.ch NITRC MacOS,Linux,Windows C,Python Stephan Gerhard Connectome Viewer is free open source cross-platform Python-based software application for visualization and analysis in connectome research. Features of the software include Connectome File Format including metadata networks surfaces volumes track files Complex network analysis toolboxes Modular plugin architecture for extensibility Mayavi2 for 3D Scientific Visualization and Plotting Interactive data manipulation and scripting capabilities Neuroimaging and Diffusion in Python libraries Connectome Viewer X11 Applications, Win32 MS Windows, English, Beta, Python, C, GIfTI, NIfTI-1, Other Format, End Users, Developers, MacOS, Three Dimensional Display, Animation, Tractography, GNU General Public License GPL, Windows, Linux, Atlas Application, Format Conversion, Volume Rendering, Surface Rendering, Two Dimensional Display http://www.nitrc.org/projects/cviewer/ connectome@unidesign.ch Public Domain Yes Moriah Thomason, moriah@wayne.edu NITRC Yes Moriah Thomason Group ICA was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children ages 9-15. We have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates. 2011-3-20 resting-state pediatric imaging template resting-state pediatric imaging template ANALYZE, Atlas Data, Public Domain http://www.nitrc.org/projects/r-spit/ moriah@wayne.edu Yes Hongjun Jia, jiahj@email.unc.edu NITRC Hongjun Jia This software package implements MABMIS Multi-Atlas-Based Multi-Image Segmentation – an algorithm for accurate and consistent segmentationlabeling on a group of images. 2011-7-28 MABMIS_20110725 MABMIS Multi-Atlas Based Segmentation http://www.nitrc.org/projects/mabmis/ jiahj@email.unc.edu Comercial Licence Rogue Research Inc. Yes Roch Comeau, roch@rogue-research.com NITRC Roch Comeau Neuronavigation system for use in human cognitive neuroscience TMS EEG NIRS and for non-human neurosurgical applications. Brainsight NIRSFNIR, Surface Rendering, EEG, EEGMEGECoG, Optical Imaging, Comercial Licence Rogue Research Inc., DICOM, NIfTI-1, MINC, MINC2, Philips PARREC http://www.nitrc.org/projects/brainsight/ roch@rogue-research.com Web Application - Free to use Yes Marc Rousseau, marc.rousseau@mcgill.ca NITRC Marc Rousseau CBRAIN is a flexible software platform with a small footprint and minimal requirements. CBRAIN was created to allow the integration the often extremely heterogeneous research HPC facilities across Canada and the World. Moreover the platforms goal was not limited to deploying national and international distributed data and compute grids for neuroimaging sites CBRAIN is an online collaborative web platform from which users transparently control their data compute and results including various forms of 2D and 3D data visualisation regardless of where these resources and data are. CBRAIN is currently deployed on 6 Compute Canada HPC clusters one German HPC cluster and 3 clusters local to McGill University Campus totaling more than 80000 potential CPU cores. Visit us at httpcbrain.mcgill.ca CBRAIN Web Application - Free to use http://www.nitrc.org/projects/cbrain/ marc.rousseau@mcgill.ca BSD License Yes Marc Niethammer, mn@cs.unc.edu NITRC Linux Yes C Marc Niethammer FRAT provides c libraries and applications for performing fluid registration based operations on 2D and 3D images. The registration method is based on the large displacement diffeomorphic mapping LDDM registration method and implements discretized fluid registration. This registration method is then applied to time series analysis cross-sectional atlas building and longitudinal atlas building. The individual tool components are LDDM Fluid registration between two images. TimeSeries Time series analysis of longitudinal data for a single subject. AtlasBuilder Cross-sectional atlas building for a population of images. LongitudinalAtlasBuilder Longitudinal atlas building for a population of subjects each with a longitudinal data set. FRATUtils A collection of utility functions for working with volumes and time series files Fluid Registration and Atlas Toolkit Console Text Based, English, Pre-Alpha, Nrrd, Other Format, C, Developers, End Users, Linux, Atlas Application, Image-to-Image, Nonlinear Warp, BSD License http://www.nitrc.org/projects/frat/ mn@cs.unc.edu 3D Slicer License Yes Harini Veeraraghavan, hariniraghav@gmail.com NITRC Harini Veeraraghavan Allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy. Faceted Search Based Ontology Visualizer 3D Slicer License http://www.nitrc.org/projects/ontologyviz/ hariniraghav@gmail.com GNU General Public License GPL Yes John West, jdwest@iupui.edu NITRC POSIXUNIX-like,Windows MATLAB,C John West SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM which creates parametric surface models using spherical harmonics. It is a matlab-based 3D shape modeling and analysis toolkit and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. 2010-6-20 Beta v1.0.0 SPHARM-MAT Win32 MS Windows, X11 Applications, Other Environment, English, Beta, ANALYZE, NIfTI-1, Other Format, MATLAB, C, End Users, Windows, POSIXUNIX-like, Spherical Harmonics, Surface Analysis, Quantitative Shape Analysis, Morphology, GNU General Public License GPL http://www.nitrc.org/projects/spharm-mat/ jdwest@iupui.edu Attribution Non-Commercial Share Alike Yes Cameron Craddock, cameron.craddock@gmail.com NITRC Yes Cameron Craddock Source code and parcellations now available Go to MediaWiki on the left for more information. Spatially constrained parcellation is a set of tools for deriving ROI atlases by whole brain clustering of task or resting state data. In addition to the tools this resource also contains several atlases derived by parcellating publicly available resting state fMRI datasets. The initial release will include python scripts and ROI atlases developed to perform the analyses described in Craddock et. al. A whole brain fMRI atlas generated via spatially constrained spectral clustering which is currently in revision in Human Brain Mapping. The scripts provide all of the tools necessary to derive an ROI atlases using spatially constrained Ncut spectral clustering. The scripts require python numpy and scipy to run. 2011-7-28 1.0 2011-7-28 1.0 Spatially Constrained Parcellation Attribution Non-Commercial Share Alike http://www.nitrc.org/projects/cluster_roi/ cameron.craddock@gmail.com GNU General Public License GPL Yes zhengjia dai, daizhengjia13@gmail.com NITRC zhengjia dai The M3 multi-modal imaging and multi-level characteristic with multi-classifier is a brain imaging classification tool which can help researchers to discriminate patients from normal controls. The M3 includes three steps feature selection maximum uncertainty linear discriminant analysis MLDA-based classification and multi-classifier. A leave-one-out cross-validation LOOCV is further used to estimate the performance of the M3. Finally the most discriminative features are identified. 