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 End Users, Developers, 5 - ProductionStableMature, Console Text Based, X11 Applications, Win32 MS Windows, OS Independent, English, Ontology, Database Application, Independent Component Analysis, Principal Component Analysis, Regression, ANALYZE, MATLAB, Brede Toolbox License, MR http://www.nitrc.org/projects/bredetoolbox/ fn@imm.dtu.dk GNU General Public License GPL Yes Michaël Zugaro, michael.zugaro@college-de-france.fr NITRC Yes Michaël Zugaro NeuroScope is an advanced viewer for electrophysiological and behavioral data it can display local field potentials EEG neuronal spikes behavioral events as well as the position of the animal in the environment. It also features limited editing capabilities. NeuroScope GNU General Public License GPL, EEGMEGECoG http://www.nitrc.org/projects/neuroscope/ michael.zugaro@college-de-france.fr GNU General Public License GPL Yes , NITRC Microsoft Yes MATLAB MEG Localization using FOCUSS and MR-FOCUSS 2012-4-30 3 - Alpha Link to website MEG Tools End Users, 3 - Alpha, GNU General Public License GPL, Microsoft, X11 Applications, Win32 MS Windows, English, Image Reconstruction, MATLAB, Other Format, EEGMEGECoG http://www.nitrc.org/projects/meg-tools/ Commercial License VPixx Yes Stephanie-Ann Seguin, sales@vpixx.com NITRC Stephanie-Ann Seguin 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 End Users, Other Audience, Stimulus Presentation, Response Monitoring, EEG, Commercial License VPixx, MR, EEGMEGECoG http://www.nitrc.org/projects/vpixx/ sales@vpixx.com Creative Commons License Yes Makoto Takemiya, takemiya@atr.jp NITRC Makoto Takemiya httpbrainliner.jp A web portal for sharing neurophysiological and behavioral data. Users can search for existing data or login with their Google Facebook or Twitter account and upload new data. Our main focus is on supporting brain-machine interface research so we encourage users to not just provide recordings of brain activity data but also information about stimuli etc. so that statistical relationships can be found between stimuli andor subject behavior and brain activity. Data on the site is freely available using mostly either CC-BY or CC-0 Creative Commons licenses though some custom licenses also exist. We also have a page at httpswww.facebook.combrainliner where you can contact us BrainLiner.jp Creative Commons License, EEGMEGECoG http://www.nitrc.org/projects/brainliner/ takemiya@atr.jp 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 MR http://www.nitrc.org/projects/medical_cvpr/ zheng.vision@gmail.com Yes Gretchen Navidi, navidig@mail.nih.gov NITRC OS Independent Yes Gretchen Navidi 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 5 - ProductionStableMature 1.0 NIH Pediatric MRI Data Repository End Users, Developers, 5 - ProductionStableMature, OS Independent, Web Environment, English, Database, Websites, Data, NIfTI-1, MINC, MINC2, DICOM, MR, Clinical Neuroinformatics http://www.nitrc.org/projects/pediatric_mri/ navidig@mail.nih.gov 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, MR, PETSPECT, CT http://www.nitrc.org/projects/pyxnat/ yannick.schwartz@gmail.com Freeware Yes Daniel Glen, glend@mail.nih.gov NITRC Linux,MacOS 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 End Users, Developers, 5 - ProductionStableMature, C, Python, Linux, MacOS, X11 Applications, English, Surface Analysis, Tensor Metric, Image Display, Rendering, Temporal Convolution - Deconvolution, Haemodynamic Response, Nonlinear, Registration, Resampling, Region of Interest, Volumetric Analysis, NIfTI-1, MINC, DICOM, ANALYZE, AFNI BRIK, Freeware, Response Monitoring, GIfTI, MR http://www.nitrc.org/projects/afni/ glend@mail.nih.gov 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 Developers, 5 - ProductionStableMature, GNU General Public License GPL, C, Console Text Based, X11 Applications, OS Independent, English, Image Reconstruction, Image Display, Simulation, NIfTI-1, DICOM, ANALYZE, MR http://www.nitrc.org/projects/od1n/ thies@jochimsen.de 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, MR http://www.nitrc.org/projects/surfacestat/ vincent-magnotta@uiowa.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.usc.eduSoftwareShapeTools at USC. ShapeTools GNU General Public License GPL, MR, PETSPECT, CT http://www.nitrc.org/projects/shapetools/ iwaterpolo@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 2012-10-08 4 - Beta v11.e SPM_SS - fMRI functional localizers End Users, Developers, 4 - Beta, MITX Consortium License, X11 Applications, Win32 MS Windows, OS Independent, English, Modeling, Linear, NIfTI-1, ANALYZE, MATLAB, MR http://www.nitrc.org/projects/spm_ss/ alfnie@gmail.com Yes Stephanie-Ann Seguin, sales@vpixx.com NITRC Yes Stephanie-Ann Seguin The PROPixx is a unique DLP LED projector which has been designed to be the most flexible display solution for vision research and neuroscience research. The PROPixx features a native resolution of 1920 x 1080 and can be driven with refresh rate up to 500Hz with deterministic timing. The PROPixx uses high brightness LEDs as a light source giving a wide colour gamut and much longer lifetime than halogen light sources. It features high-bit depth up to 12-bit per color for high-frequency full colour stimulation. For stereo vision applications our high-speed ferro-electric circular polarizer can project stereoscopic stimuli with the use of passive glasses at up to 400Hz. In addition the PROPixx includes an array of peripherals which often need to be synchronized to video during an experiment and with perfect microsecond precision. PROPixx DLP LED projector Scanner, Stimulus Presentation, Response Monitoring, Eye Tracking, MEG, EEG, Physiological Stimulation, Domain Independent http://www.nitrc.org/projects/dlp_projector/ sales@vpixx.com 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 End Users, Other Audience, 5 - ProductionStableMature, Scanner, NIRSFNIR, Commercial License Hitachi, Optical Imaging http://www.nitrc.org/projects/hitachimedical/ schnack@kf.hitachi-medical.co.jp 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 MR, EEGMEGECoG, PETSPECT, CT, Domain Independent http://www.nitrc.org/projects/qa_procedure/ dyounes@uci.edu GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The ShapeViewer httpwww.loni.usc.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.usc.eduSoftwareShapeViewer at USC. ShapeViewer GNU General Public License GPL, MR, PETSPECT, CT http://www.nitrc.org/projects/shapeviewer/ iwaterpolo@gmail.com 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 fORP 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. 2013-8-20 5 - ProductionStableMature Paradigm v2.1.0 2013-1-30 5 - ProductionStableMature Paradigm v2.0 2011-7-13 5 - ProductionStableMature Paradigm v1.0.3 Paradigm 5 - ProductionStableMature, Python, Microsoft, Win32 MS Windows, Scanner, Experimental Control, Eye Tracking, EEG, Paradigm License, MR http://www.nitrc.org/projects/paradigm/ bruno@prsemail.com GNU General Public License GPL Yes Qian Wang, qianwang@email.unc.edu NITRC Qian Wang 4DAtlas 4D Atlas Construction Toolbox provides solutions for constructing longitudinal atlases which are the necessary steps for many brain-related applications. This software package was developed in the IDEA group at UNC-Chapel Hill httpbric.unc.eduideagroup . 2013-3-26 Demo Data 2013-3-26 Documentation V1.1 2013-3-26 Software Package 2013-3-25 Software 2013-3-25 TestData 2013-3-25 Document 4D Atlas Construction GNU General Public License GPL, MR http://www.nitrc.org/projects/atlas4d/ qianwang@email.unc.edu Commercial License Yes Michael Calarco, mcalarco@trianglebiosystems.com NITRC Michael Calarco TBSI is a biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring recording and stimulation functions are needed. - Neural Recording Equipment - Neural Stimulation Equipment - Data Acquisition Hardware and Software Triangle BioSystems Other Software Resource, EEG, Commercial License, EEGMEGECoG, Computational Neuroscience http://www.nitrc.org/projects/tbsi/ mcalarco@trianglebiosystems.com 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, MR http://www.nitrc.org/projects/fandtasia/ abarmpou@cise.ufl.edu SBIA License Yes CBICA Software, software@cbica.upenn.edu NITRC CBICA Software COMPARE Generic classification tool for 3D images 2017-2-20 0.3.2 2011-2-28 COMPARE CBICA COMPARE SBIA License, MR http://www.nitrc.org/projects/compare/ software@cbica.upenn.edu SBIA License Yes CBICA Software, software@cbica.upenn.edu NITRC Yes CBICA Software 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, MR http://www.nitrc.org/projects/hammer/ software@cbica.upenn.edu Open Data Commons Public Domain Dedication and License 1.0 Yes Russell Poldrack, poldrack@mac.com NITRC Yes 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 Data, Open Data Commons Public Domain Dedication and License 1.0, MR http://www.nitrc.org/projects/openfmri/ poldrack@mac.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 5 - ProductionStableMature Talairach Client 2.4.2 2007-10-03 5 - ProductionStableMature Talairach Client 2.4 Talairach Daemon End Users, 5 - ProductionStableMature, Java, OS Independent, English, Atlas Application, Database Application, Other Format, BrainMap License, MR http://www.nitrc.org/projects/tal-daemon/ foxm@uthscsa.edu GNU General Public License GPL Yes Cinly Ooi, co224@cam.ac.uk NITRC Linux,MacOS 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 5 - ProductionStableMature Main CamBA SourceForge Package Link CamBA End Users, Developers, 5 - ProductionStableMature, GNU General Public License GPL, C, Unix Shell, Java, Linux, MacOS, X11 Applications, Other Environment, Web Environment, English, Algorithm or Reusable Library, Time Domain Analysis, Spectral Analysis, Regression, Wavelet Transformation, Affine Warp, Image-to-Template, NIfTI-1, MR http://www.nitrc.org/projects/camba/ co224@cam.ac.uk 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, MR http://www.nitrc.org/projects/webmscaleapi/ anoske@ncmir.ucsd.edu BIRN License Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project httpswww.nitrc.orgprojectsmcp. Mouse BIRN Data, BIRN License, Atlas Data, MR, Imaging Genomics http://www.nitrc.org/projects/mousebirn/ iwaterpolo@gmail.com 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 MR http://www.nitrc.org/projects/vvhistomatch/ mark-scully@uiowa.edu Textpresso License Yes Hans-Michael Muller, mueller@caltech.edu NITRC Linux,MacOS 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 End Users, 5 - ProductionStableMature, Perl, Linux, MacOS, Web Environment, English, Websites, Web Service, Knowledge Environment, Database Application, shbash, Bibliographic Resource, PDF - Portable Document Format, Textpresso License, Domain Independent http://www.nitrc.org/projects/textpresso-2-0/ mueller@caltech.edu 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 MR http://www.nitrc.org/projects/nicesign/ zheng.vision@gmail.com Yes Syam Gadde, syam.gadde@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 MR, PETSPECT, CT, Clinical Neuroinformatics http://www.nitrc.org/projects/xcede/ syam.gadde@duke.edu BSD License Yes Matthew Brett, matthew.brett@gmail.com NITRC Yes Matthew Brett 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, MR http://www.nitrc.org/projects/nibabel/ matthew.brett@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 FNIR COBI Suite, NIRSFNIR, Optical Imaging http://www.nitrc.org/projects/fnirdevices/ davood@fnirdevices.com BSDMIT-Style Open Source License Yes Frederick Bryan, frederick.w.bryan@vanderbilt.edu NITRC Frederick Bryan 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, MR http://www.nitrc.org/projects/vutools/ frederick.w.bryan@vanderbilt.edu Free For Non-Commercial Use Only Yes Yun Li, yunli@med.unc.edu NITRC Yun Li MaCH is a tool for haplotyping genotype imputation and disease association analysis developed by Goncalo Abecasis and Yun Li. 2013-3-16 1.0 MaCH Free For Non-Commercial Use Only, Domain Independent, Imaging Genomics, Imputation http://www.nitrc.org/projects/mach/ yunli@med.unc.edu BSD License Yes Anne Findlay, anne.findlay@ucsf.edu NITRC OS Independent Yes MATLAB,cshtcsh Anne Findlay 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 End Users, 5 - ProductionStableMature, BSD License, Other Environment, OS Independent, English, Surface Rendering, Three Dimensional Display, Multivariate Analysis, Principal Component Analysis, MEG Modeling, MATLAB, cshtcsh, MR, EEGMEGECoG http://www.nitrc.org/projects/nutmeg/ anne.findlay@ucsf.edu GNU General Public License GPL Yes Nitin Bangera, nitinb2@gmail.com NITRC Yes Nitin Bangera CUDA-SPHERE-FWD-MEEG is a CUDA C based toolkit which provides a GPU based implementation of the spherical model forward solution for the 306 channel Elekta Neuromag MEG system and the EEG. The 1-Sphere forward solution for the MEG and the 4-Sphere forward solution for the EEG is implemented in CUDA C and an accelerated solution is obtained using the NVIDIA GPU when the solution is calculated for a large number of dipoles on the order of 15000 and above and sensor location. Speedup by a factor of 22 and 32 is obtained for the EEG and MEG solution respectively when compared to the fastest CPU implementation available in the public domain. The complete source code and pre-compiled binaries are also made available via an open source license GPL Version 3. A CUDA enabled NVIDIA graphics card is required to use the software. 2012-2-10 1.0 CUDA accelerated spherical model MEEG GNU General Public License GPL, EEG Modeling, MEG Modeling, EEGMEGECoG http://www.nitrc.org/projects/cuda_sphere_fwd/ nitinb2@gmail.com GNU General Public License GPL Yes I Dinov, iwaterpolo@gmail.com NITRC I Dinov The Synchronized Histological Image Viewing Architecture httpwww.loni.usc.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.usc.eduSoftwareSHIVA at USC. Synchronized Histological Image View Arc GNU General Public License GPL, MR, Microscopy http://www.nitrc.org/projects/shiva/ iwaterpolo@gmail.com 3D Slicer License Yes Marcel Prastawa, marcel.prastawa@gmail.com NITRC Marcel Prastawa SCORE is a collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard ground truth. SCORE 3D Slicer License, Domain Independent http://www.nitrc.org/projects/score/ marcel.prastawa@gmail.com 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 MR http://www.nitrc.org/projects/groupwisereg/ luis.ibanez@kitware.com BIRN License Yes Syam Gadde, syam.gadde@duke.edu NITRC Linux,MacOS,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. 2015-2-20 5 - ProductionStableMature 1.11.1 2014-9-03 5 - ProductionStableMature 1.11.0 2013-1-11 5 - ProductionStableMature 1.10.7 2013-1-10 5 - ProductionStableMature 1.10.6 2012-10-16 5 - ProductionStableMature 1.10.4 2012-9-06 5 - ProductionStableMature 1.10.3 2012-8-16 5 - ProductionStableMature 1.10.2 2012-6-18 5 - ProductionStableMature 1.10.0 2012-3-12 5 - ProductionStableMature 1.9.12.2 2012-1-30 5 - ProductionStableMature 1.9.11 2011-12-21 5 - ProductionStableMature 1.9.10 2011-4-21 5 - ProductionStableMature 1.9.9.5 2011-2-24 5 - ProductionStableMature 1.9.9.4 2011-2-24 5 - ProductionStableMature 1.9.9.3 2011-1-18 5 - ProductionStableMature 1.9.9.2 2011-1-04 5 - ProductionStableMature 1.9.9.1 2010-12-20 5 - ProductionStableMature 1.9.9 2010-11-08 5 - ProductionStableMature 1.9.8.9 2010-11-08 5 - ProductionStableMature 1.9.8.8 2010-10-29 5 - ProductionStableMature 1.9.8.7 2010-8-26 5 - ProductionStableMature 1.9.8.6 2010-7-12 5 - ProductionStableMature 1.9.8.5 2010-7-09 5 - ProductionStableMature 1.9.8.4 2010-3-17 5 - ProductionStableMature 1.9.8.3 2010-3-09 5 - ProductionStableMature 1.9.8.2 2010-3-03 5 - ProductionStableMature 1.9.8.1 2010-3-02 5 - ProductionStableMature 1.9.8 2010-2-09 5 - ProductionStableMature 1.9.7.3 2010-1-13 5 - ProductionStableMature 1.9.7.2 2010-1-05 5 - ProductionStableMature 1.9.7.1 2009-12-23 5 - ProductionStableMature 1.9.7 2009-12-21 5 - ProductionStableMature 1.9.6 2009-11-17 5 - ProductionStableMature 1.9.5 2009-11-09 5 - ProductionStableMature 1.9.4 2009-10-15 5 - ProductionStableMature 1.9.3 2009-8-10 5 - ProductionStableMature 1.9.2 2009-7-08 5 - ProductionStableMature 1.9.1 2009-4-28 5 - ProductionStableMature 1.9.0 2009-4-20 5 - ProductionStableMature 1.8.65 2008-10-01 5 - ProductionStableMature 1.8.64 2008-7-29 5 - ProductionStableMature 1.8.63 BXHXCEDE Tools End Users, Developers, 5 - ProductionStableMature, C, C, Perl, Linux, Other UNIX-like, Windows, MacOS, Console Text Based, English, Quantification, Statistical Operation, NIfTI-1, MINC, DICOM, ANALYZE, MGHMGZ, Other Format, shbash, BIRN License, Format Conversion, MR http://www.nitrc.org/projects/bxh_xcede_tools/ syam.gadde@duke.edu GNU General Public License GPL Yes Keiji Harada, kharada@atr.jp NITRC Linux,MacOS,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 5 - ProductionStableMature 1.0 2011-8-03 5 - ProductionStableMature 1.0 2011-8-03 5 - ProductionStableMature 1.2.1 BrainDecoderToolbox End Users, Other Audience, 5 - ProductionStableMature, GNU General Public License GPL, Linux, Windows, MacOS, Console Text Based, English, Japanese, Application, ANALYZE, MATLAB, Other Format, MR http://www.nitrc.org/projects/bdtb/ kharada@atr.jp Freeware Yes Kai Wang, kaiwang@usc.edu NITRC Kai Wang ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes including human genome hg18 hg19 as well as mouse worm fly yeast and many others. ANNOVAR Functional annotation of genetic variants from high-throughput sequencing data Freeware, Imaging Genomics, SNPs amp;amp; Genes, Next Generation Sequencing http://www.nitrc.org/projects/annovar/ kaiwang@usc.edu 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 4 - Beta 1.1.0 2009-8-21 4 - Beta 1.0.0 Subject Library End Users, 4 - Beta, Python, Console Text Based, X11 Applications, OS Independent, English, Algorithm or Reusable Library, Other Software Resource, Database Application, Workflow, ANALYZE, MR http://www.nitrc.org/projects/subjectlibrary/ ocarmichael@ucdavis.edu Attribution Non-Commercial Yes Christoph Feenders, christoph.feenders@icbm.de NITRC Christoph Feenders 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 2013-7-04 SINOMO 2013-07 2012-1-30 2011 Release SINOMO SIngular NOde MOtifs Attribution Non-Commercial, EEGMEGECoG, Computational Neuroscience http://www.nitrc.org/projects/sinomo/ christoph.feenders@icbm.de 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 4 - Beta MBAT 2.0.13 MouseBIRN Atlasing Toolkit MBAT End Users, 4 - Beta, Java, Win32 MS Windows, Gnome, KDE, Other Environment, OS Independent, English, Information Resource, NIfTI-1, ANALYZE, BIRN License, MR http://www.nitrc.org/projects/mbat/ dlee@loni.ucla.edu 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, MR http://www.nitrc.org/projects/iviewx_mri-lr/ mark.mento@smivision.com Yes Stephanie-Ann Seguin, sales@vpixx.com NITRC Yes Stephanie-Ann Seguin The VIEWPixx 3D is a complete display toolbox which has been developed specifically to replace CRTs in vision science labs. The VIEWPixx 3D incorporates industrial LCD glass and a controller which has been custom designed to support vision research. Our innovative LED backlight design features superior display uniformity and a wide color gamut exceeding that of any CRT. In addition it includes an array of peripherals which often need to be synchronized with microsecond precision 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. It is perfectly suited for presentation of dynamic stimuli it features 1920 x 1080 resolution 10-bit intensity on each colour and true 120Hz refresh rate. VIEWPixx 3D Stimulus Presentation, Response Monitoring, Physiological Recording, Physiological Stimulation, Domain Independent http://www.nitrc.org/projects/replacement_crt/ sales@vpixx.