2011-9-26 M3 classification M3 GNU General Public License GPL http://www.nitrc.org/projects/pare/ daizhengjia13@gmail.com Yes Jennifer Elam, elam@wustl.edu NITRC Jennifer Elam The NIH Human Connectome Project is an effort to map the neural pathways that underlie human brain function. The purpose of the Project is to acquire and share data about the structural and functional connectivity of the human brain. It will advance the capabilities for imaging and analyzing brain connections resulting in improved sensitivity resolution and utility. The NIH Blueprint for Neuroscience httpwww.neuroscienceblueprint.nih.gov has funded two grants that will take complementary approaches A consortium led by Washington University in St. Louis and the University of Minnesota will enable development and utilization of advanced MRI methods to chart brain circuitry. httpwww.humanconnectome.org A consortium led by Massachusetts General Hospital and the University of California at Los Angeles will enable building a next-generation 3T MR scanner that improves the quality and spatial resolution of brain connectivity data. httpwww.humanconnectomeproject.org Human Connectome Project HCP English, ProductionStable, End Users, Developers, Community, Hardware, Software, Federal Funding Resource, Data Resource http://www.nitrc.org/projects/hcp/ elam@wustl.edu GNU General Public License GPL Yes Mingrui Xia, mingruixia@gmail.com NITRC MacOS,Linux,Windows Yes MATLAB Mingrui Xia BrainNet Viewer is a brain network visualization tool which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick easy and flexible way. 2011-10-27 ProductionStable BrainNet Viewer 1.1 Released 20111028 2011-7-07 ProductionStable BrainNet Viewer 1.00 RC1 Pre-Alpha BrainNet Viewer English, Windows, Linux, MacOS, MATLAB, Visualization, ProductionStable, Win32 MS Windows, End Users, GNU General Public License GPL http://www.nitrc.org/projects/bnv/ mingruixia@gmail.com GNU Lesser General Public License LGPL Yes William Gray, willgray@jhu.edu NITRC Yes Java William Gray This is the project page for the MR Connectome Automated Pipeline based on JIST and MIPAV. The pipeline combines structural magnetic resonance data with diffusion tensor imaging to estimate a connectome which is a comprehensive description of the wiring diagram of the brain. 2011-12-19 MRCAP Alpha Version 0.85 2011-6-30 Alpha Release Version 0.8 MR Connectome Automated Pipeline MRCAP Java, GNU Lesser General Public License LGPL, English http://www.nitrc.org/projects/mrcap/ willgray@jhu.edu Commercial License Hitachi Yes Joerg Schnackenberg, schnack@kf.hitachi-medical.co.jp NITRC Joerg Schnackenberg Hitachi Medical Corporation is a leader in fNIRS neuroimaging with more than 10 years of experience. We provide researchers and clinicians with sophisticated All-in-One solutions in the field of neuroscience. Hitachi Optical Topography System ProductionStable, End Users, Other Audience, NIRSFNIR, Scanner, Commercial License Hitachi http://www.nitrc.org/projects/hitachimedical/ schnack@kf.hitachi-medical.co.jp BSD License Yes Adrian Guggisberg, aguggis@gmail.com NITRC OS Independent MATLAB,cshtcsh Adrian Guggisberg NUTMEG Neurodynamic Utility Toolbox for Magnetoencephalography is an open-source MATLAB toolbox for reconstructing the spatiotemporal dynamics of neural activations and overlaying them onto structural MR images. More information can be found at httpwww.nitrc.orgprojectsnutmeg NUTMEG Surface Rendering, MEG Modeling, Principal Component Analysis, Multivariate Analysis, Three Dimensional Display, ProductionStable, MR, EEGMEGECoG, Other Environment, End Users, BSD License, English, OS Independent, cshtcsh, MATLAB http://www.nitrc.org/projects/nutmeg/ aguggis@gmail.com Commercial License VPixx Yes Peter April, papril@vpixx.com NITRC Peter April The DATAPixx is a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor the DATAPixx includes an array of peripherals which often need to be synchronized to video during an experiment including a stereo audio stimulator a button box port for precise reaction-time measurement triggers for electrophysiology equipment and even a complete analog IO subsystem. Because we implemented the video controller and peripheral control on the same circuit board you can now successfully synchronize all of your subject IO to video refresh with microsecond precision. DATAPixx Other Audience, End Users, Stimulus Presentation, EEG, Response Monitoring, Commercial License VPixx http://www.nitrc.org/projects/vpixx/ papril@vpixx.com Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Zarrar Shehzad, czarrar+nitrc@gmail.com NITRC C,R Zarrar Shehzad Connectir is an R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies CWAS using functional connectivity. Please see our web page for more details httpconnectir.projects.nitrc.org or click the Home Page link on the right below. connectir Software, Console Text Based, English, Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, Alpha, R, C http://www.nitrc.org/projects/connectir/ czarrar+nitrc@gmail.com Open Software License 3.0 Yes Tal Yarkoni, tyarkoni@gmail.com NITRC Tal Yarkoni The NeuroSynth framework includes software tools for automated extraction and synthesis of data from published functional neuroimaging studies a series of datasets generated using these tools and a website httpneurosynth.org for visualizing and accessing many of the tools and results. NeuroSynth Open Software License 3.0 http://www.nitrc.org/projects/neurosynth/ tyarkoni@gmail.com Analyze license Yes Analyze Direct, support@analyzedirect.com NITRC MacOS,Linux,SunOSSolaris,Windows Yes C Analyze Direct Analyze provides an integrated comprehensive set of tools for the visualization segmentation registration and analysis of multidimensional biomedical imaging data. With Analyze both anatomic structure and associated function can be studied and fused together for synergistic display and measurement of important structure-to-function relationships. Analyze Mature, C, End Users, Windows, MacOS, Linux, SunOSSolaris, Registration, Resampling, Tractography, Mesh Generation, Volumetric Analysis, Volumetric Analysis, Region of Interest, Rendering, Image Display, Platform or Development Environment, ANALYZE, DICOM, NIfTI-1, VRML, Other Format, Analyze license, English, Win32 MS Windows, X11 Applications http://www.nitrc.org/projects/analyze/ support@analyzedirect.com GNU General Public License GPL Yes David Abbott, iBrain@brain.org.au NITRC Windows NT2000,Windows Vista,MacOS,Linux,Other UNIX-like,Windows XP MATLAB David Abbott The iBrain analysis toolbox for SPM is a free toolbox that provides an automated processing pipeline for various single- or multi- subject andor multi-session functional neuroimaging experiments. The pipeline includes image conversion from scanner-specific formats pre-processing statistical analysis region-of-interest analysis and display. It is possible to specify a complete analysis stream in advance i.e. before any processing is actually performed. Analysis paradigms supported include block-design event-related simultaneous EEGfMRI and functional connectivity. This toolbox is compatible with SPM2 SPM5 and SPM8. 2011-9-23 Mature Version 3.0a 2011-9-05 Mature Version 3.0 iBrain™ analysis toolbox for SPM Modeling, Region of Interest, Workflow, Intensity Non-uniformity Correction, Image-to-Image, Image-to-Template, Resampling, Warping, Time Domain Analysis, Image Display, NIfTI-1, ANALYZE, English, Mature, MATLAB, End Users, Developers, Linux, Other UNIX-like, MacOS, Windows NT2000, Windows Vista, Windows XP, Other Format, Algorithm or Reusable Library, GNU General Public License GPL, Format Conversion, DICOM http://www.nitrc.org/projects/ibrain_spmtools/ iBrain@brain.org.au CeCill v2 Yes Maureen Clerc, Maureen.Clerc@inria.fr NITRC MacOS,POSIXUNIX-like,Windows Yes C Maureen Clerc A C package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy. OpenMEEG EEG Modeling, MEG Modeling, Algorithm or Reusable Library, ProductionStable, EEGMEGECoG, Developers, End Users, CeCill v2, MacOS, Windows, POSIXUNIX-like, C http://www.nitrc.org/projects/openmeeg/ Maureen.Clerc@inria.fr GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The Center for Computational Biology httpwww.CCB.ucla.edu provides 3 types of resources 1 Stand-alone computational software tools image and volume processing analysis visualization graphical workflow environments. 2 Infrastructure Resources Databases computational Grid services. 3 Web-services web-accessible resources for processing validation and exploration of multimodalmultichannel data including clinical data imaging data genetics data and phenotypic data. CCB is headquartered at the Laboratory of Neuro Imaging httpCCB.LONI.ucla.edu at UCLA. Center for Computational Biology CCB GNU General Public License GPL http://www.nitrc.org/projects/ccb/ iwaterpolo@gmail.com GNU Lesser General Public License LGPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The Distributome Project is an open-source open content-development project for exploring discovering navigating learning and computational utilization of diverse probability distributions. 2010-10-15 Distributome V.1 Distributome GNU Lesser General Public License LGPL http://www.nitrc.org/projects/distributome/ iwaterpolo@gmail.com ADNI License Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov Data collected as part of the ADNI study are freely available to authorized investigators through the Image Data Archive IDA. Information about obtaining access to ADNI data may be found in the How to Apply for Data section httpadni.loni.ucla.eduabout-data-samples. For more detailed information about accessing data from the IDA please review the IDA User Manual. The following ADNI data types are available Clinical Demographics Clinical Assessments Cognitive Assessments; Imaging MRI Raw pre- and post- processed image files; PET Raw pre- and post- processed image files; fMRI ADNI GO; DTI ADNI GO; Chemical Biomarker Laboratory Results; Genetic Illumina SNP genotyping; Image Analysis Results Numeric results derived from image analyses. The ADNI database is managed and housed by the Laboratory of Neuro Imaging httpwww.LONI.ucla.edu at UCLA. ADNI Database, Data, Mature, MR, PETSPECT, Web Environment, End Users, ADNI License, English, LONI Pipeline, DICOM, ANALYZE, NIfTI-1, Other Format http://www.nitrc.org/projects/adni/ iwaterpolo@gmail.com GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC Yes I Dinov The Automated Image Registration AIR tool is used for alignment of 3D and 2D images within and across subjects and across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs. AIR is distributed by the Laboratory of Neuro Imaging httpwww.LONI.ucla.eduSoftwareAIR at UCLA. 2010-11-08 5.2 Automated Image Registration AIR GNU General Public License GPL http://www.nitrc.org/projects/air/ iwaterpolo@gmail.com LONI Software License,GNU General Public License GPL Yes Bruce Liu, chengyiliu@gmail.com NITRC Windows NT2000,Windows Vista,Linux C,shbash Bruce Liu Brain Parser software uses a novel statistical-learning technique to segment brain regions of interest ROIs based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest. Brain Parser is distributed by the Laboratory of Neuro Imaging httpwww.LONI.ucla.eduSoftwareBrainParser at UCLA. 2010-4-16 Alpha 20100415 2010-4-16 Alpha 20100415 2010-4-16 Alpha 20100415 BrainParser Console Text Based, English, Alpha, C, shbash, ANALYZE, LONI Software License, End Users, Windows NT2000, Windows Vista, Linux, Anatomic, Workflow, GNU General Public License GPL http://www.nitrc.org/projects/brainparser/ chengyiliu@gmail.com 3D Slicer License Yes Lucile Bompard, lucile.bompard@gmail.com NITRC MacOS,POSIXUNIX-like Yes C Lucile Bompard shapeAnalysisMANCOVA offers statistical shape analysis based on a parametric boundary description SPHARM as the point-based model computing method. The point-based models will be analyzed with the methods here proposed using multivariate analysis of covariance MANCOVA. Here the number of variates being tested is the dimensionality of our observations. Each point of these observations is a three dimensional displacement vector from the mean. The number of contrasts is the number of equations involved in the null-hypothesis. In order to encompass varying numbers of variates and contrasts and to account for independent variables a matrix computation is