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, EEGMEGECoG http://www.nitrc.org/projects/biomag_group/ jbmckay@telus.net fMRI Grocer License Yes senhua zhu, zshtom@gmail.com NITRC senhua zhu This toolbox contains many kinds of kits that you may be interested in during fMRI data analysis. This toolbox is a homebrew kits built during practical ASLarterial spin labeling based CBF data analysis. Meanwhile this toolbox is also compatible with BOLD data analysis. Everyone would find something useful for their own data analysis This toolbox is run and tested on SPM8 with MATLAB 7.6.0R2008a under the Linux OS. Theoretically most of the functions except the menu1amp;amp;2 which are specially designed for the Batch Editor of SPM8 of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS. Feel free to give feedback to authors if you encounter any bugs or problems. Senhua Zhu Center for functional Neuroimaging University of Pennsylvania 3 W.Gates Bldg 3400 Philadelphia PA 19104 United States Email zshtomgmail.com ; senhuamail.med.upenn.edu QQ group number QQ群 60524357 Google group httpsgroups.google.comdforumfmri-grocer 2013-3-27 Grocer2.12 fMRI Grocer MR, fMRI Grocer License http://www.nitrc.org/projects/fmri_grocer/ zshtom@gmail.com g.tec Licence Yes Alexander Lechner, lechner@gtec.at NITRC Windows Yes MATLAB Alexander Lechner g.BSanalyze - gtecs Biosignal Analysis Software is an interactive environment for multimodal biosignal data processing and analysis in the fields of clinical research and life sciences. It is the most comprehensive package to analyze non-invasive and invasive brain- heart- and muscle-functions and dysfunctions. It includes many functions such as support vector machines event-related ECG support for P300 and SSVEPSSSEP BCIs zero class detection for BCIs compressed spectral array minimum energy and more g.BSanalyze consists of a base version for data import visualization transformation and pre-processing and has several dedicated toolboxes. The package comes with many sample biosignal data-sets including P300 SSVEP motor imagery CSP BCIs Tilt-Table EPs multi-unit activity CFM and ERDERS. g.BSanalyze Windows, English, Spectral Analysis, MATLAB, Other Format, ASCII, EEGMEGECoG, Event Related Potential, g.tec Licence http://www.nitrc.org/projects/gbsanalyze/ lechner@gtec.at 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 httprfmri.orgDPARSF DPARSF GNU General Public License GPL, MR http://www.nitrc.org/projects/dparsf/ ycg.yan@gmail.com Creative Commons License Yes Daniel Langstraat, daniel-langstraat@uiowa.edu NITRC C Daniel Langstraat NOTE All active development of BRAINSConstellationDetector is now being stored in a Git repository at github.com. Please go to httpsgithub.comBRAINSiaBRAINSTools 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 End Users, 5 - ProductionStableMature, C, English, Fiducial, NIfTI-1, DICOM, ANALYZE, Nrrd, Creative Commons License, MR http://www.nitrc.org/projects/brainscdetector/ daniel-langstraat@uiowa.edu 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 End Users, 4 - Beta, GNU General Public License GPL, OS Independent, Web Environment, English, Websites, Knowledge Environment, Data, MR http://www.nitrc.org/projects/bredewiki/ fn@imm.dtu.dk 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, Clinical Neuroinformatics http://www.nitrc.org/projects/pd3/ jvanhorn@loni.ucla.edu 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 MR, UCSF NCL Software License http://www.nitrc.org/projects/msc_toolbox/ liyiou@gmail.com GNU General Public License GPL Yes Christophe Phillips, c.phillips@ulg.ac.be NITRC OS Independent Yes MATLAB Christophe Phillips FASST is an EEG toolbox developed to help users with 3 specific types of data and problems simulatenous EEG-fMRI recording continuous EEG scoring e.g. sleep and handling visualisation cutting power spectrum etc. multi-channel recording of spontaneous EEG. The toolbox is written in Matlab and is specifically compatible with the BrainAmp family of EEG recorders from BrainProducts GmbH Three other data formats are now also supported the edf European Data Format exported raw-EGI data from Electrical Geodesics Inc. and the BCI2000 format.The results are directly compatible with SPM8 and are saved with SPM8 EEG data format. FASST – fMRI Artefact rejection and Sleep Scoring Toolbox End Users, Developers, 5 - ProductionStableMature, GNU General Public License GPL, OS Independent, Visualization, MATLAB, MR, EEGMEGECoG http://www.nitrc.org/projects/fasst/ c.phillips@ulg.ac.be BSD License Yes Juli Klemm, klemmj@mail.nih.gov NITRC Yes Java Juli Klemm Cancer Genome-Wide Association Studies caGWAS allows researchers to integrate query report and analyze significant associations between genetic variations and disease drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms SNPs simultaneously enabling whole genome association studies. Within the Clinical Genomic Object Model CGOM the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a semantically annotated domain model that captures associations between Study Study Participant Disease SNP Association Analysis SNP Population Frequency and SNP annotations. caGWAS End Users, BSD License, Java, Web Environment, English, Imaging Genomics, Computational Neuroscience, Genetic Association http://www.nitrc.org/projects/cagwas/ klemmj@mail.nih.gov NIH Data Access Policy Yes Matt McAuliffe, matthew.mcauliffe@nih.gov NITRC OS Independent Yes Matt McAuliffe The Federal Interagency Traumatic Brain Injury Research FITBIR informatics system was developed to share data across the entire TBI research field and to facilitate collaboration between laboratories as well as interconnectivity with other informatics platforms. Sharing data methodologies and associated tools rather than summaries or interpretations of this information can accelerate research progress by allowing re-analysis of data as well as re-aggregation integration and rigorous comparison with other data tools and methods. This community-wide sharing requires common data definitions and standards as well as comprehensive and coherent informatics approaches. FITBIR Federal Interagency Traumatic Brain Injury Research End Users, 5 - ProductionStableMature, OS Independent, Web Environment, English, Database, Web Resource, Knowledge Environment, Data, MR, Clinical Neuroinformatics, NIH Data Access Policy, Brain Injuries http://www.nitrc.org/projects/fitbir/ matthew.mcauliffe@nih.gov 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. 2015-2-13 5 - ProductionStableMature 3.0.5 SPM12 or SPM8 revision 4010 Update 2010-8-24 5 - ProductionStableMature 2.5 2007-9-09 5 - ProductionStableMature 2.4 WFU_PickAtlas End Users, 5 - ProductionStableMature, POSIXUNIX-like, Windows, X11 Applications, Win32 MS Windows, English, Atlas Application, ANALYZE, MATLAB, WFU ANSIR License, MR 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, MR http://www.nitrc.org/projects/nipy-community/ matthew.brett@gmail.com MGH CSRL License Yes Ruopeng Wang, rpwang@nmr.mgh.harvard.edu NITRC Linux,MacOS,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 5 - ProductionStableMature 0.6 2010-3-16 5 - ProductionStableMature 0.5.1 2009-12-01 5 - ProductionStableMature 0.5 2009-6-03 5 - ProductionStableMature 0.4.3 2008-6-18 5 - ProductionStableMature 0.4.2 Diffusion Toolkit TrackVis End Users, 5 - ProductionStableMature, C, Linux, Windows, MacOS, Console Text Based, X11 Applications, Win32 MS Windows, Other Environment, English, Image Reconstruction, Visualization, Diffusion MR Fiber Tracking, NIfTI-1, DICOM, ANALYZE, MGH CSRL License, MR 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 Computational Neuroscience http://www.nitrc.org/projects/sfmproject/ rohithmv@udel.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 Attribution Share Alike, Atlas Data, MR http://www.nitrc.org/projects/vervet_atlas/ clwyatt@vt.edu 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 End Users, 4 - Beta, GNU General Public License GPL, OS Independent, English, Mesh Generation, MATLAB, Other Format, MR, Optical Imaging http://www.nitrc.org/projects/iso2mesh/ 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 5 - ProductionStableMature, Python, OS Independent, Web Environment, English, Web Resource, Data, Image Display, Rendering, Web Application - Free to use, MR http://www.nitrc.org/projects/umcd/ jbrown81@gmail.com 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.usc.eduSoftwareiTools at USC. ITools Resourceome End Users, Developers, Other Audience, 4 - Beta, GNU Lesser General Public License LGPL, Java, Other Environment, OS Independent, Web Environment, English, Data Resource, Data Model, Web Resource, Ontology, Other Information Resource, Other Format, Experiment Control, LONI Pipeline, Imaging Genomics, Computational Neuroscience http://www.nitrc.org/projects/itools/ iwaterpolo@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 1 - Planning 1.1 2007-1-17 1 - Planning V0.3 Resource Ontology Discussion Group Developers, 1 - Planning, English, Ontology, Community, Domain Independent http://www.nitrc.org/projects/ontology/ jturner@mrn.org Yes Will Horton, hortonw@mir.wustl.edu NITRC POSIXUNIX-like Yes Java,Python Will Horton User contributions for XNAT. 2012-11-08 ARC Queue Tools 2012-8-08 Version 1.6.0-0 2012-6-27 Version 1.0 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 Developers, System Administrators, Python, Java, POSIXUNIX-like, Console Text Based, Other Environment, Web Environment, English, Database Application, XNAT Pipeline, MR, PETSPECT, CT http://www.nitrc.org/projects/xnat_extras/ hortonw@mir.wustl.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 End Users, Developers, Web Environment, English, Community, NIDAG, MR http://www.nitrc.org/projects/nidag/ mar@yorku.ca Commercial License VPixx Yes Stephanie-Ann Seguin, sales@vpixx.com NITRC Yes Stephanie-Ann Seguin The VIEWPixx is a complete display toolbox which has been conceived specifically to replace CRTs in vision science labs. The VIEWPixx features high-performance industrial LCD glass and a panel controller which has been custom designed to support vision research.Our innovative LED backlight design features superior display uniformity and a wide color gamut exceeding that of any CRT. In addition it 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. VIEWPixx 5 - ProductionStableMature, English, Stimulus Presentation, Response Monitoring, Physiological Recording, Commercial License VPixx, Physiological Stimulation, MR, EEGMEGECoG http://www.nitrc.org/projects/crt_replacement/ sales@vpixx.com Freeware Yes Kai Wang, kaiwang@usc.edu NITRC Kai Wang GenGen is a suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. GenGen Freeware, Imaging Genomics, SNPs amp;amp; Genes, Pathways amp;amp; Networks http://www.nitrc.org/projects/gengen/ kaiwang@usc.edu 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 1 - Planning alpha-0.1.2-Linux 2011-3-02 1 - Planning alpha-0.1.2-Mac 2011-3-02 1 - Planning alpha-0.1.2-WindowsInstaller 2011-3-01 1 - Planning alpha-0.1.2-Windows BrainCSI End Users, 1 - Planning, C, BSD License, POSIXUNIX-like, Windows, MacOS, Console Text Based, X11 Applications, Win32 MS Windows, English, Application, NIfTI-1, DICOM, MR http://www.nitrc.org/projects/braincsi/ chuck@unm.edu GNU General Public License GPL Yes Arnaud Delorme, arnodelorme@gmail.com NITRC OS Independent,MacOS,POSIXUNIX-like,Microsoft Yes MATLAB Arnaud Delorme EEGLAB is to date the most popular EEGMEGECoG software with about 100000 download worldwide since 2003. 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 spectral timefrequency and coherence analysis as well as standard methods including event-related potentials ERP. 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. For experienced Matlab users EEGLAB offers a structured programming environment for storing accessing measuring manipulating and visualizing event-related EEG data. 2012-2-06 4 - Beta EEGLAB latest release EEGLAB End Users, Developers, 4 - Beta, 5 - ProductionStableMature, GNU General Public License GPL, POSIXUNIX-like, Microsoft, MacOS, Console Text Based, X11 Applications, Win32 MS Windows, OS Independent, English, Three Dimensional Display, Two Dimensional Display, ANOVA, Fourier Time-domain Analysis, Spectral Analysis, Temporal Wavelet Analysis, Independent Component Analysis, EEG Modeling, MEG Modeling, MATLAB, Format Conversion, ASCII, EEGMEGECoG, Source Separation Analysis, Event Related Potential, EDFBDFGDF, Brain Vision Analyzer Data Exchange Format, EGI, ANT, CNT http://www.nitrc.org/projects/eeglab/ arnodelorme@gmail.com Yes Rich Pickett, rich.pickett@sdsu.edu NITRC Rich Pickett The Autism Tissue Program ATP is a research program organized to provide post-mortem brain tissue to qualified neuroscientists all over the world. Autism Tissue Program - ATP MR, Optical Imaging, Imaging Genomics, Clinical Neuroinformatics, Asperger Syndrome, Autistic Disorder, Child Development Disorders Pervasive http://www.nitrc.org/projects/atp/ rich.pickett@sdsu.edu Commercial License Yes Phan Luu, pluu@egi.com NITRC Yes Phan Luu Net Station also offers specialized tools and workflow options for both clinical and research applications allows you to save different combinations of view settings called workspaces and helps with your reporting requirements by letting you set up and print custom cover pages. For more specialized work Net Station also provides an optional electrical source estimation module GeoSource and an optional sensor location digitizer Geodesic Photogrammetry System. Netstation Animation, Spectral Analysis, Format Conversion, Commercial License, EEGMEGECoG, Event Related Potential http://www.nitrc.org/projects/netstation/ pluu@egi.com Free For Non-Commercial Use Only Yes Yun Li, yunli@med.unc.edu NITRC Yun Li mach2dat performs logistic regression using imputed SNP dosage data and adjusting for covariates. 2013-9-06 V124 2013-3-16 V121 mach2dat Free For Non-Commercial Use Only, Domain Independent, Imaging Genomics, Genetic Association http://www.nitrc.org/projects/mach2dat/ yunli@med.unc.edu Yes Sangsoo Kim, sskimb@ssu.ac.kr NITRC Sangsoo Kim A tool for the gene-set or pathway analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology KEGG pathways or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version. It has been published as amp;quot;Nam D. Kim J. Kim S. Y. amp;amp; Kim S. GSA-SNP a general approach for gene set analysis of polymorphisms. Nucleic Acids Res. 38 Suppl. 2 W749–W754 2010. GSA-SNP Imaging Genomics, Computational Neuroscience, Clinical Neuroinformatics http://www.nitrc.org/projects/gsa-snp/ sskimb@ssu.ac.kr Yes Daniel Langstraat, daniel-langstraat@uiowa.edu NITRC Daniel Langstraat NOTE All active development of BRAINSTracer is now being stored in a Git repository at github.com. Please go to httpsgithub.comBRAINSiaBRAINSTools 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 MR http://www.nitrc.org/projects/brainstracer/ daniel-langstraat@uiowa.edu GNU General Public License GPL Yes Bin He, luxxx273@umn.edu NITRC Windows XP Yes 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 End Users, GNU General Public License GPL, English, Visualization, Multivariate Analysis, Region of Interest, Forward - Inverse, MATLAB, Windows XP, EEGMEGECoG http://www.nitrc.org/projects/econnectome/ luxxx273@umn.edu 3D Slicer License Yes Antonio Tristán-Vega, atriveg@lpi.tel.uva.es NITRC Linux,MacOS,Other UNIX-like,Microsoft Yes 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. 2013-2-09 5 - ProductionStableMature Beta 1.0 Finsler tractography module for Slicer End Users, 5 - ProductionStableMature, C, Linux, Other UNIX-like, Microsoft, MacOS, Console Text Based, Other Environment, English, Diffusion MR Fiber Tracking, Direction, 3D Slicer License, Nrrd, Q-Ball, Diffusion Spectrum, MR, Connectivity Analysis http://www.nitrc.org/projects/finslertract/ atriveg@lpi.tel.uva.es Yes Angie Laird, lairda@uthscsa.edu NITRC Angie Laird Scribe encodes papers to populate the BrainMap Database Scribe MR, PETSPECT http://www.nitrc.org/projects/scribe/ lairda@uthscsa.edu BSDMIT-Style Open Source License Yes Boris Rivkin, b.rivkin@dkfz.de NITRC Boris Rivkin This projects is an open-data initiative for the distributation of common datasets for the evaluation and validation of diffusion MRI processing methods. 2017-4-03 Fiber Phantom for Kurtosis Imaging 2017-3-30 Datasets_Isotropic_Diffusion_Phantom_Star_LesionInsert 2017-3-01 MICCAI 2015 datasets for machine learning based tractography nifti and nrrd 2015-5-15 MICCAI 2015 datasets for machine learning based tractography 2015-4-01 Ground truth fibers of the replicated FiberCup dataset 2013-8-08 Fiberfox replications of the FiberCup datasets 2012-10-10 DWI data resolution phantoms 2012-10-10 DWI data single fiber string phantoms 2012-10-09 DWI data crossing fiber phantoms Diffusion MRI - In-vivo and Phantom Data NIfTI-1, Nrrd, BSDMIT-Style Open Source License, MR http://www.nitrc.org/projects/diffusion-data/ b.rivkin@dkfz.de GNU General Public License GPL Yes Olaf Dimigen, olaf.dimigen@hu-berlin.de NITRC OS Independent Yes MATLAB Olaf Dimigen EYE-EEG is a plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses imports and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLABs event structure allowing easy saccade- and fixation-related EEG analysis e.g. fixation-related potentials FRPs. Alternatively EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior e.g. pupil size microsaccades in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLABs GUI or called from the command line. EYE-EEG combined eye-tracking amp; EEG End Users, 4 - Beta, GNU General Public License GPL, Software, OS Independent, English, MATLAB, EEGMEGECoG http://www.nitrc.org/projects/eye-eeg/ olaf.dimigen@hu-berlin.de BIRN Data License Yes Timothy Brown, timothy@cis.jhu.edu NITRC Timothy Brown The long term goal of Computational Anatomy CA is to create algorithmic tools that aid basic and clinical neuroscientists in the analysis of variability in anatomical structures at different scales. The aim is to provide capability for integrating 3D Slicer application and ITK software library with the statistical shape analysis pipeline and thus enable the wider neuroimaging community to efficiently analyze anatomical variations in disease. We have constructed anatomical atlases needed for analysis of shape vectors. These atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children adolescents and young adults in neuroimaging studies of major depression disorder MDD at Washington University at St Louis. As a major public health burden MDD provides the biological testbed for the pipeline from which probabilistic atlases will be generated. Software and datasets for statistical shape analysis of anatomical structures are thus provided. Atlases of amygdala and hippocampus for pediatric populations BIRN Data License, MR http://www.nitrc.org/projects/jhucis_pedatlas/ timothy@cis.jhu.edu XNAT License,Northwestern University Schizophrenia Data and Software Tool NUSDAST Yes Lei Wang, leiwang1@northwestern.edu NITRC Yes Lei Wang The Northwestern University Schizophrenia Data and Software Tool NUSDAST is a repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia healthy controls and their respective siblings most with 2-year longitudinal follow-up. The data include Neuroimaging data Structural MR scans landmarks and surface maps and FreeSurfer parcellation and measurement Cognitive data domain scores for crystallized intelligence working memory episodic memory and executive function Clinical data demographic sibling relationship SAPS and SANS psychopathology Genetic data 20 SNPs A neuroimaging mapping analysis and visualization software tool CAWorks is also part of this resource. We have also established a web-based information retrieval portal that allows the user to efficiently search the collection. Northwestern University Schizophrenia Data and Software Tool NUSDAST Data, NIfTI-1, ANALYZE, XNAT License, Federal Funding Resource, MR, Clinical Neuroinformatics, Northwestern University Schizophrenia Data and Software Tool NUSDAST, Schizophrenia http://www.nitrc.org/projects/nusdast/ leiwang1@northwestern.edu BIRN License Yes Anthony Kolasny, akolasny@jhu.edu NITRC Yes Anthony Kolasny Current enhancements to CAWorks have focused on interactive support for landmarking of subcortical structures. Specific plugins are available for landmark placement of the hippocampus amygdala and entorhinal cortex regions. After landmarking is completed CAWorks facilitates submission for automated segmentation processing. CAWorks is being used by the Biomarkers for Older Controls At Risk for Dementia BIOCARD Resource for Quantitative Functional MRI TRD4 Validation of StructuralFunctional MRI Localization and Biomedical Informatics Research Network BIRN projects. CAWorks has been further enhanced with a browser plugin module for the Extensible Neuroimaging Archive Toolkit XNAT. The XNAT software facilitates the storage and management of neuroimaging and associated data. The XNAT browser enables the retrieval of medical image data from XNAT for analysis in CAWorks and the storage of CAWorks analysis results in XNAT. CAWorks Three Dimensional Display, BIRN License, MR http://www.nitrc.org/projects/caworks/ akolasny@jhu.edu Yes Jean-René Bélanger, jr.belanger@imeka.ca NITRC Jean-René Bélanger Imeka Tractography is a diffusion MRI service that handles the processing of diffusion data from raw data to structural connectivity including Quality Assurance. We work with neuroscience researchers who want quality diffusion data reconstruction. These researchers do not necessarily have the knowledge to perform diffusion analysis or dont have the manpower. Our service is not a black box solution we work with the researchers and make sure they can work with the tractography results and are aware of the pitfalls of the techniques by providing training sessions. We have a system to work at a distance as if we were in your lab. We can do high angular resolution HARDI reconstruction from DTI data with as little as 20 gradient directions acquisitions. State-of-the-art diffusion MRI is just one click away. Contact us right now to submit your project and have access to structural Connectome research today. Visit us at www.imeka.ca for more details Imeka Tractography Service End Users, Tractography, MR, Computational Neuroscience http://www.nitrc.org/projects/imeka_tracto/ jr.belanger@imeka.ca Free For Non-Commercial Use Only Yes Yun Li, yunli@med.unc.edu NITRC Yun Li QTL analysis based on imputed dosagesposterior_probabilities. 2013-9-06 V113 2013-3-16 V112 mach2qtl Free For Non-Commercial Use Only, Domain Independent, Imaging Genomics, Genetic Association http://www.nitrc.org/projects/mach2qtl/ yunli@med.unc.edu Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported,Attribution Non-Commercial Share Alike Yes Roberto Toro, rto@pasteur.fr NITRC OS Independent Roberto Toro The Brain Coactivation Map describes all the coactivation networks in the human brain based on the meta-analysis of more than 5400 neuroimaging articles from NeuroSynth containing more than 16000 individual experiments. It also provides a list of the MeSH tags that more closely match the structure of each network. You can use our viewer CoactivationMap httpsgithub.comr03ert0CoactivationMap.app to interactively browse the map or our command line cmtool httpsgithub.comr03ert0cmtool to query the map from a shell. 2013-11-01 cmap13 The Brain Coactivation Map OS Independent, English, Attribution Non-Commercial Share Alike, Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, MR http://www.nitrc.org/projects/cmap/ rto@pasteur.fr Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Anthony Kolasny, akolasny@jhu.edu NITRC Anthony Kolasny An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class as well where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class. This contribution is part of a shape analysis software pipeline created at Johns Hopkins. PCA will be used to develop a set of basis vectors for use with Gaussian Random Field analysis. The output of PCA will be analyzed for significance with various statistical methods such as t-tests built upon the built-in statistical capabilities of ITK. Principal Components Analysis of Scalar Vector and Mesh Vertex Data Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, Domain Independent http://www.nitrc.org/projects/pca-scalar-mesh/ akolasny@jhu.edu Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Anthony Kolasny, akolasny@jhu.edu NITRC Anthony Kolasny ITK-based processing and 3D Slicer scene management in ParaView. We believe this will broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView. KWScene MRML-based Atlas and Scene BuilderReaderWriter Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, Domain Independent http://www.nitrc.org/projects/mrml-paraview/ akolasny@jhu.edu Yes Li Shen, shenli@iu.edu NITRC Li Shen The database of Genotypes and Phenotypes dbGaP was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. dbGaP Data, Imaging Genomics, SNPs amp;amp; Genes http://www.nitrc.org/projects/dbgap/ shenli@iu.edu GNU General Public License GPL Yes Brent Foster, bfoster790@gmail.com NITRC MATLAB Brent Foster Presented here is a MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. The segmentation algorithm was presented at the 2013 IEEE International Symposium on Biomedical Imaging and IEEE Transactions on Biomedical Engineering In Press. The MATLAB GUI imports a PET image and allows the user to draw region of interests ROIs in 2D or 3D to roughly separate the object of interest from the background. Then the areas are segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax SUVmean and Volume mm^3 and can be exported into an excel sheet. We believe that there is meaningful information in the secondary groups not just the highest uptake group which is the current standard. Renderings with the functional information overlaid can also be made for visualization. 2013-11-26 V1.0.0 NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering GNU General Public License GPL, Quantification, Segmentation, ANALYZE, MATLAB, PETSPECT http://www.nitrc.org/projects/ap_seg_2013_nih/ bfoster790@gmail.com GNU Lesser General Public License LGPL Yes Nathan Churchill, nchurchill@rotman-baycrest.on.ca NITRC MATLAB Nathan Churchill This algorithm corrects for amp;quot;spikesamp;quot; in fMRI data typically caused by abrupt head motion during scanning. SPIKECOR identifies outliers using Principal Component Analysis PCA in a sliding time-window; it is sensitive to global motion artifact and stable against non-stationary signal changes. Unlike typical amp;quot;scrubbingamp;quot; protocols it is automated and identifies motion outliers using purely statistical criteria - no need to select arbitrary motion thresholds It also replaces outlier volumes with interpolated values using cubic splines which minimizes discontinuities in the data. 2014-4-10 4 - Beta SPIKECOR_2014_04_10 2013-11-30 4 - Beta SPIKECOR_2013_11_29 SPIKECOR fMRI tool for automated correction of head motion spikes 4 - Beta, GNU Lesser General Public License LGPL, English, NIfTI-1, ANALYZE, MATLAB, MR http://www.nitrc.org/projects/spikecor_fmri/ nchurchill@rotman-baycrest.on.ca Commercial License Yes Rainer Goebel, rainergoebel@mac.com NITRC Linux,MacOS,Microsoft C,C Rainer Goebel Turbo-BrainVoyager TBV is a highly optimized easy to use software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. Turbo-BrainVoyager allows to observe the working brain amp;quot;onlineamp;quot; by incrementally computing statistical maps as contrasts of a General Linear Model GLM. The program also performs real-time pre-processing including 3D motion correction spatial Gaussian smoothing and temporal filtering drift removal. 2016-1-22 5 - ProductionStableMature Turbo-BrainVoyager 3.0 2016-1-22 5 - ProductionStableMature Turbo-BrainVoyager 3.2 Turbo-BrainVoyager End Users, Developers, 5 - ProductionStableMature, C, C, Linux, Microsoft, MacOS, English, Application, DICOM, Commercial License, MR http://www.nitrc.org/projects/tbv/ rainergoebel@mac.com BIC-MNI Louis Collins Yes Vladimir Fonov, vladimir.fonov@gmail.com NITRC Vladimir Fonov Library of anatomical priors for BEaST httpwww.bic.mni.mcgill.caServicesSoftwareAdvancedImageProcessingToolsBEaST BEaST segmentation library MR, BIC-MNI Louis Collins http://www.nitrc.org/projects/beast-library/ vladimir.fonov@gmail.com GNU General Public License GPL Yes Vladimir Fonov, vladimir.fonov@gmail.com NITRC Vladimir Fonov Sample data in MINC format and collection of scripts to verify correct installation of minc-toolkit. minc-toolkit-testsuite GNU General Public License GPL, MR http://www.nitrc.org/projects/minctoolkittest/ vladimir.fonov@gmail.com GNU General Public License GPL Yes Vladimir Fonov, vladimir.fonov@gmail.com NITRC Linux,MacOS Yes C,Perl,C Vladimir Fonov Whole set of MINC-based image processing tools packaged together. Includes MINCN3BICPLEBKTSANIMALINSECTBEaSTRegisterDisplayxdisp 2015-7-15 1.0.07 2013-12-12 1.0.01 minc-toolkit GNU General Public License GPL, C, C, Perl, Linux, MacOS, Algorithm or Reusable Library, MINC, MINC2, MR http://www.nitrc.org/projects/minc-toolkit/ vladimir.fonov@gmail.com Attribution Non-Commercial Share Alike Yes Craig Stark, cestark@uci.edu NITRC Craig Stark NOTE -Some but not all of the data are are live. More will be added as time and disk space allow. Behavioral and imaging data from ~120 participants aged 18-89. Data were collected as part of a grant to use high-resolution imaging and advanced behavioral tasks to understand how aging affects the hippocampus and how this is related to age-related cognitive decline. The full dataset includes - Traditional neuropsycholgical measures - Hippocampal-specific behavioral measures - Whole-brain DTI - High-resolution DTI of the medial temporal lobes - Structural MRI including segmentation of greywhiteCSF of cortical regions Freesurfer and of hippocampal subfields 2013-12-16 Whole-brain DTI data 2013-12-02 Structural - DTI Session MPRAGE and GWCSF segmentation 2013-12-02 Behavioral and Demographics Data - Initial release Stark Cross-Sectional Aging Data, Attribution Non-Commercial Share Alike, MR, Domain Independent http://www.nitrc.org/projects/stark_aging/ cestark@uci.edu BSD License Yes Jong-Hwan Lee, jhlee.jonghwanlee@gmail.com NITRC MATLAB Jong-Hwan Lee Iterative Dual-Regression with Sparse Prior IDRwSP is aimed to better estimate an individuals neuronal activation using the results of an independent component analysis ICA method applied to a temporally concatenated group of functional magnetic resonance imaging fMRI data i.e. Tc-GICA method. An ordinary DR approach estimates the spatial patterns SPs of neuronal activation and corresponding time courses TCs specific to each individuals fMRI data with two steps involving least-squares LS solutions. The proposed approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs i.e. minimally overlapping SPs based on L1-norm minimization. See the reference paper. Kim YH Kim J Lee JH. Iterative approach of dual regression with a sparse prior enhances the performance of independent component analysis for group functional magnetic resonance imaging fMRI data. Neuroimage. 2012. 2013-12-25 4 - Beta v20131226 Iterative dual-regression with sparse prior 4 - Beta, BSD License, Application, NIfTI-1, MATLAB, MR http://www.nitrc.org/projects/iterdrwsp/ jhlee.jonghwanlee@gmail.com GNU General Public License GPL Yes Awais Mansoor, awais.mansoor@gmail.com NITRC Windows Yes C Awais Mansoor Open-source software for automatic segmentation of lung in CT images. The software is an segmentation tool for the segmentation of lung from CT images. The sofware can be run in two modes a fully automatic and b semi-automatic with manual seeding by the user. The software also allows the user perform basic filtering operations and manual correction to the segmentation if needed. The VTK-based rendering implemntation along with option to view in axial coronal and saggital provide user with better visualization of the segmented lung. A short video on the working of the software can be viewed here httpwww.youtube.comwatchv=VD3GQ0O7weE The algorithm driving the software has been tested on a publically available database LOLA Challenge 11 httpwww.lola11.com. The results based on the overlap score can viewed on the challenge website. 2014-6-19 v1.2.0-win32 2014-6-19 v1.2.0-win64 2013-12-26 v1.0.2-linux 2013-12-26 v1.0.2-win64 2013-11-27 v1.0.1-win32 2013-11-27 v1.0.1-win64 NIH-CIDI Lung Segmentation Tool GNU General Public License GPL, C, Windows, Win32 MS Windows, English, Segmentation, Volumetric Analysis, ANALYZE, CT http://www.nitrc.org/projects/nihlungseg/ awais.mansoor@gmail.com Non-Commercial Software License Agreement Yes Hesamoddin Salehian, h.salehyan@gmail.com NITRC OS Independent MATLAB Hesamoddin Salehian Intrinsic Unscented Kalman Filter IUKF is a recently introduced tractography algorithm for HARDI. IUKF provides a relatively accurate and efficient fiber tracking mechanism compared to most existing tractography methods. Following are the key features of IUKF • Given HARDI data sets it is capable of tracking in the presence of complex local geometries such as crossing and kissing fibers. • Unlike many existing techniques IUKF does not require one to reconstruct the multi-tensor field a priori because reconstruction is only performed at the voxels along estimated fibers. This significantly increases the tracking speed. • IUKF reconstructs a bi-tensor model for underlying signal and exploits intrinsic operations on the space of diffusion tensors symmetric positive definite matrices. This will provide more accurate and smooth estimates of the underlying signal and the fiber orientations compared to its non-intrinsic counterparts. 2014-6-30 IUKF Tractography v1.1 2014-1-02 IUKF Tractography v1.0 Intrinsic Unscented Kalman Filter IUKF Tractography Software v1.0 OS Independent, MATLAB, Non-Commercial Software License Agreement, MR http://www.nitrc.org/projects/iukf_2013/ h.salehyan@gmail.com GPL-Style Open Source Yes Jonathan Lisinski, jlisinski@vtc.vt.edu NITRC POSIXUNIX-like Yes C Jonathan Lisinski 3dsvm is a command-line program and plugin for AFNI httpwww.nitrc.orgprojectsafni built around SVM-Light httpsvmlight.joachims.org. It performs support vector machine SVM analysis on fMRI data and runs on UnixX11Motif systems including SGI Solaris Linux and Mac OS X. 3dsvm C, POSIXUNIX-like, English, NIfTI-1, AFNI BRIK, GPL-Style Open Source, MR http://www.nitrc.org/projects/afni_3dsvm/ jlisinski@vtc.vt.edu 3D Slicer License Yes Xiafoeng Liu, xiaofeng.liu@ge.com NITRC Xiafoeng Liu MABMIS is a module for Slicer 4 that implements a multi-atlas based multi-image method for group-wise segmentation. H. Jia P-T Yap D. Shen amp;quot;Iterative multi-atlas-based multi-image segmentation with tree-based registrationamp;quot; NeuroImage 59422-430 2012. The method utilizes a novel tree-based groupwise registration method for concurrent alignment of both the atlases and the target images and an iterative groupwise segmentation method for simultaneous consideration of segmentation information propagated from all available images including the atlases and other newly segmented target images. MABMIS contains a training step and a testing step. In the training step a groupwise registration is performed to generate a tree structure for the atlases. In the testing step a group of target images are simultaneously and iteratived segmented using the pre-constructed atlas tree. Prior to applying MABMIS the atlas images and target images need be skullstripped and linearly transformed to a common space. 2014-1-08 MABMIS manual 2014-1-08 Test Data 2014-1-08 Macosx_x64_precompiled 2014-1-08 Linux_x64_precompiled 2014-1-08 Windows_x64_vs9_precompiled MABMIS for Slicer 4 Multi-Atlas Based Multi-Image Segmentation 3D Slicer License, MR http://www.nitrc.org/projects/mabmis_slicer4/ xiaofeng.liu@ge.com Attribution Yes Kendrick Kay, kendrick@post.harvard.edu NITRC OS Independent Yes MATLAB Kendrick Kay GLMdenoise is a MATLAB toolbox for denoising task-based fMRI data. The basic idea is to derive noise regressors from voxels unrelated to the experimental paradigm and to use these regressors in a general linear model GLM analysis of the data. The technique is fast and automated and general it requires only a design matrix indicating the experimental design and an fMRI dataset. In the published paper Kay et al. Frontiers in Neuroscience 2013 it is shown that GLMdenoise outperforms other popular denoising methods such as using motion parameters as noise regressors ICA-based denoising and RETROICORRVHRCOR. GLMdenoise a fast automated technique for denoising task-based fMRI data End Users, Developers, 5 - ProductionStableMature, OS Independent, English, Algorithm or Reusable Library, MATLAB, Attribution, MR http://www.nitrc.org/projects/glmdenoise/ kendrick@post.harvard.edu Free For Non-Commercial Use Only Yes Pew-Thian Yap, mind.unc@gmail.com NITRC Linux,MacOS,Windows C Pew-Thian Yap Displacement field viewer or DFViewer is a simple tool for visualizing displacement fields estimated in association with image registration. Based on the displacement vector field a mesh is generated for visualization. The mesh can be color mapped with the jacobian determinant at each point for better localization of regions that undergo compression or expansion. Key features 1 Jacobian determinant color mapping. 2 View synchronization. 3 SaveLoad view configurations. 4 Conversion from deformation fields. 5 Conversion from HAMMER displacement fields. 6 Drag-and-drop mechanism for opening file. 7 Adjustable mesh resolution. 8 Option to save mesh in VTK format. 9 Option to view mesh in different image planes. 