performed. This matrix represents the multidimensional aspects of the correlation significance and it can be transformed into a scalar measure by manipulation of its eigenvalues. Details of the methods can be found in its Insight Journal publication httphdl.handle.net103803124 shapeAnalysisMANCOVA - SPHARM tools Console Text Based, English, ProductionStable, 3D Slicer License, Statistical Operation, Surface Analysis, Spherical Harmonics, C, Developers, End Users, MacOS, POSIXUNIX-like http://www.nitrc.org/projects/shape_mancova/ lucile.bompard@gmail.com MITX Consortium License Yes Alfonso Nieto-Castanon, alfnie@gmail.com NITRC OS Independent Yes MATLAB Alfonso Nieto-Castanon This spm-toolbox performs ROI-level and voxel-level between-subjects analyses of functional MRI data restricting the analyses to those areas identified using subject-specific functional localizers. Methods The toolbox implements ROI-level and voxel-level analyses and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest as well as automatically-defined ones GcSS procedure Fedorenko et al. 2010. General linear model second-level analyses are implemented including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs T F and Wilks lambda statistics This toolbox requires Matlab and SPM5SPM8. httpweb.mit.eduevelina9wwwfuncloc.html 2010-11-08 Beta v10.a SPM_SS - fMRI functional localizers End Users, ANALYZE, NIfTI-1, MATLAB, Developers, OS Independent, Linear, Modeling, MITX Consortium License, Win32 MS Windows, X11 Applications, English, Beta http://www.nitrc.org/projects/spm_ss/ alfnie@gmail.com BIRN Data License Yes Bennett Landman, bennett.landman@vanderbilt.edu NITRC Bennett Landman We have acquired scan-rescan imaging sessions on 21 healthy volunteers no history of neurological disease. Imaging modalities include MPRAGE FLAIR DTI resting state fMRI B0 and B1 field maps ASL VASO quantitative T1 mapping quantitative T2 mapping and magnetization transfer imaging. All data have been converted to NIFTI format. This is intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic amp;quot;1 houramp;quot; session at 3T. Please cite Bennett. A. Landman Alan J. Huang Aliya Gifford Deepti S. Vikram Issel Anne L. Lim Jonathan A.D. Farrell John A. Bogovic Jun Hua Min Chen Samson Jarso Seth A. Smith Suresh Joel Susumu Mori James J. Pekar Peter B. Barker Jerry L. Prince and Peter C.M. van Zijl. “Multi-Parametric Neuroimaging Reproducibility A 3T Resource Study” NeuroImage. 2010 NIHMSPMC252138 doi10.1016j.neuroimage.2010.11.047 2012-1-26 BIRN DTI Reproducibility 45 DTI datasets over 3 sessions 2010-9-07 Intrasession Scan-Rescan 2010-6-23 Kirby 21 2009 Multi-Modal MRI Reproducibility Resource Data, MR, Developers, End Users, BIRN Data License, Java Image Science Toolkit, NIfTI-1 http://www.nitrc.org/projects/multimodal/ bennett.landman@vanderbilt.edu GNU General Public License GPL Yes Javier Lopez-Calderon, matlabiano@gmail.com NITRC Javier Lopez-Calderon ERPLAB Toolbox is a set of open source freely available Matlab routines for analyzing ERP data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind amp;amp; Brain with financial support from NIMH. ERPLAB GNU General Public License GPL http://www.nitrc.org/projects/erplab/ matlabiano@gmail.com 3D Slicer License Yes Beatriz Paniagua, beatriz_paniagua@med.unc.edu NITRC Beatriz Paniagua We have developed a sequence of fully automated voxel-wise rigid registration that utilizes stable structures of reference for assessment of craniofacial changes overtime.The major strengths of this method are that registration does not depend on the precision of the 3D surface models and that a “stable structure of reference” can be used without the simple “best fit” of all surfaces. CMFreg 3D Slicer License http://www.nitrc.org/projects/cmfreg/ beatriz_paniagua@med.unc.edu BSD License Yes Clement Vachet, cvachet@unc.edu NITRC Linux Yes C Clement Vachet GAMBIT is an end-to-end application developped at UNC-Chapel Hill allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements. This cross-platform tool can be run within 3D Slicer as an external module or directly as a command line. 2011-5-23 Beta GAMBIT_Executables_1.3 2010-10-08 Beta GAMBIT_Executables_1.2 2010-10-08 Beta GAMBIT_Executables_1.1 2010-6-15 Beta GAMBIT_Tutorial_example_1.0 2010-6-15 Beta GAMBIT_Executables_1.0 GAMBIT English, Beta, ANALYZE, Nrrd, Other Format, C, BSD License, Workflow, Thickness, Mesh Generation, End Users, Developers, Linux http://www.nitrc.org/projects/gambit/ cvachet@unc.edu GNU General Public License GPL Yes Arnaud Delorme, arnodelorme@gmail.com NITRC OS Independent MATLAB Arnaud Delorme EEGLAB provides an interactive graphic user interface GUI allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis ICA andor timefrequency analysis as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows plus a command history function that eases users transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics both at the level of individual EEGLAB datasets andor across a collection of datasets brought together in an EEGLAB studyset. For experienced Matlab users EEGLAB offers a structured programming environment for storing accessing measuring manipulating and visualizing event-related EEG data as well as sharing new methods by publishing EEGLAB plug-in functions. EEGLAB Federal Funding Resource, Mature, EEGMEGECoG, End Users, GNU General Public License GPL, English, OS Independent, MATLAB, ASCII http://www.nitrc.org/projects/eeglab/ arnodelorme@gmail.com MITX Consortium License Yes Christian Dansereau, christiandansereau@gmail.com NITRC Linux,Windows Other Programming Language,MATLAB Christian Dansereau The pipeline system for Octave and Matlab PSOM is a lightweight library to manage complex multi-stage data processing. A pipeline is a collection of jobs i.e. Matlab or Octave codes with a well identified set of options that are using files for inputs and outputs. To use PSOM the only requirement is to generate a description of a pipeline in the form of a simple MatlabOctave structure. PSOM then automatically offers the following services Run jobs in parallel using multiple CPUs or within a distributed computing environment. Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis. Handle job failures successful completion of jobs is checked and failed jobs can be restarted. Handle updates of the pipeline change options or add jobs and let PSOM figure out what to reprocess 2011-11-08 Beta PSOM release 0.9 2011-1-17 Beta 0.8.8 2010-12-07 Beta 0.8.7 2010-11-23 Beta 0.8.6 2010-5-18 Beta 0.8.5 2009-12-21 Beta 0.8.3 Pipeline system for Octave and Matlab Developers, Windows, Linux, Algorithm or Reusable Library, Workflow, MITX Consortium License, English, Beta, MATLAB, Other Programming Language http://www.nitrc.org/projects/psom/ christiandansereau@gmail.com Yes Lori Sanfratello, lsanfratello@mrn.org NITRC OS Independent Lori Sanfratello MEGSIM httpcobre.mrn.orgmegsim contains realistic simulated MEG datasets ranging from basic sensory to oscillatory sets that mimic functional connectivity; as well as basic visual auditory and somatosensory empirical sets. The simulated sets were created for the purpose of testing analysis algorithms across the different MEG systems when the truth is known. MEG baseline recordings were obtained from 5 healthy participants using three MEG systems VSMCTF Omega Elekta Neuromag Vectorview 4-D Magnes 3600. Simulated signals were embedded within the CTF and Neuromag 306 baseline recordings 4-D to be added. Participant MRIs are available. Averaged simulation files are available as netcdf files. Neuromag 306 averaged simulations are also available in fif format. Also available single trials of data where the simulated signal is jittered about a mean value continuous fif files where the simulated signal is marked by a trigger and simulations with oscillations added to mimic functional connectivity. MEGSIM Other, Model, Test Data, EEGMEGECoG, Web Environment, Developers, End Users, English, OS Independent http://www.nitrc.org/projects/megsim/ lsanfratello@mrn.org GNU General Public License GPL Yes Torsten Rohlfing, torsten@synapse.sri.com NITRC Other OS,MacOS,Linux,SunOSSolaris,Cygwin,Windows Yes C,C,shbash Torsten Rohlfing A software toolkit for computational morphometry of biomedical images CMTK comprises a set of command line tools and a back-end general-purpose library for processing and IO. The command line tools primarily provide the following functionality registration affine and nonrigid; single and multi-channel; pairwise and groupwise image correction MR bias field estimation; interleaved image artifact correction; EPI unwarping processing filters; combination of segmentations via voting and STAPLE; shape-based averaging statistics t-tests; general linear model. CMTK is implemented in C with parallel processing using POSIX Threads SMP OpenMP SMP Grand Central Dispatch SMP and CUDA GPU. Supported file formats include Analyze rw NIFTI rw Nrrd rw DICOM read BioRad read. Data exchange with other toolkits such as ITK FSL AFNI SPM etc. is thus easily accomplished. 2012-1-10 Mature 2.1.1 Computational Morphometry Toolkit CMTK Algorithm or Reusable Library, Image-to-Image, Anatomic, Artifact Removal, Resampling, Warping, Principal Component Analysis, Linear, Two Dimensional Display, Workflow, Format Conversion, Atlas Application, Image Reconstruction, GNU General Public License GPL, ANALYZE, DICOM, Other Format, NIfTI-1, Nrrd, Console Text Based, X11 Applications, English, Mature, C, C, shbash, Developers, End Users, MacOS, Linux, Cygwin, Windows, Other OS, SunOSSolaris http://www.nitrc.org/projects/cmtk/ torsten@synapse.sri.com Attribution Non-Commercial Share Alike Yes xiujuan geng, gxjsusan@gmail.com NITRC xiujuan geng Human DTI brain atlases have been generated at UNC-Chapel Hill for several age groups by iterative joint deformable registration of training datasets into a single unbiased DTI average image. Atlases packages include an atlas DTI tensor image atlas DTI property images FA MD AD RD and single tensor tractography based fiber tracts of major tracts with related 3D planes for fiber profile information genu splenium anterior and posterior limb of internal capsule uncinate fasciculus. UNC Human DTI Brain Atlas Data, End Users, Attribution Non-Commercial Share Alike, Atlas Data http://www.nitrc.org/projects/dti_brain_atlas/ gxjsusan@gmail.com BSD License Yes Chris Rorden, rorden@gatech.edu NITRC MacOS,Linux,Windows Yes Pascal Chris Rorden MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcroGL is a variant of MRIcron that uses OpenGL for very fast rendering but requires a modern NVidia or ATI graphics card. 2011-11-26 Mature MRIcronNPMdcm2nii 111111 for OSX 10.4 or later 2011-11-26 Mature Missingness in Neuroimaging Data MIND ALPHA 2011-11-26 Mature MRIcroGL 111111 source 2011-11-26 Mature MRIcroGL 111111 Windows 2011-11-26 Mature MRIcroGL 111111 Linux GTK2 x86 64-bit 2011-11-26 Mature MRIcroGL 111111 Linux GTK2 x86 32-bit 2011-11-26 Mature MRIcroGL 111111 OSX 10.4 Intel 2011-4-12 Mature MRIcroGL 42011 Windows 2011-4-12 Mature MRIcroGL 42011 Linux 32-bit GTK2 2011-4-12 Mature MRIcroGL 42011 Linux 64-bit GTK2 2011-4-12 Mature MRIcroGL 42011 Macintosh OSX Intel 10.4 2011-4-12 Mature MRIcroGL 42011 Source 2011-4-07 Mature MRIcron 42011 Windows 2011-4-07 Mature MRIcron 42011 Linux 32-bit GTK1 2011-4-07 Mature MRIcron 42011 Linux 32-bit GTK2 2011-4-07 Mature MRIcron 42011 Linux 64-bit GTK2 2011-4-07 Mature MRIcron 42011 Linux 64-bit GTK1 2011-4-07 Mature MRIcron 42011 Macintosh OSX PPCIntel 10.4 2011-4-07 Mature MRIcron 42011 source  2010-11-05 Mature MRIcron 112010 Windows 2010-11-05 Mature MRIcron 112010 Linux 32-bit GTK2 2010-11-05 Mature MRIcron 112010 Linux 32-bit GTK1 2010-11-05 Mature MRIcron 112010 Linux x86-64 GTK2 2010-11-05 Mature MRIcron 112010 Linux x86-64 GTK1 2010-11-05 Mature MRIcron 112010 Macintosh OSX PPCIntel 10.4 2010-11-05 Mature MRIcron 112010 Source 2010-7-15 Mature MRIcroGL 62010 Windows 2010-7-15 Mature MRIcroGL 62010 Linux 32-bit GTK2 2010-7-15 Mature MRIcroGL 62010 Linux 64-bit GTK2 2010-7-15 Mature MRIcroGL 62010 Macintosh OSX Intel 10.4 2010-7-15 Mature MRIcroGL 62010 Source 2010-4-01 Mature MRIcroGL 42010 Windows 2010-4-01 Mature MRIcroGL 42010 Linux 32-bit GTK2 2010-4-01 Mature MRIcroGL 42010 Macintosh OSX Intel 10.4 2010-4-01 Mature MRIcron 42010 Source 2010-4-01 Mature MRIcron 42010 Windows 2010-4-01 Mature MRIcron 42010 Macintosh OSX PPCIntel 10.4 2010-4-01 Mature MRIcron 42010 Linux 32-bit GTK2 2010-4-01 Mature MRIcron 42010 Linux 32-bit GTK1 2010-4-01 Mature MRIcron 42010 Linux 64-bit GTK2 2010-4-01 Mature MRIcron 42010 Linux 64-bit GTK1 2010-4-01 Mature MRIcroGL 42010 Linux 64-bit GTK2 2010-2-05 Mature MRIcron 22010 Source 2010-2-05 Mature MRIcron 22010 Windows 2010-2-05 Mature MRIcron 22010 Macintosh OSX PPCIntel 2010-2-05 Mature MRIcron 22010 Linux 64-bit GTK-2 2010-2-05 