10 Glyph arrow view. 11 Accepts multiple image formats including NIfTI .nii.gz or .nii NRRD .nrrd or .nhdr and MetaImage .mha or .mhd. 2014-1-13 Sample Data 2014-1-13 DFViewer 1.1.0 2013-12-20 DFViewer 1.0.0 Displacement Field Viewer End Users, C, Linux, Windows, MacOS, English, Visualization, NIfTI-1, Other Format, Nrrd, Free For Non-Commercial Use Only, Computational Neuroscience http://www.nitrc.org/projects/dfviewer/ mind.unc@gmail.com GNU General Public License GPL Yes Derek Beaton, derekbeaton@utdallas.edu NITRC OS Independent R Derek Beaton Exposition is defined as a comprehensive explanation of an idea. In the world of high dimensional data analysis and multivariate analysis one technique stands out because of its versatility and ubiquity The singular value decomposition SVD. With the ExPosition packages for R a comprehensive explanation of your data will be provided with minimal effort. ExPosition Packages End Users, Developers, 5 - ProductionStableMature, GNU General Public License GPL, OS Independent, English, Visualization, Discriminant Analysis, Principal Component Analysis, R, Domain Independent, Imaging Genomics, Other Omics http://www.nitrc.org/projects/exposition/ derekbeaton@utdallas.edu GNU General Public License GPL Yes Peter Andrews, Peter.Andrews@dartmouth.edu NITRC Peter Andrews Multifactor Dimensionality Reduction MDR is a nonparametric and genetic model-free machine learning alternative to logistic regression for detecting and characterizing nonlinear interactions among discrete genetic and environmental attributes. The MDR method combines attribute selection attribute construction and classification with cross-validation and permutation testing to provide a comprehensive and powerful approach to detecting epistasis. MDR has been successfully applied to numerous different diseases and is currently being adapted to genome-wide assoication studies GWAS. MDR Multifactor Dimensionality Reduction GNU General Public License GPL, Imaging Genomics, Genetic Association http://www.nitrc.org/projects/mdr/ Peter.Andrews@dartmouth.edu BIC-MNI Louis Collins Yes Vladimir Fonov, vladimir.fonov@gmail.com NITRC Vladimir Fonov bic-mni-models anatomical brain template library includes models from ICBM 2009 template httpwww.bic.mni.mcgill.caServicesAtlasesICBM152NLin2009 bic-mni-models MR, BIC-MNI Louis Collins http://www.nitrc.org/projects/bic-mni-models/ vladimir.fonov@gmail.com GNU General Public License GPL Yes Kaushik Bhaganagarapu, kaushik@brain.org.au NITRC MATLAB Kaushik Bhaganagarapu SOCK Spatially Organized Component Klassifikator is a software toolbox that can automatically identify many of the artifact components that are often present in independent component analysis ICA of functional MRI fMRI. The method • Does not require temporal information about the fMRI paradigm. • Does not require the user to train the algorithm. • Requires only the EPI images additional acquisition of anatomical images is not required. • Is able to identify a high proportion of artifact-related ICs without removing components that are likely to be of neuronal origin. • Can be applied to resting-state fMRI. • Is automated requiring minimal or no human intervention. The method is described in the following paper Bhaganagarapu K Jackson GD Abbott DF. An automated method for identifying artifact in Independent Component Analysis of resting-state fMRI. Frontiers in Human Neuroscience 73431-16 2013. httpdx.doi.org10.3389fnhum.2013.00343 2015-6-17 SOCK version 1.3 2015-3-03 SOCK version 1.2 2013-7-16 SOCK version 1.0 SOCK End Users, GNU General Public License GPL, Application, MATLAB, MR http://www.nitrc.org/projects/sock/ kaushik@brain.org.au Freeware Yes Jose Antonio Lojo Ramírez, jalojoram@gmail.com NITRC Jose Antonio Lojo Ramírez The Striatal Subregional VOImap is intended to provide accurate data in terms of specific uptake location to make the BP quantitation. Available in .obj format. The VOIs were manually drawn with software Analyze 90 Mayo Clinic in 18F-DOPA brain image after spatial normalization with a 18F-DOPA Template developed by our group available at httpswww.nitrc.orgprojectsspmtemplates. Each striatum was divided into 6 sub-regions ventral caudate anterior dorsal caudate posterior dorsal caudate ventral putamen anterior dorsal putamen and posterior dorsal putamen based on Mawlawi et al. J Cereb Blood Flow Metab.2001;211034–57 and Oh et al. J Nucl Med.2012;53399–406 segmentation. A nonspecific background volume was drawn in the occipital cortex. Terms of use The Striatal Subregional VOImap is intended for free use by the neuroimaging community. However we do ask that you please cite. J.A. Lojo-Ramírez F.J. García-Gómez amp;amp; D. García-Solís. Contact jalojoramgmail.com The Striatal Subregional VOImap Freeware, PETSPECT, Parkinson Disease http://www.nitrc.org/projects/striatalvoimap/ jalojoram@gmail.com GNU General Public License GPL,OtherProprietary License Yes Robert Oostenveld, r.oostenveld@donders.ru.nl NITRC OS Independent Yes MATLAB,C Robert Oostenveld FieldTrip is the Matlab software toolbox for MEG and EEG analysis that is being developed at the Donders Institute for Brain Cognition and Behaviour at the Radboud University Nijmegen the Netherlands together with collaborating institutes. The toolbox includes algorithms for simple and advanced analysis of MEG EEG and invasive electrophysiological 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 End Users, Developers, 5 - ProductionStableMature, GNU General Public License GPL, C, OtherProprietary License, Console Text Based, OS Independent, English, Algorithm or Reusable Library, Visualization, Workflow, Multivariate Analysis, Fourier Time-domain Analysis, Spectral Analysis, Independent Component Analysis, Registration, EEG Modeling, MEG Modeling, NIfTI-1, MINC, MINC2, DICOM, ANALYZE, MATLAB, AFNI BRIK, Other Format, MR, EEGMEGECoG http://www.nitrc.org/projects/fieldtrip/ r.oostenveld@donders.ru.nl Free For Non-Commercial Use Only Yes Pierrick Coupé, pierrick.coupe@gmail.com NITRC OS Independent Yes MATLAB Pierrick Coupé The proposed Matlab package DWIdenoisingPackage contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means local PCA and Oracle DCT methods. Based on image redundancy andor sparsity the proposed filters provide efficient denoising while preserving fine structures. The package is compiled for Linux 64 bits Windows 64 bits and MAC 64bits. The proposed GUI enables the processing of several .nii files in 2-clicks to make easier the processing of large database. 2014-3-25 4 - Beta r01 DTI denoising End Users, 4 - Beta, Other Environment, OS Independent, English, Algorithm or Reusable Library, NIfTI-1, MATLAB, Free For Non-Commercial Use Only, MR http://www.nitrc.org/projects/dti-denoising/ pierrick.coupe@gmail.com Free For Non-Commercial Use Only Yes Pierrick Coupé, pierrick.coupe@gmail.com NITRC OS Independent Yes MATLAB Pierrick Coupé The Matlab package MRIdenoisingPackage contains five denoising filters and a noise estimation method for 3D MRI. The package includes nonlocal means Oracle DCT and locally adaptive NLM methods. Based on image redundancy andor sparsity the proposed filters provide efficient denoising while preserving fine structures. The package is compiled for Linux 64 bits Windows 64 bits and MAC 64bits. The proposed GUI enables the processing of several .nii files in 2-clicks to make easier the processing of large database. 2014-3-25 4 - Beta r01 MRI denoising End Users, 4 - Beta, OS Independent, English, Algorithm or Reusable Library, NIfTI-1, MATLAB, Free For Non-Commercial Use Only, MR http://www.nitrc.org/projects/mri-denoising/ pierrick.coupe@gmail.com Commercial License ASA Software Yes Maarten Van de Velde, mvelde@ant-neuro.com NITRC Microsoft Yes 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 End Users, Microsoft, Artifact Removal, Wavelet Transformation, Fourier Transform, EEG Modeling, MEG Modeling, DICOM, ANALYZE, ASCII, EEGMEGECoG, Commercial License ASA Software, Event Related Potential, EDFBDFGDF, Brain Vision Analyzer Data Exchange Format, EGI, ANT, CTF, M4D, FIF, CNT http://www.nitrc.org/projects/asa/ mvelde@ant-neuro.com GNU General Public License GPL Yes Youngjin Yoo, youngjin.yoo@alumni.ubc.ca NITRC OS Independent C Youngjin Yoo This tool is developed to offer a fast algorithm for computing myelin maps from multiecho T2 relaxation data using parallel computation with multicore CPUs and graphics processing units GPUs. The tool also provides non-local spatial regularization to produce more accurate and reliable myelin maps for noisy T2 relaxation data. The details of the method are given the following papers Yoo Youngjin et al. amp;quot;Fast computation of myelin maps from MRI T2 relaxation data using multicore CPU and graphics card parallelization.amp;quot; Journal of Magnetic Resonance Imaging 2014. Yoo Youngjin and Roger Tam. amp;quot;Non-local spatial regularization of MRI T2 relaxation images for myelin water quantification.amp;quot; In Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013 pp. 614-621. Springer Berlin Heidelberg 2013. The JMRI paper stated that we intented to contribute to Gadgetron but we found that NITRC seems to be a better fit so we have decided to share our code through NITRC. 2016-8-23 5 - ProductionStableMature POSIX style command line interface and 48-echo input data 2014-9-29 5 - ProductionStableMature memory corruption problem in NNLS_CPU.cpp has been fixed. 2014-3-26 5 - ProductionStableMature Initial source code release Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation Developers, 5 - ProductionStableMature, GNU General Public License GPL, C, Curses, Newt, OS Independent, English, Algorithm or Reusable Library, NIfTI-1, MR, Multiple Sclerosis http://www.nitrc.org/projects/nlsrnnls/ youngjin.yoo@alumni.ubc.ca GNU General Public License GPL Yes Awais Mansoor, awais.mansoor@gmail.com NITRC Windows C,Pascal Awais Mansoor A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence QLF images. Please cite our paper Mansoor A.; Patsekin V.; Scherl D.; Robinson J.; Rajwa B. amp;quot;A Statistical Modeling Approach to Computer-Aided Quantification of Dental Biofilmamp;quot; Biomedical and Health Informatics IEEE Journal of URL httpieeexplore.ieee.orgstampstamp.jsptp=amp;amp;arnumber=6758338amp;amp;isnumber=6363502 2014-4-24 BiofilmQuant BiofilmQuant End Users, GNU General Public License GPL, C, Pascal, Windows, Win32 MS Windows, English, Volumetric Analysis, Other Format, Optical Imaging http://www.nitrc.org/projects/biofilmquant/ awais.mansoor@gmail.com GNU General Public License GPL Yes Won Hwa Kim, wonhwa@cs.wisc.edu NITRC MATLAB Won Hwa Kim Wisconsin CTA toolbox is a Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. In particular this tool is useful for multi-resolutional analysis of such cortical thickness signals and detecting group differences. We find that compared to standard analysis this method is much more sensitive in detecting such differences. It is based on the Spectral Graph Wavelet Transform SGWT toolbox httpwiki.epfl.chsgwt and provides plug and play methods for deriving Wavelet Multiscale Descriptor WMD cortical thickness smoothing using SGWT Multivariate General Linear Model MGLM False Discovery Rate FDR and so on. Won Hwa Kim httppages.cs.wisc.edu~wonhwa 2014-4-02 CTA_toolbox_v1.1 Wisconsin Cortical Thickness Analysis CTA Toolbox GNU General Public License GPL, Thickness, MATLAB, Computational Neuroscience http://www.nitrc.org/projects/cta_toolbox/ wonhwa@cs.wisc.edu GNU General Public License GPL Yes Vamsi Ithapu, ithapu@wisc.edu NITRC MATLAB Vamsi Ithapu Matlab implementation for efficient permutation testing httppages.cs.wisc.edu~vamsipt_fast.html. Permutation testing is a non parametric procedure to estimate the distribution of max null statistic. However it computationally very expensive particularly in neuroimaging and biostatistics studies where dimensionality of data is on the order of millions. We proposed an efficient procedure to estimate this max null using matrix completion. A speed up of atleast 50 times is achieved while estimating the max null upto a high degree of accuracy. For complete details please refer to the project website link above. Please cite the following paper upon usage of the tool. C. Hinrichs V. K. Ithapu Q. Sun V. Singh S. C. Johnson Speeding up Permutation Testing in Neuroimaging Neural Information Processing Systems NIPS 2013 2014-4-06 Errors corrected New version 2014-1-16 2014-01-16 Efficient Permutation Testing GNU General Public License GPL, Algorithm or Reusable Library, MATLAB, Domain Independent http://www.nitrc.org/projects/efficient_pt/ ithapu@wisc.edu GNU General Public License GPL Yes Guorong Wu, grwu@med.unc.edu NITRC Yes Guorong Wu MARS Multi-Atlas Robust Segmentation provides the automatic solutions for efficent segmentationlabeling anatomcial structures from medical images. Specifically this software has integrated several state-of-the-art multi-atlas based segmentation methods such as majority voting local weighted voting and non-local patch based segmentation methods. More importantly we also included our recently-developed joint sparse patch based segmentation method in this software. Compared with convention methods our method has the following advantages 1 add sparsity constraint to suppress the influence of misleading patches; 2 reduce the joint risk of two patches jointly making the same segmentation errors and 3 use iterative framework to correct the possible mis-segmentations. This software package was developed in the IDEA group at UNC-Chapel Hill httpbric.unc.eduideagroup. Wu et. al. amp;quot;A generative probability model of joint label fusion for multi-atlas based brain segmentationamp;quot; MIA 2013. 2014-5-15 MARS_V1.0 users manual corrected 2014-5-15 MARS_V1.0 users manual 2014-5-15 MARS_V1.0_MAC_OS_X_10.9 2014-5-15 MARS_V1.0_LINUX64 2014-5-15 MARS_V1.0_WIN64 2014-5-01 TestData 2014-5-01 MARS_V1.0 MARS Multi-Atlas Robust Segmentation GNU General Public License GPL, MR, CT, Computational Neuroscience http://www.nitrc.org/projects/mars/ grwu@med.unc.edu GNU General Public License GPL Yes Babak Afshin-Pour, bafshinpour@research.baycrest.org NITRC MATLAB Babak Afshin-Pour gCCA is a multivariate method for fMRI data analysis based on generalized canonical correlation analysis gCCA to maximize SPM reproducibility without adopting any model for the hemodynamic response or other temporal brain responses. The underlying assumption is that there are multiple subjects that share an unknown spatial response or spatial map to the common experimental manipulation but may show different temporal responses to external stimulation. For each subject our gCCA explores a broad range of temporal responses in fMRI time-series space while maximizing the mean of correlation coefficients between the pair-wise spatial maps of the subjects. 1 Afshin-Pour B. et. al 2012. Enhancing reproducibility of fMRI statistical maps using generalized canonical correlation analysis in NPAIRS framework. NeuroImage 604 1970-1981. 2 Afshin-Pour et. al 2014. Evaluation of spatio-temporal decomposition techniques for group analysis of fMRI resting state data sets. NeuroImage 87 363-382. 2014-5-14 5 - ProductionStableMature Version 1 gCCA 5 - ProductionStableMature, GNU General Public License GPL, Multivariate Analysis, NIfTI-1, ANALYZE, MATLAB, MR http://www.nitrc.org/projects/gcca/ bafshinpour@research.baycrest.org GNU Lesser General Public License LGPL Yes Erik Kastman, ekk@medicine.wisc.edu NITRC Yes Ruby Erik Kastman Ruby NIfTI is a pure-ruby gem library for handling NIfTI data in the Ruby programming language. Ruby NIfTI currently supports basic read and write access to NIfTI files including basic amp;amp; extended header information and image information. More information on ruby-nifti can be found on the github page; please use the Github Issue Tracker for any questions httpsgithub.combrainmapnifti INSTALLATION ------------ gem install nifti or add this to your Gemfile and `bundle install` gem nifti ~amp;gt;0.0.2 USAGE ------ Read file obj = NIFTINObject.newamp;quot;T1.niiamp;quot; Display some key information about the file puts obj.headersform_code_descr =amp;gt; amp;quot;NIFTI_XFORM_SCANNER_ANATamp;quot; Retrieve the pixel data in a Ruby Array image = obj.get_image Full Documentation is at httprdoc.infogemsniftiframes Ruby NIfTI Developers, GNU Lesser General Public License LGPL, Ruby, NIfTI-1, MR http://www.nitrc.org/projects/ruby-nifti/ ekk@medicine.wisc.edu Artistic License Yes Andrada Ianus, andrada.ianus@gmail.com NITRC Yes MATLAB Andrada Ianus Microstructure Imaging Sequence Simulation Toolbox MISST is a practical diffusion MRI simulator for development testing and optimisation of novel MR pulse sequences for microstructure imaging. MISST is based on a matrix method approach and simulates the signal for a large variety of pulse sequences and tissue models. Its key purpose is to provide a deep understanding of the restricted diffusion MRI signal for a wide range of realistic fully flexible scanner acquisition protocols in practical computational time. 2016-9-15 version 0.93 MISST - Microstructure Imaging Sequence Simulation ToolBox Artistic License, Simulation, MATLAB, MR http://www.nitrc.org/projects/misst/ andrada.ianus@gmail.com Attribution Non-Commercial Yes Yong Liu, yongliu.lab@gmail.com NITRC Yong Liu Brainnetome fMRI toolkit brat refers to the construction and assessment of brain network used to evaluated brain network architecture about fMRI imaging data. These ideas have been instantiated in software that is called Brainnetome fRMI toolkitbrat. The brat package has been designed for the analysis of brain network based on spm httpwww.fil.ion.ucl.ac.ukspm. The images can from different cohorts or time-series from the same subject. The current release is designed for the analysis of fMRI EEG. It includes the proprecessing steps functional connectivity analysis network analysis and network view etc. 2016-4-21 Brant 2015-11-25 brat_beta2.15 2015-6-13 2.0 beta 2014-12-19 brat beta 1.0 2014-5-28 brat beta20120529 Brainnetome fMRI toolkit Attribution Non-Commercial, MR http://www.nitrc.org/projects/brat/ yongliu.lab@gmail.com Artistic License Yes Sung Yu, syu@mprc.umaryland.edu NITRC Linux,MacOS,Windows Yes C Sung Yu BrainVisa Morphologist is collaborative BrainVisa extension library that provides computational tools for performing Object Based Morphology measurements to assess groupwise differences and track morphological changes to study aging development neurological and neurodegenerative disorders and genetic factors that affect them. This library includes source codes and methods for computation of regional GM thickness multi-threaded and single thread 3D gyrification index sulcal lenght and depth and sulcal span and gyral white matter span. These tools are distributed as plugins for a popular analysis package BrainVisa 2016-7-26 5 - ProductionStableMature RIC toolbox for brainvisa-4.5.0 2013-2-06 5 - ProductionStableMature BrainVisa Morphologist 4.1.1 Linux version 2012-2-16 5 - ProductionStableMature Windows Version of Plugins 2012-2-16 5 - ProductionStableMature Linux version of PlugIns 2012-2-16 5 - ProductionStableMature MacOS Version of plugins 2012-2-16 5 - ProductionStableMature Source Code for 411 update and multiple bug fixes 2011-6-24 5 - ProductionStableMature Reprint of a manuscript 2011-6-24 5 - ProductionStableMature Version 4.1 plugins Mac 2011-6-24 5 - ProductionStableMature Version 4.1 plugins Linux 2011-6-24 5 - ProductionStableMature Version 4.1 plugins 2011-6-24 5 - ProductionStableMature Source code for 4.1 version 2011-5-02 5 - ProductionStableMature Version 4.02 plugins Linux x32 2011-5-02 5 - ProductionStableMature Version 4.02 plugins Mac OS10.X 2011-5-02 5 - ProductionStableMature Version 4.02 plugins Windows 2011-5-02 5 - ProductionStableMature Eclipse Workspace with Source Code for 4.02 version 2010-8-25 5 - ProductionStableMature Linux OS 2010 version of Plugin Including Gyral Span 2010-8-25 5 - ProductionStableMature Mac OS 2010 Version of Plugins including Gyral Span 2010-8-25 5 - ProductionStableMature MS Windows 2010 Version including Gyral Span 2010-8-25 5 - ProductionStableMature Eclipse Workspace 2008-9-29 5 - ProductionStableMature brainvisa_ext_3.1_all_plugins_single_package BrainVisa Morphologist extensions End Users, 5 - ProductionStableMature, Artistic License, C, Linux, Windows, MacOS, X11 Applications, English, Shape Analysis, Image Display, Morphology, NIfTI-1, ANALYZE, Other Format, MR http://www.nitrc.org/projects/brainvisa_ext/ syu@mprc.umaryland.edu Attribution Non-Commercial Yes Frederike Beyer, frederike.beyer@neuro.uni-luebeck.de NITRC Frederike Beyer This dataset contains diffusion tensor images of 93 healthy young male subjects. Subject infomration age 18-30 mean age 23 86 right-handed 7 left-handed no psychiatric or neurological diseases DTI-images were recorded on a 3-T Philips Achieva scanner with the following specifications 8-channel head coil 32 gradient directions 70 axial slices slice thickness 2 mm single-shot EPI sequence TR = 7852 ms TE = 60 ms flip angle 90° FOV = 224 mm matrix = 112 x 112 YMDTI Diffusion Tensor Images of Healthy Young Males Data, Attribution Non-Commercial, MR http://www.nitrc.org/projects/ymdti/ frederike.beyer@neuro.uni-luebeck.de Yes Chris Gorgolewski, krzysztof.gorgolewski@gmail.com NITRC Yes Python Chris Gorgolewski NeuroVault makes uploading statistical maps easy and straightforward. In addition it provides permanent links to attractive volumetric and 3D surface based visualisations of your data. NeuroVault End Users, 4 - Beta, Python, Web Environment, English, Database, NIfTI-1, MR, PETSPECT http://www.nitrc.org/projects/neurovault/ krzysztof.gorgolewski@gmail.com GNU GPL v2 Yes Erik Ziegler, erik.ziegler@ulg.ac.be NITRC Linux,MacOS Python Erik Ziegler This project aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation TMS and transcranial direct current stimulation. Human skin skull cerebrospinal fluid and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to startstop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included. Forward Accurate finite element electromagnetic head models 4 - Beta, Python, Linux, MacOS, English, Algorithm or Reusable Library, NIfTI-1, MR, EEGMEGECoG, Domain Independent, GNU GPL v2 http://www.nitrc.org/projects/forward/ erik.ziegler@ulg.ac.be GNU General Public License GPL Yes Anders Eklund, andek034@gmail.com NITRC POSIXUNIX-like,Windows Yes Other Programming Language,C,Unix Shell Anders Eklund Analysis of functional magnetic resonance imaging fMRI data is becoming ever more computationally demanding as temporal and spatial resolutions improve and large publicly available data sets proliferate. Moreover methodological improvements in the neuroimaging pipeline such as non-linear spatial normalization non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches can dramatically increase the computational burden. Here we therefore present BROCCOLI a free software package written in OpenCL Open Computing Language that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI running on a GPU can perform non-linear spatial normalization to a 1 mm brain template in 4–6 s and run a second level permutation test with 10000 permutations in about a minute. The new software is freely available under GNU GPL3 and can be downloaded from github httpsgithub.comwanderineBROCCOLI. BROCCOLI GNU General Public License GPL, C, Unix Shell, POSIXUNIX-like, Other Programming Language, Windows, NIfTI-1, MR http://www.nitrc.org/projects/broccoli/ andek034@gmail.com GNU General Public License GPL Yes Francois Tadel, francois.tadel@gmail.com NITRC OS Independent Yes MATLAB,Java 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 - Pre-processing frequency filtering resampling artifact detection and correction epoching averaging - Visualization of recordings time series 2D3D topographies - MRIEEGMEG co-registration - Powerful database explorer Source estimation - Forward modeling spherical models overlapping spheres BEM - Inverse modeling minimum norm dSPM sLORETA beamformers - Visualization of sources cortex surface MRI volume normalization to atlases Post-processing - Regions of interests at cortical level - Time-frequency analysis Morlet wavelets Hilbert transform FFT PSD - Group analysis Registration of individual brains on a template t-test permutations 2009-9-24 5 - ProductionStableMature Brainstorm3 daily update Brainstorm End Users, Developers, 5 - ProductionStableMature, GNU General Public License GPL, Java, OS Independent, English, Algorithm or Reusable Library, Atlas Application, Database Application, Spatial Transformation, Statistical Operation, Temporal Transformation, Time Domain Analysis, Visualization, Mesh Generation, EEG Modeling, MEG Modeling, NIfTI-1, ANALYZE, MATLAB, MGHMGZ, Other Format, Format Conversion, MR, EEGMEGECoG, Connectivity Analysis http://www.nitrc.org/projects/bst/ francois.tadel@gmail.com GNU Lesser General Public License LGPL Yes Mathias Goldau, math@informatik.uni-leipzig.de NITRC Mathias Goldau OpenWalnut is an open source tool for multi-modal medical and brain data visualization. Its universality allows it to be easily extended and used in a large variety of application cases. It is both a tool for the scientific user and a powerful framework for the visualization researcher. OpenWalnut is licensed under the terms of the GNU Lesser General Public License version 3. Written entirely in Standard C and using a number of portable libraries e.g. Qt Boost and OpenSceneGraph it runs on common GNULinux operating systems Mac OSX and Windows. For more information including system requirements see OpenWalnut. OpenWalnut GNU Lesser General Public License LGPL, MR, EEGMEGECoG, CT, Domain Independent http://www.nitrc.org/projects/openwalnut/ math@informatik.uni-leipzig.de BSD License Yes James Bednar, jbednar@inf.ed.ac.uk NITRC James Bednar Topographica is a software package for computational modeling of neural maps developed as part of the NIMH Human Brain Project under grant 1R01-MH66991. The goal is to help researchers understand brain function at the level of the topographic maps that make up sensory and motor systems. Topographica is intended to complement the many good low-level neuron simulators that are available such as Genesis and Neuron. Those simulators focus on modeling the detailed internal behavior of neurons and small networks of them. Topographica instead focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. Topographica provides a general-purpose framework for building models at this level at an appropriate level of detail and complexity as determined by the available computing power phenomena of interest and amount of biological data available for validation. Topographica BSD License, Computational Neuroscience http://www.nitrc.org/projects/topographica/ jbednar@inf.ed.ac.uk BIRN Data License Yes James MacFall, james.macfall@duke.edu NITRC James MacFall The ELUDE dataset is a longitudinal study of late-life depression at Duke University. There are 281 depressed subjects and 154 controls included. An MR scan of each subject was obtained every 2 years for up to 8 years total of 1093 scans. Clinical assessments occurred more frequently and consists of a battery of psychiatric tests including several depression-specific tests. Efficient Longitudinal Upload of Depression in the Elderly ELUDE BIRN Data License, MR, Clinical Neuroinformatics http://www.nitrc.org/projects/elude/ james.macfall@duke.edu MITX Consortium License Yes julien cohen-adad, jcohen@nmr.mgh.harvard.edu NITRC Linux,MacOS Yes C,Python,shbash julien cohen-adad The Spinal Cord Toolbox is a comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. The toolbox includes a template and several atlases white and gray matter spinal tracts spinal and vertebral levels etc. along with state-of-the-art methods to register any data to the template. It also includes useful scripts for data preprocessing extraction of centerline automatic segmentation slice-wise motion correction etc. Check this out Spinal Cord Toolbox End Users, 5 - ProductionStableMature, C, Python, MITX Consortium License, Linux, MacOS, Console Text Based, English, Atlas Application, Segmentation, Workflow, NIfTI-1, shbash, MR http://www.nitrc.org/projects/sct/ jcohen@nmr.mgh.harvard.edu ADNI License Yes Xiaowei Zhang, zhangxw@lzu.edu.cn NITRC Xiaowei Zhang Researches have shown that Depression and Schizophrenia is a dynamic nonstatic phenomenon. Accordingly it appears to be more important to prevent the worsening of these diseases over time and early assessment and prediction for these diseases can play an important role in achieving early intervention and reducing the incidence of them. In our research we plan to explore the tool and resource about how to predict Depression and Schizophrenia based on Demographics and physiological informationEEG ERPs Genetics MRI fMRI etc.. Ultimately we hope this research can lay the theoretical foundation for the application of prediction for Depression and Schizophrenia. Prediction and Diagnosis for Depression and Schizophrenia ADNI License, MR, EEGMEGECoG, Computational Neuroscience, Clinical Neuroinformatics http://www.nitrc.org/projects/zhangxw/ zhangxw@lzu.edu.cn BSD License Yes Daniel Blezek, blezek.daniel@mayo.edu NITRC OS Independent JavaScript,Java Daniel Blezek Notion PACS =========== Notion is a stand-alone PACShttpen.wikipedia.orgwikiPicture_archiving_and_communication_system designed to be used by radiology researchers for storage and anonymization of research images. Why use Notion If you have a need to - store DICOM images but do not wanthave a dedicated research PACS - anonymize DICOM images - map Names IDs and Accession numbers during anonymization - maintain separation of image data across projects - scale to 100s of independant research projects Why not use Notion If you - already have a research PACS - do not need to anonymize data - do not care about isolation between research projects - are happy using manual anonymization tools 2015-9-14 5 - ProductionStableMature 3.1.0 2015-6-01 5 - ProductionStableMature 3.0 2014-7-03 5 - ProductionStableMature 2.1 2014-1-31 5 - ProductionStableMature 1.0 Notion ResearchPACS End Users, System Administrators, 5 - ProductionStableMature, BSD License, Java, OS Independent, Web Environment, JavaScript, Application, DICOM, MR, PETSPECT, CT, Domain Independent, Clinical Neuroinformatics http://www.nitrc.org/projects/notion/ blezek.daniel@mayo.edu GNU General Public License GPL Yes Awais Mansoor, awais.mansoor@gmail.com NITRC C Awais Mansoor Dicom Converteris based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to Analyze .hdr MetaImage .mhd Nrrd .nhdr .nrrd In addition the application supports drop directory support. Please check for updates and leave feedback at Dr Awais Mansoor awais.mansoorgmail.com and Dr. Ulas Bagci Ulasbagcigmail.com. Center for Infectious Disease Imaging CIDI Department of Radiology and Imaging Sciences National Institutes of Health NIH Bethesda MD. 2014-6-19 v1.0.0-linux 2014-6-19 v1.0.0-win64 DICOMConvert End Users, GNU General Public License GPL, Software, C, English, NIfTI-1, DICOM, ANALYZE, Nrrd, Domain Independent http://www.nitrc.org/projects/dicomconvert/ awais.mansoor@gmail.com BSD License Yes Marius Staring, m.staring@lumc.nl NITRC OS Independent Yes C Marius Staring Welcome to elastix a toolbox for rigid and nonrigid registration of images. elastix is open source software based on the well-known Insight Segmentation and Registration Toolkit ITK. The software consists of a collection of algorithms that are commonly used to solve medical image registration problems. The modular design of elastix allows the user to quickly configure test and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets by means of scripting. The website is found at httpelastix.isi.uu.nl. A paper describing elastix contains more details S. Klein M. Staring K. Murphy M.A. Viergever J.P.W. Pluim amp;quot;elastix a toolbox for intensity based medical image registrationamp;quot; IEEE Transactions on Medical Imaging vol. 29 no. 1 pp. 196 - 205 January 2010. elastix End Users, Developers, Other Audience, 5 - ProductionStableMature, C, BSD License, Console Text Based, OS Independent, English, Algorithm or Reusable Library, Registration, Resampling, NIfTI-1, ANALYZE, Other Format, Nrrd, Philips PARREC, Domain Independent http://www.nitrc.org/projects/elastix/ m.staring@lumc.nl GNU General Public License GPL Yes Xilin Shen, xilin.shen@yale.edu NITRC SunOSSolaris,Windows NT2000,BSD,Linux,MacOS,IRIX Yes C,TclTk Xilin Shen BioImage Suite is a general purpose registrationsegmentationvisualization suite. It also has facilities for DTI and fMRI processing. 2015-10-14 5 - ProductionStableMature 1.0 2013-8-01 5 - ProductionStableMature Functional Brain Atlas from Shen et al Neuroimage 2013 2011-3-18 5 - ProductionStableMature BioImage Suite 3.01 2008-1-30 5 - ProductionStableMature BioImage Suite 2.5 2008-1-16 5 - ProductionStableMature 2.5RC2 2007-10-17 5 - ProductionStableMature 2.5 RC1 2007-9-26 5 - ProductionStableMature Introduction to Programming for Image Analysis with VTK 2007-9-26 5 - ProductionStableMature NonLinear MNI 2 Talairach 1.0 2007-9-26 5 - ProductionStableMature BioImage Suite 2.0 BioImage Suite End Users, Developers, 5 - ProductionStableMature, GNU General Public License GPL, C, TclTk, Linux, BSD, SunOSSolaris, IRIX, Windows NT2000, MacOS, Console Text Based, X11 Applications, Win32 MS Windows, English, Web Resource, Animation, Volume Rendering, Three Dimensional Display, Fiber Tracking, Image-to-Template, Intermodal, Intersubject, Active Contour, Expectation Minimization, Morphology, Volumetric Analysis, NIfTI-1, MINC2, ANALYZE, MR http://www.nitrc.org/projects/bioimagesuite/ xilin.shen@yale.edu Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Andreas Schaefer, schaefer@cbs.mpg.de NITRC Yes Andreas Schaefer Structural brain data is key for the understanding of brain function and brain networks i.e. connectomics. Here we present data sets available from the ‘atlasing of the basal ganglia ATAG’ consortium which provides ultra-high resolution 7Tesla T magnetic resonance imaging MRI scans from young middle-aged and elderly participants. The ATAG data sets include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. Also these atlases can be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinson’s disease and neuropsychiatric diseases. Our results indicate that ATAG data sets allow direct visualization of smallest structures in the subcortex as well as of the brain stem. 2014-10-16 Elderly 62-75 2014-10-16 Middle 40-60 2014-10-16 Young 19-28 2014-7-29 Metadata 7T Structural MRI scans ATAG NIfTI-1, Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, MR http://www.nitrc.org/projects/atag_mri_scans/ schaefer@cbs.mpg.de 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 MR http://www.nitrc.org/projects/miview/ gbook@gbook.org GNU GPL v2 Yes Aaron Carass, aaron_carass+nitrc@jhu.edu NITRC Yes Aaron Carass The Image Synthesis Tools are a collection of software tools developed for medical image synthesis of typically magnetic resonance MR brain images however the approaches have been used to create computed tomography CT images from MR input. The goal of image synthesis is to recover MR images with a desired optimal contrast for further processing by either registration or segmentation. Image synthesis can be thought of as a new image restoration technique that recovers images with both the desired tissue contrast and a normalized intensity profile. 2017-3-31 Image Synthesis of Whole Head Image 2016-12-02 MIMECS v13 2016 Nov 5 2015-11-06 MIMECS v13 2015 Nov 3 2015-10-21 MIMECS v13 2015 Oct 20 2015-8-06 MIMECS v13 2015 Jul 24 2015-1-07 MIMECS v13 2015 Jan 7 2014-10-14 MIMECS v13 2014 Oct 14 Image Synthesis MR, CT, GNU GPL v2 http://www.nitrc.org/projects/image_synthesis/ aaron_carass+nitrc@jhu.edu SBIA License Yes CBICA Software, software@cbica.upenn.edu NITRC CBICA Software Meta-project providing datasets associated with various CBICA projects Mouse Brain Facial ExpressionSchizophrenia Prostate etc. CBICA Datasets SBIA License, MR, Domain Independent, Computational Neuroscience, Clinical Neuroinformatics http://www.nitrc.org/projects/cbica_datasets/ software@cbica.upenn.edu GNU GPL v2 Yes Andreas Berger, andreas.berger.01@gmail.com NITRC POSIXUNIX-like Yes R Andreas Berger This package contains tools for doing group analysis of FreeSurfer httpssurfer.nmr.mgh.harvard.edu surface data using the general linear model in R lm. Results can be rendered in FreeSurfers freeview or AFNIs SUMA. Plots for selected vertices can be rendered in R with ggplot2. 2014-7-21 4 - Beta freesurfR 0.5 freesurfR 4 - Beta, Software, POSIXUNIX-like, MGHMGZ, R, MR, GNU GPL v2 http://www.nitrc.org/projects/freesurf_r/ andreas.berger.01@gmail.com BSD License Yes Jochen Weber, jw2661@columbia.edu NITRC Linux,MacOS,Windows Yes MATLAB Jochen Weber NeuroElf is a Matlab-based toolbox initially created for reading writing and processing of BrainVoyager QX files in Matlab. Some additional routines are available such as the scripting of preprocessing using SPM or second-level statistics. The toolbox is freely available. 2014-6-06 4 - Beta NeuroElf v0.9d - prerelease NeuroElf End Users, Developers, 4 - Beta, BSD License, Linux, Windows, MacOS, English, Other Software Resource, Statistical Operation, Time Domain Analysis, Workflow, NIfTI-1, DICOM, ANALYZE, MATLAB, AFNI BRIK, Other Format, Format Conversion, Philips PARREC, MR http://www.nitrc.org/projects/bvqxtools/ jw2661@columbia.edu Freeware Yes Giorgio Ascoli, ascoli@gmu.edu NITRC Giorgio Ascoli The L-Neuron program creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups and in particular Hillmans Tamori and Burkes. These rules are local and recursive. The L-Neuron algorithms read in experimental data to generate virtual structures. The experimental data are in the form of statistical distributions for example bifurcation angles in Purkinje cells can be represented with a Gaussian distribution with a certain average and standard deviation. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic random fashion during dendritic growth. Therefore with the same set of parameter distributions the program can generate an unlimited number of virtual neurons. L-Neuron End Users, 5 - ProductionStableMature, Win32 MS Windows, Other Environment, Simulation, Freeware, Computational Neuroscience, Neuronal Modeling http://www.nitrc.org/projects/l-neuron/ ascoli@gmu.edu GNU General Public License GPL Yes Jeffrey Krichmar, jkrichma@uci.edu NITRC Jeffrey Krichmar Installation see httpwww.socsci.uci.edu~jkrichmaCARLsimindex.html Supported platforms Linux Windows Dependencies NVIDIA CUDA SDK The code has been predominately developed under Linux and the build instructions reflect that. While the code should function under MS Windows these instructions are not applicable. We will hopefully release instructions in the future on how to setup the code base under Visual Studio on Windows based systems. Detailed installation instructions can be found in the file INSTALL in the code package. CARLsim a GPU-accelerated SNN Simulator GNU General Public License GPL, Computational Neuroscience http://www.nitrc.org/projects/carlsim/ jkrichma@uci.edu GNU General Public License GPL Yes Matthew Nolan, mattnolan@mac.com NITRC Yes Matthew Nolan PSICS is software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes Parallel Stochastic Ion Channel Simulator GNU General Public License GPL, Computational Neuroscience http://www.nitrc.org/projects/psics/ mattnolan@mac.com GNU General Public License GPL Yes Hermann Cuntz, hermann.neuro@gmail.com NITRC Yes Hermann Cuntz 1. Tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. 2. The basic tools to edit visualize and analyze dendritic and axonal trees. 3. Methods for quantitatively comparing branching structures between neurons. 4. Tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance. This software package is written in Matlab Mathworks Natick MA the most widely used scientific programming language. We hope that other groups will benefit from this package and that they will add their own code to the TREES toolbox based on their own specific applications. The code is therefore freely distributed. When publishing scientific work using this toolbox please cite the paper amp;quot;Cuntz H Forstner F Borst A Häusser M 2010. One rule to grow them all A general theory of neuronal branching and its practical application. PLoS Comput Biol 68 e1000877.amp;quot; TREES toolbox GNU General Public License GPL, Computational Neuroscience http://www.nitrc.org/projects/treestoolbox/ hermann.neuro@gmail.com GNU Lesser General Public License LGPL Yes Libsbml Team, libsbml-team@caltech.edu NITRC SunOSSolaris,Windows Vista,Windows NT2000,BSD,Linux,MacOS,AIX,Other UNIX-like,Cygwin,Windows XP Yes MATLAB,Java,C,Python,C,R Libsbml Team LibSBML is a free open-source programming library to help you read write manipulate translate and validate SBML files and data streams. Its not an application itself though it does come with example programs but rather a library you embed in your own applications. libSBML Developers, 5 - ProductionStableMature, GNU Lesser General Public License LGPL, C, C, Python, Java, Linux, BSD, SunOSSolaris, AIX, Other UNIX-like, Windows NT2000, MacOS, English, Algorithm or Reusable Library, MATLAB, Windows Vista, Windows XP, Cygwin, R, Computational Neuroscience http://www.nitrc.org/projects/libsbml/ libsbml-team@caltech.edu Attribution Non-Commercial Share Alike Yes Robert G Smith, rob@retina.anatomy.upenn.edu NITRC Robert G Smith Neuron-C is a simulation language for modeling biophysically realistic neural circuits. Neuron-C Attribution Non-Commercial Share Alike, Computational Neuroscience http://www.nitrc.org/projects/neuron-c/ rob@retina.anatomy.upenn.edu GNU General Public License GPL Yes Kili P, pohl.kilian@gmail.com NITRC POSIXUNIX-like Yes shbash Kili P This is a lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script shbash which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing. While the framework is not very powerful deliberately so it is extremely simple and easy to apply. There is no need to provide any command wrappers. An existing processing script or sequence of shell commands can be turned into a data-driven cluster-safe pipeline by adding just a few extra lines of shell code. 2013-12-03 5 - ProductionStableMature 1.0.1 Lightweight Data Pipeline Developers, 5 - ProductionStableMature, GNU General Public License GPL, POSIXUNIX-like, English, Algorithm or Reusable Library, shbash, Domain Independent http://www.nitrc.org/projects/lwdp/ pohl.kilian@gmail.com BSD License Yes Ted Carnevale, ted.carnevale@yale.edu NITRC OS2,Linux,Other UNIX-like,Windows Yes Ted Carnevale NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building managing and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data especially those that involve cells with complex anatomical and biophysical properties. For a more detailed description see httpwww.neuron.yale.eduneuronwhat_is_neuron NEURON End Users, 5 - ProductionStableMature, BSD License, Linux, Other UNIX-like, Windows, OS2, Computational Neuroscience http://www.nitrc.org/projects/neuron/ ted.carnevale@yale.edu Yes Daniel Margulies, daniel.margulies@gmail.com NITRC Daniel Margulies brainhack.org seeks to provide a forum for collaborative projects in the field of brain science. We invite everyone to submit projects either existing ones that you want to see featured or new ones that you want launch and work on in a collaborative open way. brainhack.org is an effort of the Neuro Bureau neuro-collaboration in action. brainhack2014 Developers, Other, Domain Independent http://www.nitrc.org/projects/brainhack2014/ daniel.margulies@gmail.com BSD License Yes Grigori Yourganov, grigori.yourganov@gmail.com NITRC OS Independent,Linux,MacOS,Microsoft Yes MATLAB Grigori Yourganov NiiStat is a set of Matlab scripts for analyzing neuroimaging data from clinical populations. 