Mature MRIcron 22010 Linux 64-bit GTK1 2010-2-05 Mature MRIcron 22010 Linux 32-bit GTK2 2010-2-05 Mature MRIcroGL 22010 Source 2010-2-05 Mature MRIcroGL 22010 Windows 2010-2-05 Mature MRIcroGL 22010 Macintosh OSX 2010-2-05 Mature MRIcroGL 22010 Linux 64-bit GTK2 2010-2-05 Mature MRIcron 22010 Linux 64-bit GTK2 2010-2-05 Mature MRIcroGL 22010 Linux 32-bit GTK2 2009-12-28 Mature MRIcron 122009 Linux 64-bit GTK2 2009-12-28 Mature MRIcron 122009 Linux 64-bit GTK1 2009-12-28 Mature MRIcron 122009 Linux 32-bit GTK1 2009-12-28 Mature MRIcron 122009 Linux 32-bit GTK2 2009-12-28 Mature MRIcron 122009 Source 2009-12-28 Mature MRIcron 122009 Windows 2009-12-28 Mature MRIcron 122009 Mac OSX IntelPPC 2009-12-28 Mature MRIcroGL 122009 Linux 32-bit GTK2 2009-12-28 Mature MRIcroGL 122009 Linux 64-bit GTK2 no scripting 2009-12-28 Mature MRIcroGL 122009 Source 2009-12-28 Mature MRIcroGL 122009 Windows 2009-12-28 Mature MRIcroGL 122009 Mac OSX Intel 2009-10-22 Mature ezDICOM standalone activex and console applications and source 2009-10-16 Mature MRIcron September 2009 - source 2009-10-16 Mature MRIcron September 2009 - Windows 2009-10-16 Mature MRIcron September 2009 - Linux OSX PPCIntel 2009-10-16 Mature MRIcron September 2009 - Linux GTK1 32-bit 2009-10-16 Mature MRIcron September 2009 - Linux GTK2 32-bit 2009-10-16 Mature MRIcron September 2009 - Linux GTK1 64-bit 2009-10-16 Mature MRIcron September 2009 - Linux GTK2 64-bit 2009-10-14 Mature MRIcroGL 92009 Source 2009-10-14 Mature MRIcroGL 92009 Linux x86-32bit GTK2 2009-10-14 Mature MRIcroGL 92009 Wiindows 2009-10-14 Mature MRIcroGL 92009 Mac OSX 2009-9-02 Mature MRIcroGL 92009 Linux GTK2-64bit no scripting 2009-7-08 Mature MRIcron July 2009 - Linux QT 32-bit 2009-7-08 Mature MRIcron July 2009 - Linux GTK2 64-bit 2009-7-08 Mature MRIcron July 2009 - Linux GTK1 64-bit 2009-7-08 Mature MRIcron July 2009 - Linux GTK2 32-bit 2009-7-08 Mature MRIcron July 2009 - Linux GTK1 32-bit 2009-7-08 Mature MRIcron July 2009 - Source 2009-7-08 Mature MRIcron July 2009 - OSX IntelPPC 2009-7-08 Mature MRIcron July 2009 - Windows 2009-6-15 Mature MRIcroGL IPodVideo beta 2009-6-15 Mature MRIcroGL 62009 Linux GTK2 2009-6-15 Mature MRIcroGL 62009 source 2009-6-15 Mature MRIcroGL 62009 Mac OSX 2009-6-15 Mature MRIcroGL 62009 Windows 2009-6-03 Mature MRIcroGL 52009 source 2009-6-03 Mature MRIcroGL 52009 Linux GTK2 2009-6-03 Mature MRIcroGL 52009 Mac OSX 2009-6-03 Mature MRIcroGL 52009 Windows 2008-11-06 Mature MRIcroGL 2008-9-26 Mature mricro 1.4 for Windows 2008-9-08 Mature mricrogl MRIcron Win32 MS Windows, Gnome, KDE, Other Environment, English, End Users, BSD License, Pascal, Center of Mass, MacOS, Windows, Two Dimensional Display, Regression, Linux, ANALYZE, NIfTI-1, DICOM, Console Text Based, Clipping, Mature, Volume Rendering http://www.nitrc.org/projects/mricron/ rorden@gatech.edu MITX Consortium License Yes Alfonso Nieto-Castanon, alfnie@gmail.com NITRC OS Independent Yes MATLAB Alfonso Nieto-Castanon Toolbox for functional connectivity analyses of fMRI data Seed-to-voxel analyses Analyze the connectivity between one or multiple seed areas and the whole brain ROI-to-ROI analyses Analyze the connectivity between multiple ROIs as well as graph-theoretical properties of the resulting networks Voxel-to-voxel analyses Analyze the whole-brain connectome without using a priori seedsROIs Available for resting state data as well as task-related block designs. Gui and automated batch processing Method highlights Complete spatial preprocessing pipeline; CompCor method for removing physiological and movement confounds; Multiple seed-to-voxel and ROI-to-ROI linear connectivity measures; Whole-brain multivariate pattern analyses of connectivity maps and estimation of several descriptive connectivity indexes; Univariate and multivariate group-level analyses mixed within- between-subjects designs Dependencies Matlab SPM httpweb.mit.eduswgsoftware.htm 2011-11-20 Beta conn v.13.i 2011-10-19 Beta documentation 2011-10-18 Beta batch processing example scriptsdatasets 2010-6-23 Beta conn v.12.p previous stable release CONN - fMRI functional connectivity Correlation, Multivariate Analysis, Visualization, Modeling, Principal Component Analysis, Regression, Beta, End Users, Developers, MITX Consortium License, English, OS Independent, MATLAB, ANALYZE, NIfTI-1 http://www.nitrc.org/projects/conn/ alfnie@gmail.com GNU General Public License GPL Yes Matthew Kempton, matthew.kempton@kcl.ac.uk NITRC Yes Matthew Kempton ALVIN - Automatic Lateral Ventricle delIneatioN is a fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants adults and patients with Alzheimers disease ICCamp;gt;0.95. ALVIN is insensitive to different scanner sequences ICCamp;gt;0.99 8 different sequences 1.5T and 3T and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject. Download from here or visit our main website httpsites.google.comsitemrilateralventricle 2011-12-14 ALVIN v1.01 ALVIN - Lateral Ventricle Segmentation Volumetric Analysis, Region of Interest, Volume Measurement, GNU General Public License GPL http://www.nitrc.org/projects/alvin_lv/ matthew.kempton@kcl.ac.uk Creative Commons License Yes Samir Das, samirdas99@gmail.com NITRC Samir Das LORIS is a modular and extensible web-based data management system that integrates all aspects of a multi-center study from heterogeneous data acquisition imaging clinical behavior genetics to storage processing and ultimately dissemination. LORIS Creative Commons License http://www.nitrc.org/projects/loris/ samirdas99@gmail.com Yes Pontus Holm, pontus.holm@incf.org NITRC OS Independent Yes Pontus Holm The INCF is a professional organization devoted to advancing the field of neuroinformatics. One of its aims is to develop an international neuroinformatics infrastructure which promotes the sharing of data and computing resources to the international research community. A second objective of INCF is to help develop scalable portable and extensible applications that can be used by neuroscience laboratories worldwide. 