2017-1-26 4 - Beta NiiStat v9.oct.2016 2014-11-02 4 - Beta NiiStat 0.9.2 2014-9-26 4 - Beta 0.9.1 NiiStat End Users, 4 - Beta, BSD License, Linux, Microsoft, MacOS, Win32 MS Windows, Other Environment, OS Independent, English, Algorithm or Reusable Library, NIfTI-1, MATLAB, MR, PETSPECT, CT, Aphasia, Apraxias, Stroke http://www.nitrc.org/projects/niistat/ grigori.yourganov@gmail.com GNU General Public License GPL Yes David Boas, dboas@nmr.mgh.harvard.edu NITRC Linux Yes C David Boas 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 3 - Alpha 20030113 SVV End Users, 3 - Alpha, GNU General Public License GPL, C, Linux, X11 Applications, English, Surface Rendering, NIfTI-1, MR, PETSPECT, CT, Attention Deficit Disorder with Hyperactivity, Depression, Holoprosencephaly, Huntington Disease, Obsessive-Compulsive Disorder, Schizophrenia, Cocaine-Related Disorders http://www.nitrc.org/projects/dave1/ dboas@nmr.mgh.harvard.edu GNU General Public License GPL Yes Morten Mørup, morten.morup@gmail.com NITRC Yes Morten Mørup The open source toolbox ERPWAVELAB is developed for multi-channel time- frequency analysis of event related activity of EEG and MEG data. The toolbox provides tools for data analysis and visualization of the most commonly used mea- sures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way tensor factorization. The decomposi- tions provided can accommodate additional dimensions like subjects conditions or repeats and as such they are perfected for group analysis. Furthermore the toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain. ERPwavelab GNU General Public License GPL, Fourier Time-domain Analysis, Temporal Wavelet Analysis, EEGMEGECoG, Event Related Potential http://www.nitrc.org/projects/erpwavelab/ morten.morup@gmail.com Attribution Share Alike Yes Christophe Phillips, c.phillips@ulg.ac.be NITRC Python Christophe Phillips This project contains data and analysis pipelines for a set of 53 subjects in a cross-sectional Parkinsons disease PD study. The dataset contains diffusion-weighted images DWI of 27 PD patients and 26 age sex and education-matched control subjects. The DWIs were acquired with 120 unique gradient directions b=1000 and b=2500 smm2 and isotropic 2.4 mm3 voxels. The acquisition used a twice-refocused spin echo sequence in order to avoid distortions induced by eddy currents. Processing scripts for the paper can be found on Github httpsgithub.comCyclotronResearchCentreparktdi_scripts 2014-9-23 Demographic data 2014-6-18 Motion-corrected diffusion-weighted images 2014-6-18 Normalized TDI Maps High-quality diffusion-weighted imaging of Parkinsons disease Python, English, Data, NIfTI-1, Attribution Share Alike, NiPyPe, MR, Clinical Neuroinformatics, Parkinson Disease http://www.nitrc.org/projects/parktdi/ c.phillips@ulg.ac.be Yes Taylor Hanayik, hanayik@gmail.com NITRC Yes Taylor Hanayik The clinical toolbox is useful for normalizing data from individuals with brain injury andor modalities popular in the clinical environment CT as described by Rorden et al. 2012 PMID 22440645. The latest version supports either enantiomorphic PMID 18023365 or lesion-masked PMID 11467921 normalization. It can be either scripted or used with SPMs simple graphical interface. 2014-10-14 Clinical Toolbox 82014 requires SPM and Matlab Clinical Toolbox for SPM MR, CT http://www.nitrc.org/projects/clinicaltbx/ hanayik@gmail.com Yes Steven Potkin, sgpotkin@uci.edu NITRC Yes Steven Potkin This international symposium was held initially to assess the new technology and innovation in the various established fields of genetics and imaging and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics. Over the past decade the conference has helped to define and document progress in the field and to create a dialogue for the challenges and opportunities it faces. International Imaging Genetics Conference Websites, Community, Imaging Genomics http://www.nitrc.org/projects/iigc/ sgpotkin@uci.edu GNU GPL v2 Yes Shaun Purcell, shaun.purcell@mssm.edu NITRC Shaun Purcell PLINK is a free open-source whole genome association analysis toolset designed to perform a range of basic large-scale genetic analyses. PLINK Imaging Genomics, GNU GPL v2 http://www.nitrc.org/projects/plink/ shaun.purcell@mssm.edu 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 httploni.usc.eduSoftwareAIR at USC. 2010-11-08 5.2 Automated Image Registration AIR GNU General Public License GPL, MR http://www.nitrc.org/projects/air/ iwaterpolo@gmail.com Yes Ayla Khan, ayla@sci.utah.edu NITRC Linux,MacOS,Windows 95982000 Yes C Ayla Khan map3d supports interactive visualization of surface based time signals such as high resolution EEG MEG and ECG. map3d C, Linux, Windows 95982000, MacOS, X11 Applications, Win32 MS Windows, Visualization, Forward - Inverse, Other Format, EEGMEGECoG http://www.nitrc.org/projects/map3d/ ayla@sci.utah.edu Free For Non-Commercial Use Only Yes Christopher Kovach, christopher-kovach@uiowa.edu NITRC OS Independent MATLAB,C Christopher Kovach GazeReader is a toolbox for a point-process derived GLM analysis of eye tracking data in Matlab Mathworks Nattick MA. It was developed with the following goals in mind 1. Flexible yet well ordered integration of the steps involved in linear model specification fitting selection and review. 2. Ease of use and efficiency in specifying and comparing numerous alternate models through both a graphical interface and Matlab scripting. 3. Simple error checking and review of model fitting and procedures. 4. The ability to display model data side by side with raw eye-tracking data along with any appropriate stimulus related background images in order to facilitate interpretation. 5. Efficiency of numerical model fitting. Data loading model specification fitting and review are organized into a sequence of events each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment GUIDE. GazeReader C, OS Independent, MATLAB, Other Format, Eye Tracking, Free For Non-Commercial Use Only, Domain Independent http://www.nitrc.org/projects/gazereader/ christopher-kovach@uiowa.edu BSD License Yes Yangming Ou, ouymcn@gmail.com NITRC Yangming Ou 4D 3Dtime or spatial-temporal consistent deformable registration build on top of 3D pair-wise DRAMMS registration. - to quantify tumor changes in multiple visits; - to quantify voxel-wise neuro-development or structural growth. 4D Spatio-Temporal DRAMMS Registration BSD License, Domain Independent http://www.nitrc.org/projects/dramms4d/ ouymcn@gmail.com NIH Data Access Policy Yes yuai hua, yuaih@email.unc.edu NITRC Yes yuai hua The aim of this tool is to implement a functional analysis pipeline for the joint analysis of longitudinally measured functional data and clinical data for example age gender and disease status. FMPM consists of a functional mixed effects model for characterizing the association of functional response with covariates of interest by incorporating complex spatial–temporal correlation structure an efficient method for spatially smoothing varying coefficient functions an estimation method for estimating the spatial– temporal correlation structure a test procedure with local and global test statistics for testing hypotheses of interest associated with functional response and a simultaneous confidence band for quantifying the uncertainty in the estimated coefficient functions. 2014-10-06 FMPMv1.0 Functional Mixed Processes Models Imaging Genomics, NIH Data Access Policy http://www.nitrc.org/projects/fmpm/ yuaih@email.unc.edu Apache License 2.0 Yes Juan Prieto, jprieto@med.unc.edu NITRC Linux Yes Juan Prieto This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps - Affine Registration with BRAINSFit - Non Linear Registration with GreedyAtlas A final step will apply the transformations to the original DTI images so that the final average can be computed. The main function writes a python script that will be executed to compute the Atlas. By running DTIAtlasBuilder you will need to fill in informations in a Graphical User Interface and then compute the Atlas. You can also run the tool in command line no GUI. Using the GUI you will be able to save or load a dataset file or a parameter file. The tool needs these other tools to work so be sure to have these installed on your computer - ImageMath - ResampleDTIlogEuclidean - CropDTI - dtiprocess - BRAINSFit - GreedyAtlas - dtiaverage - DTI-Reg - unu - MriWatcher requires glut library This package is also available as an extension of 3D Slicer httpwww.slicer.org 2014-3-05 5 - ProductionStableMature DTIAtlasBuilder_v1.3.2_linux64_noQt 2013-6-26 5 - ProductionStableMature DTIAtlasBuilder_v1.3_linux64 2013-5-01 5 - ProductionStableMature DTIAtlasBuilder v1.2 DTI Atlas Builder End Users, 5 - ProductionStableMature, Linux, Console Text Based, X11 Applications, Win32 MS Windows, Application, Apache License 2.0, MR http://www.nitrc.org/projects/dtiatlasbuilder/ jprieto@med.unc.edu Apache License 2.0 Yes Juan Prieto, jprieto@med.unc.edu NITRC Yes Juan Prieto This tool computes an automatic segmentation of neonatal brain MRI. Automatic segmentation of these images is a challenging task mainly due to the low intensity contrast and the non-uniformity of white matter intensities where white matter can be divided into early myelination regions and non-myelinated regions. The degree of myelination is a fractional voxel property that represents regional changes of white matter as a function of age. Our method makes use of a registered probabilistic brain atlas to select training samples and to be used as a spatial prior. Neoseg Apache License 2.0, MR http://www.nitrc.org/projects/neoseg/ jprieto@med.unc.edu GNU General Public License GPL,GNU GPL v2 Yes Feng Xue, xfgavin@gmail.com NITRC Linux shbash Feng Xue A set of BASH scripts for MRI data management FSL automation and web application 2015-2-22 3 - Alpha XFSL PACS scripts 2015-2-16 3 - Alpha Updated xfsl_vbm scripts 2015-2-09 3 - Alpha Link XFSL An FSL toolbox End Users, 3 - Alpha, GNU General Public License GPL, Linux, English, Other Software Resource, shbash, MR, GNU GPL v2 http://www.nitrc.org/projects/xfsl/ xfgavin@gmail.com Apache License 2.0 Yes Juan Prieto, jprieto@med.unc.edu NITRC MacOS,POSIXUNIX-like Yes C Juan Prieto 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 End Users, Developers, 5 - ProductionStableMature, C, POSIXUNIX-like, MacOS, Console Text Based, English, Surface Analysis, Statistical Operation, Spherical Harmonics, Apache License 2.0, MR http://www.nitrc.org/projects/shape_mancova/ jprieto@med.unc.edu Yes Carlos Platero, carlos.platero@upm.es NITRC MATLAB,C Carlos Platero We present a label fusion method based on minimizing an energy function by using graph-cut techniques. We use a conditional random field CRF model that allow us to incorporate shape appearance and context information efficiently. This model is characterized by a pseudo Boolean function defined on unary pairwise and higher order potentials. To evaluate the performance and the robustness of the proposed label fusion method we employ two available database of T1-weighted T1W magnetic resonance MR images of human brains. We compare our approach with other label fusion methods in the hippocampal automatic segmentation from T1W-MR images. 2015-1-17 lf_CRF_v0.0.0_matlab_mexw64 A label fusion using CRF C, MATLAB, MR http://www.nitrc.org/projects/lf_crf/ carlos.platero@upm.es Yes Juan Prieto, jprieto@med.unc.edu NITRC Juan Prieto Connectivity Orientation Spherical distribution Tool COST - This tool implements the method from the paper amp;quot;Efficient Graph-based White Matter Connectivity from Orientation Distribution Functions via Multi-directional Graph Propagationamp;quot; Proc. of SPIE 2011; 796279620S1-8. However with it we also seek to modify the method into a minimum cost-based approach and eventually test it on applications. COST MR http://www.nitrc.org/projects/cost_unc/ jprieto@med.unc.edu Attribution Non-Commercial Share Alike Yes Madeline Pool, madeline.pool@mail.mcgill.ca NITRC OS Independent Yes Madeline Pool NeuriteTracer is a set of ImageJ plugins for automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. NeuriteTracer End Users, OS Independent, Attribution Non-Commercial Share Alike, Computational Neuroscience http://www.nitrc.org/projects/neuritetracer/ madeline.pool@mail.mcgill.ca GNU General Public License GPL Yes Juan Prieto, jprieto@med.unc.edu NITRC Yes Juan Prieto 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. 2013-8-28 MriWatcher v2.3 2012-1-25 Mriwatcher 1.1 MacOS 10.7 MriWatcher GNU General Public License GPL, MR http://www.nitrc.org/projects/mriwatcher/ jprieto@med.unc.edu Yes Ioannis Kakadiaris, ioannisk@uh.edu NITRC Ioannis Kakadiaris ORION I is a software designed for automatic 3D morphological reconstruction of neurons. The input of a software is a 3D image stack RAW format representing the neuron or a sequence of 3D image stacks with the provide translation parameters to align the stacks. The output is the 3D morphological reconstruction of the neuron represented in a 3D acyclic graph as the standard SWC format. ORION I Computational Neuroscience http://www.nitrc.org/projects/orion_1/ ioannisk@uh.edu Non-Commercial Software License Agreement Yes Chris Thornton, c.thornton@ncl.ac.uk NITRC Chris Thornton The Virtual Electrode Recording Tool for EXtracellular potentials VERTEX is a Matlab tool for simulating extracellular potential recordings in spiking neural network SNN models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular spatially-organised networks containing thousands or hundreds of thousands of neurons. VERTEX’s interface and model specification options were designed with this particular task in mind. It is therefore less flexible than other neural simulators but the limited scope has allowed us to simplify the user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls. Virtual Electrode Recording Tool for EXtracellular potentials VERTEX Non-Commercial Software License Agreement, Computational Neuroscience http://www.nitrc.org/projects/vertex/ c.thornton@ncl.ac.uk GNU GPL v2 Yes Aaron Carass, aaron_carass+nitrc@jhu.edu NITRC Yes MATLAB Aaron Carass The dissemination of software for the analysis of optical coherence tomography scans of the retina including the macula. 2015-2-15 2.11 2015-1-20 1.2 AURA tools AUtomated Retinal Analysis tools MATLAB, Optical Imaging, Clinical Neuroinformatics, GNU GPL v2 http://www.nitrc.org/projects/aura_tools/ aaron_carass+nitrc@jhu.edu GNU General Public License GPL Yes Younes Zerouali, younes_zerouali@hotmail.com NITRC Yes MATLAB Younes Zerouali Are you interested in estimating the spatial extent of EEGMEG sources Are you interested in localizing oscillatory patterns Are you interested in localizing synchronous cortical sources We introduce here the toolbox BEst – amp;quot;Brain Entropy in space and timeamp;quot; that implements several EEGMEG source localization techniques within the “Maximum Entropy on the Mean MEM” framework. These methods are particularly dedicated to estimate accurately the source of EEGMEG generators together with their spatial extent along the cortical surface. Assessing the spatial extent of the sources might be very important in some application context and notably when localizing spontaneous epileptic discharges. We also proposed two other extensions of the MEM framework within the time frequency domain dedicated to localize oscillatory patterns in specific frequency bands and synchronous sources. Brain Entropy in space and time BEst End Users, 5 - ProductionStableMature, GNU General Public License GPL, English, Algorithm or Reusable Library, EEG Modeling, MEG Modeling, MATLAB, MEG, EEG, EEGMEGECoG, Epilepsy http://www.nitrc.org/projects/best/ younes_zerouali@hotmail.com Yes Arnaud Delorme, arnodelorme@gmail.com NITRC Yes Arnaud Delorme Pbrain is a collection of applications for the analysis of EEG and medical image data. Currently there are two applications eegview and loc3d. loc3d is a 3D image analysis application for localizing identifying and labeling objects in image data which we use primarily for locating electrodes in CT data. eegview is an eeg visualization and analysis application which has facilities for displaying the EEG mapped onto the spatial coordinates output from loc3d. pBrain Surface Rendering, EEGMEGECoG, Event Related Potential http://www.nitrc.org/projects/pbrain/ arnodelorme@gmail.com Freeware Yes pascal vallotton, pascal.vallotton@csiro.au NITRC pascal vallotton Diatrack powerful particle tracking win64 Benchmark object tracking software for 2D and 3D applications such as biological imaging rheology or single molecule imaging. Reliably follow and characterize hundreds of objects simultaneously with a precision that reaches 0.01 pixels depending on data. DiaTrack provides a compelling set of tools to extract quantitative information from image sequences. Diatrack can be downloaded under www.diatrack.orgcontact.html zip file is about 30MB; additional Mathworks libraries are automatically downloaded and installed by Setup. Diatrack particle tracking software Freeware, Domain Independent http://www.nitrc.org/projects/diatrack/ pascal.vallotton@csiro.au Attribution Non-Commercial No Derivatives Yes Lotta Ellingsen, lotta@jhu.edu NITRC Yes Lotta Ellingsen Longitudinal Multiple Sclerosis MS Lesion Imaging Archive provides Training data consisting of longitudinal images from 5 patients and Testing data from 14 patients. Each longitudinal dataset includes T1-w T2-w PD-w and T2-w FLAIR MRI with 3-5 time points acquired on a 3T MR scanner. With the multiple time points this constitutes 82 individual data sets. To minimize the dependency of the results on registration performance and brain extraction all images are already rigidly co-registered to the baseline T1-w image with automatically computed skull stripping masks. Unprocessed data is also included. The Training data also contains manual segmentations of the MS lesions from two different raters for each of the time points provided. The main page regarding the challenge is httpwww.iacl.jhu.eduMSChallenge and the data is available from the Smart Stats Website httpssmart-stats-tools.orgnode26 2017-3-07 Link to Data Site Longitudinal Multiple Sclerosis Lesion Imaging Archive Attribution Non-Commercial No Derivatives, MR, Computational Neuroscience, Clinical Neuroinformatics http://www.nitrc.org/projects/longitudinal_ms/ lotta@jhu.edu Yes Tian Ge, tge1@mgh.harvard.edu NITRC Yes Tian Ge A MATLAB toolbox for fast and flexible high-dimensional heritability analysis using genome-wide single nucleotide polymorphism SNP data from unrelated individuals developed in the article amp;quot;Massively Expedited Genome-wide Heritability Analysis MEGHAamp;quot;. Massively Expedited Genome-wide Heritability Analysis MEGHA Imaging Genomics http://www.nitrc.org/projects/megha2015/ tge1@mgh.harvard.edu Comercial Licence Rogue Research Inc. Yes Roch Comeau, roch@rogue-research.com NITRC Yes Roch Comeau Neuronavigation system for use in human cognitive neuroscience TMS EEG NIRS and for non-human neurosurgical applications. Brainsight Surface Rendering, NIfTI-1, MINC, MINC2, DICOM, Philips PARREC, EEG, NIRSFNIR, Comercial Licence Rogue Research Inc., MR, EEGMEGECoG, Optical Imaging http://www.nitrc.org/projects/brainsight/ roch@rogue-research.com Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Wouter Boekel, weboekel@gmail.com NITRC Wouter Boekel This data-set contains all 3T MRI and behavioural data used in Boekel et al. in press in which we aimed to replicate several structural brain behaviour SBB correlations. The data-set consists of - 36 T1 images acquired on a 3T MRI scanner - 36 DWI images acquired on a 3T MRI scanner - Behavioral data for 2 computerized tasks and 3 questionnaires. The behavioral data occasionally contains only a subset of the 36 subjects due to questionnairescomputer-tasks not having been completed fully or properly. Documents containing behavioural data contain subject numbers e.g. 1244 to match MRI subject numbers e.g. sc1244. The full reference of the article is Boekel W. Wagenmakers E. J. Belay L. Verhagen A.J. Brown S. D. Forstmann B. U. in press A purely confirmatory replication study of structural brain-behavior correlations. Cortex. 