2008-8-31 ProductionStable INCF Software Center INCF MR, Web Environment, Developers, End Users, Other Audience, English, OS Independent, Websites, Web Service, Community, Database, ProductionStable, Computational Neuroscience, EEGMEGECoG http://www.nitrc.org/projects/incf/ pontus.holm@incf.org Yes Marcel Prastawa, prastawa@sci.utah.edu NITRC Yes Marcel Prastawa TumorSim is a cross-platform simulation software that generates pathological ground truth from a healthy ground truth e.g. the BrainWeb data. The software requires an input directory that describes a healthy anatomy anatomical probabilities mesh diffusion tensor image etc. Example output simulation images are available for download for validating various image analysis algorithms such as registration and segmentation algorithms. The simulation method is described in the following paper Marcel Prastawa Elizabeth Bullitt and Guido Gerig. Simulation of Brain Tumors in MR Images for Evaluation of Segmentation Efficacy. Medical Image Analysis MedIA Vol 13 No 2 April 2009 Pages 297-311. 2011-12-14 TumorSim 1.1 2011-12-14 TumorSim 1.0 TumorSim http://www.nitrc.org/projects/tumorsim/ prastawa@sci.utah.edu Non-Commercial Software License Agreement Yes Hasan Ayaz, hasan.ayaz@gmail.com NITRC Hasan Ayaz MazeSuite is a complete set of tools that enables researchers to perform spatial and navigational behavior experiments within interactive easy to create and extendable e.g. multiple rooms 3D virtual environments. MazeSuite can be used to designedit adapted 3D environments where subjects’ behavioral performance can be tracked. MazeSuite consists of three main applications; an editing program to create and alter maps MazeMaker a visualizationrendering module MazeWalker and finally an analysismapping tool MazeAnalyzer. Additionally MazeSuite has the capabilities of sending signal pulses to physiological recording devices using standard computer ports. MazeSuite with all 3 applications is a unique and complete toolset for researchers who want to easily and rapidly deploy interactive 3D environments. For more information and related publications please see www.mazesuite.com MazeSuite Non-Commercial Software License Agreement http://www.nitrc.org/projects/mazesuite/ hasan.ayaz@gmail.com FSL License Yes Matthew Webster, mwebster@fmrib.ox.ac.uk NITRC Windows NT2000,MacOS,Linux,SunOSSolaris Yes C,C Matthew Webster FSL is a comprehensive library of image analysis and statistical tools for FMRI MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group FMRIB Oxford UK. 2011-11-18 ProductionStable Current 2011-5-15 ProductionStable 4.1.8 2010-7-01 ProductionStable fsl 4.1.6 2010-2-04 ProductionStable 4.1.5 2009-6-09 ProductionStable 4.1.4 2008-8-13 ProductionStable 4.1.0 2007-7-31 ProductionStable 4.0.4 FSL Affine Warp, Independent Component Analysis, Temporal Transformation, Tensor Metric, Tractography, Image Display, Volumetric Analysis, Segmentation, Registration, ProductionStable, MR, Console Text Based, X11 Applications, End Users, FSL License, English, Linux, Windows NT2000, MacOS, SunOSSolaris, C, C, NIfTI-1, ANALYZE http://www.nitrc.org/projects/fsl/ mwebster@fmrib.ox.ac.uk Yes Phan Luu, pluu@egi.com NITRC Phan Luu APIs for Net Station data files. APIs are available for C C and Java. Net Station http://www.nitrc.org/projects/netstation_api/ pluu@egi.com MPT Yes Nima Bigdely-Shamlo, nima@sccn.ucsd.edu NITRC Nima Bigdely-Shamlo This toolbox is an EEGLAB plugin for performing Measure Projection Analysis. Measure Projection Analysis MPA is a novel probabilistic multi-subject inference method that overcomes EEG Independent Component IC clustering issues by abandoning the notion of distinct IC clusters. Instead it searches voxel by voxel for brain regions having event-related IC process dynamics that exhibit statistically significant consistency across subjects andor sessions as quantified by the values of various EEG measures. Local-mean EEG measure values are then assigned to all such locations based on a probabilistic model of IC localization error and inter-subject anatomical and functional differences. 2012-1-06 Latest Release Measure Projection Toolbox MPT MPT http://www.nitrc.org/projects/measure_project/ nima@sccn.ucsd.edu GNU General Public License GPL Yes Alois Schloegl, alois.schloegl@ist.ac.at NITRC Alois Schloegl Biosig provides tools for processing of electroencephalogram EEG and other biomedical signals like ECG EOG EMG etc. Biosig contains tools for quality control artifact processing time series analysis feature extraction classification and machine learning and tools for statistical analysis. Many tools are able to handle data with missing values statistics time series analysis machine learning. Another feature is that more then 40 different data formats are supported and a number of converters for EEG ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces BCI sleep research and ECG and HRV analysis. It provides software interfaces several programming languages C C MatlabOctave Python and it provides also an interactive viewing and scoring software for adding and editing of annotations markers and events. BioSig GNU General Public License GPL http://www.nitrc.org/projects/biosig/ alois.schloegl@ist.ac.at Yes Charles Peterson, charlesp@txbiomedgenetics.org NITRC Charles Peterson The goal of this project is to merge two important research directions in modern science genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far however standard imaging tools are unable to deal with large-scale genetics data and standard genetics tools in turn are unable to accommodate large size and binary format of the image data. Thus we are developing software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. Our focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability pleiotropy quantitative trait loci QTL and genome-wide association GWAS gene expression and methylation analyses optimized for traits derived from structural and functional brain imaging data 2012-1-13 Solar Eclipse Imaging Genetics Workshop Hand Out 2012-1-03 SOLAR manual pages 2012-1-03 SOLAR software for Linux computers 2012-1-03 SOLAR software for Windows PC computers 2012-1-03 SOLAR software for intel-based MAC_OS computers Solar Eclipse Imaging Genetics tools http://www.nitrc.org/projects/se_linux/ charlesp@txbiomedgenetics.org BSD License Yes Luis Ibanez, luis.ibanez@kitware.com NITRC Luis Ibanez ParaView is an open-source multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaViews batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data. ParaView BSD License http://www.nitrc.org/projects/paraview/ luis.ibanez@kitware.com Yes Jennifer Elam, elam@wustl.edu NITRC MacOS,Linux,Windows Yes C Jennifer Elam THE HUMAN CONNECTOME PROJECT WU-Minn Consortium The Consortium will acquire and analyze several modalities of neuroimaging data plus behavioral and