2015-1-28 BVECS_FIXED 2014-12-15 MRI files 2014-12-11 behavioral files and readme 3T MRI data set on structural brain-behavior correlations Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, MR http://www.nitrc.org/projects/confrep2014/ weboekel@gmail.com Data License Yes Farshid Sepehrband, fsepehrband@gmail.com NITRC Farshid Sepehrband For information about lo-DWI and the data please visit httpssites.google.comsitelopdwihome lop-DWI Data License, MR http://www.nitrc.org/projects/lop-dwi/ fsepehrband@gmail.com Free For Non-Commercial Use Only,Freeware Yes Insular Cortex, cirongliu@gmail.com NITRC Yes Insular Cortex This is a multi-mode T1w and DTI brain template of monkeys during late infancy based on longitudinal data from 6 months to 16 months which will help spatial normalization voxel-based and tract-based analyses in non-human primates. Lots efforts were made to ensure the quality 1 we manually skull-striped brains for all T1wamp;amp;DTI data 120 brains. The time-consuming procedure guaranteed more accurate brain extraction than automatic methods 3dSkullStrip or BET. 2 We had tested different methods and the best ones were chosen to build the T1w by ANTS and DTI by DTI-TK templates. 3 We also made high quality template-related files including parcellation maps tissue probability maps inferior cingulum mask for TBSS and templates for each time point. Detailed information about monkeys and methods of building templates can be found in LiuC et al. amp;quot;Rhesus monkey brain development during late infancy and the effect of phencyclidine a longitudinal MRI and DTI study.amp;quot; NeuroImage 2015. 2014-12-15 Infant_Monkey_Template_v1_beta_20141216 Infant Macaque MRI And DTI Templates Freeware, Free For Non-Commercial Use Only, MR http://www.nitrc.org/projects/infant_monkey/ cirongliu@gmail.com GSP Open Access Data Use Terms Yes Timothy OKeefe, timothy_okeefe@harvard.edu NITRC Timothy OKeefe Large scale imaging data sets are necessary to address complex questions regarding the relationship between brain and behavior. The Brain Genomics Superstruct Project Open Access Data Release exposes a carefully vetted collection of neuroimaging behavior cognitive and personality data for over 1500 human participants. Each neuroimaging data set includes one high-resolution Magnetic Resonance Imaging MRI acquisition and one or more resting-state functional MRI acquisitions. Each functional acquisition is accompanied by a fully-automated quality assessment and pre-computed brain morphometrics are also provided. Instructions for accessing the GSP Open Access Data may be found at httpneuroinformatics.harvard.edugsp. Brain Genomics Superstruct Project GSP Open Access Data Release MR, Clinical Neuroinformatics, GSP Open Access Data Use Terms http://www.nitrc.org/projects/gspdata/ timothy_okeefe@harvard.edu GNU Affero General Public License v3 Yes Jussi Lindgren, jussi-tapio.lindgren@inria.fr NITRC Linux,Windows Yes MATLAB,C,Python Jussi Lindgren OpenViBE is a software platform dedicated to designing testing and using brain-computer interfaces BCI. The package includes an Acquisition Server application to stream data from various hardware devices and a Designer tool to create and run real-time signal-processing chains assembled with a graphical design language. OpenViBE package includes several BCI demo applications based on e.g. P300 SSVEP Motor Imagery etc which are ready for use. OpenViBE End Users, Developers, 5 - ProductionStableMature, C, Python, Linux, Windows, X11 Applications, Win32 MS Windows, English, Platform or Development Environment, MATLAB, EEGMEGECoG, EDFBDFGDF, GNU Affero General Public License v3 http://www.nitrc.org/projects/openvibe/ jussi-tapio.lindgren@inria.fr Attribution Non-Commercial Share Alike Yes Diego Salas-Gonzalez, diegosortilegio@gmail.com NITRC Diego Salas-Gonzalez The FP-CIT SPECT brain template has been created using a fully automatic procedure involving posterization of the source image to three levels background brain and striatum. We performed a spatial affine registration of these 40 posterized source images to a posterized reference image in the MNI space. The intensity values of the transformed images is normalized linearly assuming that the histogram of the intensity values follows an alpha-stable distribution. Lastly we built the 123IFP-CIT SPECT template by the mean of the transformed and normalized images. More info 1 Salas-Gonzalez et al. Building a FP-CIT SPECT brain template using a posterization approach. Accepted in Neuroinformatics. 2 Salas-Gonzalez et al. Linear intensity normalization of FP-CIT SPECT brain images using the alpha-stable distribution. NeuroImage Volume 65 2013 pp. 449-455. httpdx.doi.org10.1016j.neuroimage.2012.10.005 123I FP-CIT SPECT brain template in MNI space Attribution Non-Commercial Share Alike, PETSPECT http://www.nitrc.org/projects/fp_cit_atlas/ diegosortilegio@gmail.com GNU General Public License GPL Yes Douglas Garrett, garrett@mpib-berlin.mpg.de NITRC OS Independent Yes MATLAB Douglas Garrett VarTbx measures within-voxel time series variability in fMRI data. The VarTbx structure is intended to be similar to a standard SPM first-level analysis. You can then proceed to pass those first-level variability-based images to a level-2 SPM analysis in order to model group effects of interest. However the first-level NIFTI output files could also be used within other statistics programs of your choice e.g. FSL AFNI PLS. VarTbx currently supports modeling block designs with a boxcar model and computes temporal variability using measures such as detrended variance VAR detrended standard deviation SD mean squared successive difference MSSD and SQRTMSSD. We plan to add additional modeling approaches and variability measures in future releases. 2015-1-21 4 - Beta vartbx VarTbx – Variability Toolbox End Users, Developers, 4 - Beta, GNU General Public License GPL, OS Independent, English, Time Domain Analysis, NIfTI-1, MATLAB, MR http://www.nitrc.org/projects/vartbx/ garrett@mpib-berlin.mpg.de DKE License Yes Emilie McKinnon, mckinnon@musc.edu NITRC Windows Vista,Windows XP Yes MATLAB,C Emilie McKinnon Diffusional Kurtosis Estimator DKE is a software tool for post-processing diffusional kurtosis imaging DKI datasets that includes a suite of command-line programs along with a graphical user interface GUI. DKE supports 32- 64-bit Windows and linux. DKE generates a set of kurtosis axial mean radial KFA MKT parametric maps with a given set of diffusion weighted images acquired from a valid DKI protocol. Diffusivity axial mean radial and fractional anisotropy maps using either DKI or diffusion tensor imaging signal models are also calculated in the processing. DKE features include DICOM NIfTI and Bruker format support interactive GUI as well as batch mode command-line processing and rigid-body motion correction. DKE implements the methods described in the following paper Tabesh A Jensen JH Ardekani BA and Helpern JA. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Mag Reson Med. 2011 Mar;653823-36. httpwww.ncbi.nlm.nih.govpubmed21337412 2015-7-23 3 - Alpha Version 1 2015-2-25 3 - Alpha 2.6 2012-12-28 3 - Alpha 2.5.1 Diffusional Kurtosis Estimator 3 - Alpha, C, Win32 MS Windows, English, Quantification, NIfTI-1, DICOM, MATLAB, Windows Vista, Windows XP, Super Tensor, MR, DKE License http://www.nitrc.org/projects/dke/ mckinnon@musc.edu GNU GPL v2 Yes Kenny Vaden, vaden@musc.edu NITRC Kenny Vaden BOLDR is a set of scripts that we have developed and used to perform General Linear Model GLM and Generalized Linear Mixed Model GLMM-based logistic regression analyses with fMRI data in the R-statistics environment. The R-code distributed in the BOLDR toolkit ZIP file can be edited to perform logistic regression analyses similar to ours in which we predicted trial-level correctincorrect word recognition on the basis of BOLD measured just prior to the presentation Vaden et al. 2015. Although the scripts are preliminary at this time we will revise the code along with documentation - in part based on feedback from the users. If you can edit and use these scripts without any problems feel free to tell us too. We anticipate that the code and documentation will develop throughout 2015 so check this page for newer versions. Please note that these scripts are potentially dependent on specific versions of R-packages and the R-statistics software. R-Scripts for Predicting Trial Level Performance MR, GNU GPL v2 http://www.nitrc.org/projects/boldr/ vaden@musc.edu Open Software License 3.0 Yes Simon Warfield, simon.warfield@childrens.harvard.edu NITRC Simon Warfield The CRL has developed a mathematical framework for the generation of an unbiased deformable spatiotemporal atlas of the fetal brain from magnetic resonance imaging MRI of normal fetuses scanned prenatally. Our atlas serves to capture the inter-subject anatomic variability of the fetal brain over the fetal brain growth period and is currently available between 27 weeks gestational age to 35 weeks. The atlas has been constructed following an unbiased minimum distance template estimation approach which utilizes symmetric diffeomorphic deformation and the cross-correlation CC similarity metric integrated with kernel regression in age. Visit httpcrl.med.harvard.eduresearchfetal_brain_atlas for more information. Unbiased Deformable Spatiotemporal Atlas of the Fetal Brain Open Software License 3.0, MR http://www.nitrc.org/projects/crl_fetal_atlas/ simon.warfield@childrens.harvard.edu Freeware Yes Francisco Javier Garcia Gomez, javier191185@gmail.com NITRC Francisco Javier Garcia Gomez The 18F-DOPA and 123I-FP-CIT Ioflupane - DaTSCAN templates are intended for use as templates for SPM automated normalisation. Created for SPM8 but SPM12 compatible. Available in NifTI file format. The updated Templates are symmetrical and adjusted to MNI-space templates from 12 18F-DOPA and 30 controls without evidence of nigrostriatal degeneration 123I-FP-CIT. Authors I. Huertas J.A. Lojo F.J. García-Gómez amp;amp; D. García-Solís. Contact javier191185gmail.com Terms of use These images are intended for free use by the neuroimaging community. However we do ask that you please cite the following reference in any publications which make use of these images previous version García-Gómez FJ García-Solís D Luis-Simón FJ Marín-Oyaga VA Carrillo F Mir P Vázquez-Albertino RJ. Elaboration of the SPM template for the standardization of SPECT images with 123I-Ioflupane. Rev Esp Med Nucl Imagen Mol. 2013 Nov-Dec;326350-6. 18F-DOPA PET and 123I-FP-CIT Ioflupane - DaTSCAN SPECT templates for SPM normalisation. Freeware, PETSPECT, Parkinson Disease http://www.nitrc.org/projects/spmtemplates/ javier191185@gmail.com BSD License Yes Paul Morgan, paul.morgan@nottingham.ac.uk NITRC OS Independent,Linux,MacOS,Windows Yes C Paul Morgan dcm2nii is a popular tool for converting images from the complicated formats used by scanner manufacturers DICOM PARREC to the simple NIfTI format used by many scientific tools. dcm2nii works for all modalities CT MRI PET SPECT and sequence types. Note dcm2nii has traditionally been included with MRIcron downloads. This project describes the next generation version which we refer to as dcm2niix. Future releases will supersede the legacy dcm2nii distributed with MRIcron. 2016-9-21 dcm2nii source code please download MRIcroGL for compiled version dcm2nii C, BSD License, Linux, Windows, MacOS, OS Independent, English, NIfTI-1, DICOM, MR, PETSPECT, CT http://www.nitrc.org/projects/dcm2nii/ paul.morgan@nottingham.ac.uk MriCloud Agreement Yes Susumu Mori, susumu@mri.jhu.edu NITRC OS Independent Yes Susumu Mori MriCloud is a cloud-based platform that provides several advanced features including; 1 Fully automated cloud service for brain parcellation of MPRAGE images based on Multiple-Atlas Likelihood Fusion MALF algorithm Tang et al. PLoS ONE 2013 JHU multi-atlas inventories with 286 defined structures and our Ontology Level Control OLC technology Djamanakova et al. NeuroImage 2014. 2 Fully automated cloud service for DTI tensor calculation and extensive quantitative reports for quality control Li et al. PLoS ONE 2013. MriCloud End Users, OS Independent, Web Environment, English, Atlas Application, Tensor Metric, Segmentation, NIfTI-1, MR, Alzheimer Disease, MriCloud Agreement http://www.nitrc.org/projects/mricloud/ susumu@mri.jhu.edu Yes Nolan Nichols, nolan.nichols@gmail.com NITRC Nolan Nichols Aloha Registration is now open for the 3rd Annual OHBM Hackathon taking place at the Hawaii Convention Center in Hawaii on the beautiful island of Oahu from June 12-14 2015. During this three day event the first two days will focus on collaborative and open neuroscience projects in data analysis and methods development. See brainhack.org for examples of previous projects and to submit your project ideas The third and final day of the event will feature a FREE morning course on “Brain Hacking 101” where participants will be introduced to brain imaging as a data science. The afternoon will feature a session freely available to all OHBM attendees on the hackathon project outcomes. The spirit of the Hackathon will continue into the OHBM Annual Meeting June 14-18 in Honolulu through an on-site collaboration space available throughout the conference. Dates June 12-14 2015 Location Hawaii Convention Center Honolulu HI OHBM 2015 website Project website www.brainhack.org HBM Hackathon End Users, Developers, 5 - ProductionStableMature, English, Websites, Community, MR, EEGMEGECoG, Imaging Genomics, Computational Neuroscience http://www.nitrc.org/projects/ohbm_hack/ nolan.nichols@gmail.com Yes Daniel Rueckert, d.rueckert@imperial.ac.uk NITRC Daniel Rueckert The IXI Dataset is a collection of nearly 600 MR images from normal healthy subjects. The MR image acquisition protocol for each subject includes T1 T2 and PD-weighted images MRA images and diffusion-weighted images 15 directions. The data was collected at three different hospitals in London using 1.5T and 3T scanners. IXI Dataset Data, NIfTI-1, MR http://www.nitrc.org/projects/ixi_dataset/ d.rueckert@imperial.ac.uk Yes Gregory Lee, gregory.lee@cchmc.org NITRC Gregory Lee The CMIND database contains brain imaging data collected on 3T MRI scanners from over 200 normally developing healthy children from birth to 18 years. There is also longitudinal data collected from a sub-group of children ages 0-3 and 7-9 years who returned scans for three consecutive years. The imaging data stored in the C-MIND database are DTI HARDI 3DT1W 3DT2W concurrent ASL-BOLD scans during two language tasks Stories amp;amp; Sentence-Picture Matching Resting State fMRI and Baseline ASL scans. The database also hosts extensive age-appropriate behavioral measures for all the subjects. The data and their behavioral measures can be downloaded from a public database httpscmind.research.cchmc.org. Registration to this website is available and the information can be found in the opening page httpscmind.research.cchmc.orgauthconsent. A tool using python was developed to process the data and templates of various age ranges are available at bitbucket httpsbitbucket.orggrlee77cmind-py. C-MIND Database MR http://www.nitrc.org/projects/cmind_2014/ gregory.lee@cchmc.org GNU General Public License GPL Yes Vamsi Ithapu, ithapu@wisc.edu NITRC Vamsi Ithapu The toolbox provides Matlab codes for learning randomized denoisiging autoencoders rDA based imaging marker for neuroimaing studies. rDA is an ensemble of neural networks based on denoising autoencoders that take imaging data as inputs and produce singlemulti dimensional summary score. Parameters are learned from training data. rDA can be used for any learning task classification regression for designing imaging disease markers. The unbiased and low variance of rDAs outputs are highly relevant for designing efficient clinical trials. Further details about the model are in the following paper please cite it if the codes are used. V. K. Ithapu V. Singh O. Okonkwo S. C. Johnson Randomized denoising autoencoders for smaller and efficient imaging based AD clinical trials Medical Image Computing and Computer Assisted Intervention MICCAI 2014 2015-8-10 rdacodes-version2 2015-3-17 v01 Randomized Denoising Autoencoders for Neuroimaging GNU General Public License GPL, MR, EEGMEGECoG, PETSPECT, Computational Neuroscience http://www.nitrc.org/projects/rdacodes/ ithapu@wisc.edu Data License Yes Natasha Lepore, nlepore@chla.usc.edu NITRC OS Independent Yes MATLAB Natasha Lepore This resource provides simulated DW-MRI brain images and quantitative tools for evaluating the performance of diffusion analysis methods in terms of fiber orientation estimation and false-positive-negative fiber rates which are of fundamental importance to tractography based studies. The data and tools aim to encourage greater understanding of the fiber estimation abilities of existing methods by use of standardized metrics for evaluation and comparison and help development of improved diffusion analysis methods. DW data was generated using a multi-tensor model at SNRs of 9 18 and 36 for sets of 20 30 40 60 90 and 120 gradient directions. For each combination of SNR and gradient direction set 10 realizations of data are provided. All data is simulated with a diffusion-weighting of b=1000 as is common for clinical acquisitions. amp;gt;amp;gt; See amp;quot;Docsamp;quot; for all documentation and citation information. amp;gt;amp;gt; See amp;quot;Downloadsamp;quot; for data and quantitative tools. amp;gt;amp;gt; Published in NeuroImage Vol 109 April 2015. 