genetic data from 1200 healthy adults 300 twin pairs and siblings. The project will yield invaluable information about brain connectivity its relationship to behavior and contributions of genetic and environmental factors to individual differences in brain circuitry. Data will be shared with the scientific community via a user-friendly platform for data mining analysis and visualization. Phase I involves optimization of data acquisition and analysis methods. Phase II 2012-2015 will involve data acquisition from 400 subjectsyear. The Consortium includes investigators at 10 institutions co-lead institutions Washington U. and the U. of Minnesota Oxford U. St. Louis U. Advanced MRI Technologies with UC Berkeley Indiana U. the U. G. d’Annunzio Radboud U. Nijmegen the Ernst Strüngmann Institute and Warwick U. www.humanconnectome.org HCP WU-Minn Consortium Linux, Windows, XNAT Pipeline, C, GIfTI, NIfTI-1, DICOM, CIFTI, Data, Database, Scanner, Independent Component Analysis, MEG, Time Domain Analysis, Registration, Surface Rendering, Diffusion MR Fiber Tracking, Animation, Three Dimensional Display, Two Dimensional Display, Atlas Data, Alpha, Domain Independent, EEGMEGECoG, MR, Other Environment, End Users, English, MacOS http://www.nitrc.org/projects/hcp_wuminn/ elam@wustl.edu MITX Consortium License Yes tom Fogal, tfogal@sci.utah.edu NITRC tom Fogal Note ImageVis3D development is hosted elsewhere -- see httpwww.imagevis3d.org ImageVis3D is a new volume rendering program developed by the NIHNCRR Center for Integrative Biomedical Computing CIBC. The main design goals of ImageVis3D are simplicity scalability and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility as shown in the images. Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation the user can interactively explore terabyte sized data sets. Finally the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it such as the rendering core. This rendering core for instance is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with our collaborators. ImageVis3D MITX Consortium License http://www.nitrc.org/projects/imagevis3d/ tfogal@sci.utah.edu GNU General Public License GPL Yes Rob Ellis, robjellis@gmail.com NITRC Yes Rob Ellis A simple menu-driven toolbox for SPM software that provides the user with several options 1 a histogram of all non-zero voxel values in an brain image; 2 a scatter plot quantile-quantile plot or Bland-Altman plot of statistic values at all corresponding voxel locations in two brain images; 3 a surface plot of all voxel values at a particular axial slice. Note the toolbox calls various SPM functions and also makes use of several functions within the MATLAB amp;quot;statsamp;quot; toolbox. Both SPM either 5 or 8 and the stats toolbox should be installed. For further information and documentation visit httptools.robjellis.net 2012-1-20 vis_2012.01.21 2012-1-20 vis_2012.01.20 vis SPM Visualized Statistics toolbox Visualization, Quantification, Statistical Operation, GNU General Public License GPL, ANALYZE, NIfTI-1 http://www.nitrc.org/projects/vis/ robjellis@gmail.com Attribution Yes John Bushnell, john.bushnell@icb.ucsb.edu NITRC John Bushnell A free database of fMRI data used in peer reviewed studies fMRIDC. The database of studies can be browsed and searched and data is provided via download links that are emailed to users in response to specific requests. All of the data has been rendered anonymous is free and can be used in further studies. Any published findings based on these datasets should credit the authors of the original study as well as the fMRI Data Center including the accession number. The fMRI Data Center MR, Attribution http://www.nitrc.org/projects/fmridatacenter/ john.bushnell@icb.ucsb.edu BSD License Yes Eun Young Kim, eunyoung-kim@uiowa.edu NITRC Eun Young Kim NOTE All new development is being managed in a github repository. Please visit httpsgithub.comBRAINSiaBRAINSStandAlone BRAINSCut is a software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper amp;quot;Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures.amp;quot; PMID 17904870. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. BRAINSCut BSD License http://www.nitrc.org/projects/brainscut/ eunyoung-kim@uiowa.edu Yes Joy Matsui, joymatsui@gmail.com NITRC Yes Joy Matsui NOTE All active development of BRAINSConstellationDetector is now being stored in a Git repository at github.com. Please go to httpsgithub.comBRAINSiaBRAINSStandAlone BrainDemonsWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit www.ITK.org for all the computations and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration including diffeomorphic demons registration originating from Tom Vercauteren at INRIA . 2009-1-20 1.0 2008-10-20 TestData 2008-10-20 CDash Testing Dashboard BRAINSDemonWarp http://www.nitrc.org/projects/brainsdemonwarp/ joymatsui@gmail.com TurtleSeg License Yes Rafeef Abugharbieh, rafeef@ece.ubc.ca NITRC Windows NT2000,Windows Vista,Windows XP Yes C Rafeef Abugharbieh TurtleSeg is an interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process. TurtleSeg Intensity Contour, Mature, CT, MR, Win32 MS Windows, End Users, TurtleSeg License, English, Windows Vista, Windows XP, Windows NT2000, C, ANALYZE, DICOM, MINC, NIfTI-1, Other Format http://www.nitrc.org/projects/turtleseg/ rafeef@ece.ubc.ca LIBRA license Yes Yakang Dai, daiyakang@gmail.com NITRC Linux Yes C,Perl,MATLAB,C,Unix Shell Yakang Dai LIBRA is a toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal or single-time-point multimodality including T1 T2 and FA or single-modality data can be processed using the toolbox. Main functions of the software step by step include image preprocessing brain extraction tissue segmentation and brain labeling. The software is developed by the IDEA group at the University of North Carolina at Chapel Hill directed by Dr. Dinggang Shendinggang_shenmed.unc.edu. Linux operating system is required for the stand-alone executable software. The graphical user interfaces and overall framework of the LIBRA software are implemented in MATLAB. The image processing functions are implemented with the combination of CC MATLAB Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing. 2011-11-29 LIBRA 1.0 LIBRA Linux, MATLAB, C, C, Perl, Unix Shell, ANALYZE, Segmentation, Atlas Data, Atlas Application, Registration, Resampling, Image Display, MR, LIBRA license http://www.nitrc.org/projects/libra/ daiyakang@gmail.com