2013-12-03 Simulated diffusion-weighted brain images Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations Developers, OS Independent, Algorithm or Reusable Library, Data, Tractography, NIfTI-1, MATLAB, Test Data, Data License, MR http://www.nitrc.org/projects/sim_dwi_brain/ nlepore@chla.usc.edu GNU General Public License GPL Yes Chris Veigl, chris.veigl@gmail.com NITRC Chris Veigl Brainbay supports Human-Computer-Interface functions and the NeuroServer Software Framework to transmit live recordings via Internet LAN. BrainBay is a part of the OpenEEG project and provides graphical musical feedback and feedback-games. BrainBay GNU General Public License GPL, EEGMEGECoG http://www.nitrc.org/projects/brainbay/ chris.veigl@gmail.com Commercial License Yes Jarek Foltynski, jfolt@yahoo.com NITRC Jarek Foltynski Visual designer software for Biofeedback BioEra Commercial License, EEGMEGECoG http://www.nitrc.org/projects/bioera/ jfolt@yahoo.com BSD License Yes Martin Rajchl, voxelsurfer@gmail.com NITRC MATLAB,Other Programming Language,C Martin Rajchl Advanced Segmentation Tools ASETS - Fast Continuous Max Flow variants in CUDACMatlab Attention This is a beta version. We appreciate any bug reports and feedback on how to improve usability. For installation and usage please refer to the readme.md. - Fast parallel continuous max flow solvers in 2D3D -- Binary max flow -- Multi-region Potts model Ishikawa model Hierarchical Max Flow -- In two different implementations full flow and pseudo flow solvers - Implemented in multiple languages -- MatlabmexC -- MatlabCUDA - Application examples for medical image segmentation -- Interactive max flow graph cuts -- Regularization of probabilistic label maps as in atlas-based segmentation -- High-performance multi-phase levelsets -- Post-processing of flawed manual segmentations with contrast sensitive regularization -- L1 intensity segmentation - Resources httpwww.advancedsegmentationtools.org Advanced Segmentation Tools ASeTs 4 - Beta, C, BSD License, Other Programming Language, Algorithm or Reusable Library, Atlas Application, Segmentation, MATLAB, Domain Independent http://www.nitrc.org/projects/asets/ voxelsurfer@gmail.com Free For Non-Commercial Use Only Yes Aditya Bade, aditya.bade@unmc.edu NITRC Yes Aditya Bade In vivo MEMRI-based Rat Brain Atlas provides a reference MEMRI data of Wistar rat brain and corresponding 40 structure labels. Using the reference MRI and the atlas data users can perform regional specific MRI parametric and volumetric analysis. In vivo MEMRI-based Rat Brain Atlas Free For Non-Commercial Use Only, MR http://www.nitrc.org/projects/memriratbrains/ aditya.bade@unmc.edu GPL-Style Open Source Yes Erika Nixon, enixon.umm@gmail.com NITRC Linux,Windows Yes MATLAB,R Erika Nixon Bayesian Connectivity analysis software BCA is a pipeline for connectivity matrix analysis. A general user is a researcher who is interested in brain network analysis and has basic knowledge of LinuxUnix R and Matlab. 2015-4-09 BCA Bayesian Connectivity Analysis software BCA Software, Linux, Windows, MATLAB, R, GPL-Style Open Source, MR, Computational Neuroscience, Clinical Neuroinformatics http://www.nitrc.org/projects/bca/ enixon.umm@gmail.com Yes Hester Breman, breman@brainvoyager.com NITRC Yes MATLAB,Java,C Hester Breman The Neuroimaging Informatics Technology Initiative NIfTI and NIfTI Data Format Working Group creator and maintainer of the NIfTI-1 and NIfTI-2 data formats. 2011-11-08 5 - ProductionStableMature Structural 2010-7-19 5 - ProductionStableMature nifticlib-2.0.0 2008-8-06 5 - ProductionStableMature nifticonverter for BrainVoyager QX 2007-9-30 5 - ProductionStableMature 0.20070930.1 2006-4-05 5 - ProductionStableMature niftimatlib-1.0 2006-3-20 5 - ProductionStableMature niftijlib-0.2 NIfTI Developers, 5 - ProductionStableMature, C, Java, English, Algorithm or Reusable Library, Other Information Resource, NIfTI-1, MATLAB, MR, PETSPECT, CT http://www.nitrc.org/projects/nifti/ breman@brainvoyager.com Yes Bob Dewsnap, rdewsnap@techen.com NITRC Bob Dewsnap CWx Optical Imaging System is a real-time data acquisition system used widely for functional NIRS measurements. Data from the CWx Systems is specific to fNIRS and directly compatible with Homer2 fNIRS analysis software. The Current CW6 system offers up to 32 lasers and 32 detectors in any combination for maximum channel count with an adjustable output data sample rate. Typical sample rate is 50Hz for most configurations. The CWx Software includes SDGui used to create compatible source-detector probe geometry files designed by the user. CWx Optical Imaging System Optical Imaging http://www.nitrc.org/projects/techen_cwx/ rdewsnap@techen.com GNU GPL v2 Yes Babak Afshin-Pour, bafshinpour@research.baycrest.org NITRC Babak Afshin-Pour We proposed a fully automatic iterative reclustering framework in which a small number of spatially large heterogeneous networks are initially extracted to maximize spatial reproducibility. Then the large networks of the brain are iteratively subdivided to create spatially reproducible subnetworks until the overall within-network homogeneity does not increase substantially. Here you may download the experimental results generated using the proposed clustering method. The results include a meaningful pattern for spatially hierarchical structure of the brain. Shams et al. amp;quot;Automated Iterative Reclustering Framework for Determining Hierarchical Functional Networks in Resting State fMRIamp;quot;. Human Brain Mapping Accepted. 2014-12-03 31 subjects resting-state results Hierarchical Functional Networks in Resting State fMRI MR, GNU GPL v2 http://www.nitrc.org/projects/iterative_clust/ bafshinpour@research.baycrest.org Apache License 2.0 Yes SUN HYUNG KIM, shykim@email.unc.edu NITRC SUN HYUNG KIM ShapeComplexityIndex tool calculate the local complexity as the difference between the observed distributions of local surface topology to its best-fit basic topology model within a given local kernel. The reference paper was published in httpproceedings.spiedigitallibrary.orgproceeding.aspxarticleid=2211519amp;amp;resultClick=1 ShapeComplexityIndex Apache License 2.0, Computational Neuroscience http://www.nitrc.org/projects/shapecomplexity/ shykim@email.unc.edu MOCA License Yes Yonggang Shi, yonggans@usc.edu NITRC Yes Yonggang Shi MOCA stands for amp;quot;Metric Optimization for Computational Anatomyamp;quot;. It is a collection of software tools for the computational analysis of brain anatomy with MRI data. It includes automated software tools from surface reconstruction to their mapping via metric optimization in the Laplace-Beltrami embedding space. It is general and can be applied to a wide range of anatomical structures including cortical sub-cortical and fiber bundle surfaces. 2015-5-27 MOCA_LINUX 2015-5-27 MOCA_Windows MOCA End Users, Surface Analysis, Shape Analysis, Mesh Generation, MR, Connectivity Analysis, Alzheimer Disease, Depression, Multiple Sclerosis, MOCA License http://www.nitrc.org/projects/moca_2015/ yonggans@usc.edu volBrain is free for non-commercial and non-medical purposes Yes Pierrick Coupé, pierrick.coupe@gmail.com NITRC Pierrick Coupé volBrain is an online MRI brain segmentation system. It is intended to help researchers all over the world to obtain automatically volumetric brain information from their MRI data without the need for any infrastructure in their local sites. volBrain works in a fully automatic manner and is able to provide brain structure volumes without any human interaction. We encourage you to use the system hoping you find it useful. 2015-5-23 volBrainv1 volBrain online MRI segmentation MR, volBrain is free for non-commercial and non-medical purposes http://www.nitrc.org/projects/volbrain/ pierrick.coupe@gmail.com 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 4 - Beta BETA2 Brainscape End Users, 4 - Beta, OS Independent, Web Environment, English, Database, Data, Statistical Operation, Correlation, DICOM, MR http://www.nitrc.org/projects/brainscape/ dmarcus@wustl.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, MR http://www.nitrc.org/projects/brainscope/ dx2103@columbia.edu GNU General Public License GPL Yes Xiaoyun Liang, imagetechliang@gmail.com NITRC Xiaoyun Liang Dual-tree complex wavelet combined with non-local means ASL fMRI denoising is a software toolbox that can denoise MR images especially ASL fMRI images. The software 1 Reads and writes images in analyze format; 2 Pre-processes ASL fMRI images and provides denoised images for further analysis; 3 Achieves variable denoising outcomes by changing certain parameters; 4 Can be employed for denoising other MR images such as diffusion MRIetc. The method is described in the following paper Voxel-wise functional connectomics using arterial spin labeling fMRI the role of denoising. Xiaoyun Liang Alan Connelly Fernando Calamante 2015. Brain connectivity. DOI 10.1089brain.2014.0290. 2016-11-22 dt-cwt-nlm 2015-5-28 dt-cwt-nlm1.0 Dual-tree complex wavelet combined with non-local means for ASL fMRI denoising GNU General Public License GPL, MR http://www.nitrc.org/projects/dt-cwt-nlm/ imagetechliang@gmail.com Yes James Bursley, bursley@fas.harvard.edu NITRC James Bursley This is structural and functional MRI data from 35 healthy volunteers that accompanies Bursley et al. 2015 amp;quot;Awake Offline Processing During Associative Learning.amp;quot; Subjects encoded paired associates and then performed a distractor task before being probed on associate pairs. Pattern analyses suggest that encoded memories were reactivated during the distractor task and performance of the distractor task led to superior recall for the associate pairs compared to a control condition in which no distractor task was performed. Offline Processing MRI Other, MR http://www.nitrc.org/projects/offprocmri/ bursley@fas.harvard.edu GNU General Public License GPL Yes Martin Göttlich, martin.goettlich@neuro.uni-luebeck.de NITRC Linux,Windows Yes MATLAB Martin Göttlich BASCO BetA-Series COrrelation is a software tool with GUI for investigating inter-regional functional connectivity in event-related fMRI data and allows you to assess the modulation of functional connectivity by an experimental condition. This tool is inspired by an approach introduced by Rissman and colleagues 2004. The method is based on a general linear model GLM where the evoked activity in each trial is modeled by a separate covariate. This renders a series of beta-values for each voxel which is related to a given experimental condition. The functional connectivity between brain regions is derived from correlating voxel beta-series. BASCO offers the following analysis approaches i Seed-based functional connectivity analysis. ii ROI-based network analysis. Given a parcellation of the brain the mean beta-series are extracted for each ROI and a network matrix is calculated correlating all ROI beta-series. iii Voxel-based whole brain network analysis. 2015-6-04 4 - Beta BASCO Manual v2.1 2015-6-03 4 - Beta BASCO Tutorial Data v1.0 2015-6-03 4 - Beta BASCO v2.0 BetA-Series COrrelation 4 - Beta, GNU General Public License GPL, Linux, Windows, MATLAB, MR, Connectivity Analysis http://www.nitrc.org/projects/basco/ martin.goettlich@neuro.uni-luebeck.de BSD License Yes Yangming Ou, ouymcn@gmail.com NITRC Yangming Ou The Personalized Congregation of Algorithms for Skull Stripping Optimization PICASSO tool is a general skull stripping for T1-weighted brain MRIs a in multiple imaging sites; b by scanners of various vendors GESiemensPhilips; c by scanners of various magnetic field strengths 1.0T1.5T3T7T; d by various T1-weighted pulse sequences MPRAGE SPGR etc; e with various fields-of-view even containing neck and shoulders; f from subjects of various ages infants pediatrics young adults elderly adults; g from subjects of different health conditions normative dementia tumor-bearing; h with various image resolutions from 1x1x1mm to 1.5x1.5x6mm; and i with various image contrasts high or low SNRs. The PICASSO tool runs in the unix command line. It is compatible with a single linuxmac computer or preferably with high-performance parallel clusters PBS or SGE. Publication pending. PICASSO skull stripping tool BSD License, MR http://www.nitrc.org/projects/picasso/ ouymcn@gmail.com Attribution Yes Heath Pardoe, heath.pardoe@nyumc.org NITRC Heath Pardoe - NIFTI format corpus callosum segmentation data - NIFTI format brain segmentations Both derived from ABIDE database 2015-6-09 Corpus callosum and brain segmentations from ABIDE autism database Corpus callosum and brain segmentations from ABIDE database NIfTI-1, Attribution, MR, Autistic Disorder http://www.nitrc.org/projects/cc_abide/ heath.pardoe@nyumc.org Attribution Non-Commercial Yes Aditya Bade, aditya.bade@unmc.edu NITRC Yes Aditya Bade In vivo MEMRI-based Mouse Brain Atlas provides a reference MEMRI data of NSG mouse brain and corresponding 41 structure labels. Using the reference MRI and the atlas data users can perform regional specific MRI parametric and volumetric analysis. In vivo MEMRI-based Mouse Brain Atlas Attribution Non-Commercial, MR http://www.nitrc.org/projects/memribrainatlas/ aditya.bade@unmc.edu BSD License Yes Jingping Xu, xujingping@mail.bnu.edu.cn NITRC Jingping Xu FC-NIRS is a Functional Connectivity Analysis Tool for near-infrared spectroscopy dataThe package’s functions include preprocessing quality control FC calculation and network analysis. 2015-6-13 FC_NIRS-v1.0Beta20150613 2015-6-13 FC_NIRS.exe 2014-12-28 141229 2014-10-29 141029 2014-10-29 141030 2014-9-25 Beta Functional Connectivity Analysis Tool for near-infrared spectroscopy data BSD License, Optical Imaging http://www.nitrc.org/projects/fcnirs/ xujingping@mail.bnu.edu.cn Creative Commons License Yes Juha Pajula, juha.pajula@iki.fi NITRC Juha Pajula The use of standardizable computing environments offers a promise for enhancing the reproducibility of neuroimaging computational workflows. In this hackathon project we seek to develop a reproducibility assessment framework for testing and validating similar workflows run under different conditions. For a given workflow which can be run on a local computer system as a virtual machine or in a cloud computing environment we want to assess the potential variances introduced in workflow results as a function of the operating environment. This framework can then be extended to assessment of variations due to additional factors such as software versioning workflow parameters and input data. The end result of this project would be a stand alone application that details the reproducibility of workflowresult pair in the context of the various execution variables. This project hopes to leverage the NITRC-CE nipype testkraut and existing shared datashared results. Cloud Reproducibility Challenge Developers, 2 - Pre-Alpha, English, Creative Commons License, MR http://www.nitrc.org/projects/cloudrepro/ juha.pajula@iki.fi Academic Free License amp;quot;AFLamp;quot; Yes Qingtian Zhang, forgettingzqt@gmail.com NITRC Qingtian Zhang FMRI data set for phoneme coding in the auditory cortex with 7 subjects and 9 Chinese CV syllables. 2015-6-11 subject7 2015-6-11 subject6 2015-6-10 subject5 2015-6-10 subject4 2015-6-09 subject3 2015-6-09 subject2 2015-6-09 subject1 Phoneme-Syllable Tsinghua University CSamp;T 2011 Academic Free License amp;quot;AFLamp;quot;, MR http://www.nitrc.org/projects/tsinghua_2011/ forgettingzqt@gmail.com BSD License Yes Scott Vendemia, vendemis@mailbox.sc.edu NITRC Linux,MacOS,Windows Yes Pascal Scott Vendemia 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. MRIcron is a mature and useful tool however you may want to consider the more recent MRIcroGL as an alternative. 2016-10-12 5 - ProductionStableMature MRIcronNPMdcm2nii 2MAY2016 2012-12-27 5 - ProductionStableMature MRIcron 122012 2012-12-27 5 - ProductionStableMature MRIcroGL 122012 for OSX 2012-12-27 5 - ProductionStableMature MRIcroGL 122012 for Windows 2012-12-27 5 - ProductionStableMature MRIcroGL 122012 for Linux 64 bit 2012-12-27 5 - ProductionStableMature MRIcroGL 122012 for Linux 32 bit 2012-12-27 5 - ProductionStableMature MRIcroGL 122012 source code 2012-7-20 5 - ProductionStableMature MRIcron 72012 2012-7-20 5 - ProductionStableMature MRIcroGL 62012 2011-11-26 5 - ProductionStableMature MRIcronNPMdcm2nii 111111 for OSX 10.4 or later 2011-11-26 5 - ProductionStableMature Missingness in Neuroimaging Data MIND ALPHA 2011-11-26 5 - ProductionStableMature MRIcroGL 111111 source 2011-11-26 5 - ProductionStableMature MRIcroGL 111111 Windows 2011-11-26 5 - ProductionStableMature MRIcroGL 111111 Linux GTK2 x86 64-bit 2011-11-26 5 - ProductionStableMature MRIcroGL 111111 Linux GTK2 x86 32-bit 2011-11-26 5 - ProductionStableMature MRIcroGL 111111 OSX 10.4 Intel 2011-4-12 5 - ProductionStableMature MRIcroGL 42011 Windows 2011-4-12 5 - ProductionStableMature MRIcroGL 42011 Linux 32-bit GTK2 2011-4-12 5 - ProductionStableMature MRIcroGL 42011 Linux 64-bit GTK2 2011-4-12 5 - ProductionStableMature MRIcroGL 42011 Macintosh OSX Intel 10.4 2011-4-12 5 - ProductionStableMature MRIcroGL 42011 Source 2011-4-07 5 - ProductionStableMature MRIcron 42011 Windows 2011-4-07 5 - ProductionStableMature MRIcron 42011 Linux 32-bit GTK2 2011-4-07 5 - ProductionStableMature MRIcron 42011 Linux 32-bit GTK1 2011-4-07 5 - ProductionStableMature MRIcron 42011 Linux 64-bit GTK2 2011-4-07 5 - ProductionStableMature MRIcron 42011 Linux 64-bit GTK1 2011-4-07 5 - ProductionStableMature MRIcron 42011 Macintosh OSX PPCIntel 10.4 2011-4-07 5 - ProductionStableMature MRIcron 42011 source  2010-11-05 5 - ProductionStableMature MRIcron 112010 Windows 2010-11-05 5 - ProductionStableMature MRIcron 112010 Linux 32-bit GTK2 2010-11-05 5 - ProductionStableMature MRIcron 112010 Linux 32-bit GTK1 2010-11-05 5 - ProductionStableMature MRIcron 112010 Linux x86-64 GTK2 2010-11-05 5 - ProductionStableMature MRIcron 112010 Linux x86-64 GTK1 2010-11-05 5 - ProductionStableMature MRIcron 112010 Macintosh OSX PPCIntel 10.4 2010-11-05 5 - ProductionStableMature MRIcron 112010 Source 2010-7-15 5 - ProductionStableMature MRIcroGL 62010 Windows 2010-7-15 5 - ProductionStableMature MRIcroGL 62010 Linux 32-bit GTK2 2010-7-15 5 - ProductionStableMature MRIcroGL 62010 Linux 64-bit GTK2 2010-7-15 5 - ProductionStableMature MRIcroGL 62010 Macintosh OSX Intel 10.4 2010-7-15 5 - ProductionStableMature MRIcroGL 62010 Source 2010-4-01 5 - ProductionStableMature MRIcroGL 42010 Windows 2010-4-01 5 - ProductionStableMature MRIcroGL 42010 Linux 32-bit GTK2 2010-4-01 5 - ProductionStableMature MRIcroGL 42010 Macintosh OSX Intel 10.4 2010-4-01 5 - ProductionStableMature MRIcron 42010 Source 2010-4-01 5 - ProductionStableMature MRIcron 42010 Windows 2010-4-01 5 - ProductionStableMature MRIcron 42010 Macintosh OSX PPCIntel 10.4 2010-4-01 5 - ProductionStableMature MRIcron 42010 Linux 32-bit GTK2 2010-4-01 5 - ProductionStableMature MRIcron 42010 Linux 32-bit GTK1 2010-4-01 5 - ProductionStableMature MRIcron 42010 Linux 64-bit GTK2 2010-4-01 5 - ProductionStableMature MRIcron 42010 Linux 64-bit GTK1 2010-4-01 5 - ProductionStableMature MRIcroGL 42010 Linux 64-bit GTK2 2010-2-05 5 - ProductionStableMature MRIcron 22010 Source 2010-2-05 5 - ProductionStableMature MRIcron 22010 Windows 2010-2-05 5 - ProductionStableMature MRIcron 22010 Macintosh OSX PPCIntel 2010-2-05 5 - ProductionStableMature MRIcron 22010 Linux 64-bit GTK-2 2010-2-05 5 - ProductionStableMature MRIcron 22010 Linux 64-bit GTK1 2010-2-05 5 - ProductionStableMature MRIcron 22010 Linux 32-bit GTK2 2010-2-05 5 - ProductionStableMature MRIcroGL 22010 Source 2010-2-05 5 - ProductionStableMature MRIcroGL 22010 Windows 2010-2-05 5 - ProductionStableMature MRIcroGL 22010 Macintosh OSX 2010-2-05 5 - ProductionStableMature MRIcroGL 22010 Linux 64-bit GTK2 2010-2-05 5 - ProductionStableMature MRIcron 22010 Linux 64-bit GTK2 2010-2-05 5 - ProductionStableMature MRIcroGL 22010 Linux 32-bit GTK2 2009-12-28 5 - ProductionStableMature MRIcron 122009 Linux 64-bit GTK2 2009-12-28 5 - ProductionStableMature MRIcron 122009 Linux 64-bit GTK1 2009-12-28 5 - ProductionStableMature MRIcron 122009 Linux 32-bit GTK1 2009-12-28 5 - ProductionStableMature MRIcron 122009 Linux 32-bit GTK2 2009-12-28 5 - ProductionStableMature MRIcron 122009 Source 2009-12-28 5 - ProductionStableMature MRIcron 122009 Windows 2009-12-28 5 - ProductionStableMature MRIcron 122009 Mac OSX IntelPPC 2009-12-28 5 - ProductionStableMature MRIcroGL 122009 Linux 32-bit GTK2 2009-12-28 5 - ProductionStableMature MRIcroGL 122009 Linux 64-bit GTK2 no scripting 2009-12-28 5 - ProductionStableMature MRIcroGL 122009 Source 2009-12-28 5 - ProductionStableMature MRIcroGL 122009 Windows 2009-12-28 5 - ProductionStableMature MRIcroGL 122009 Mac OSX Intel 2009-10-22 5 - ProductionStableMature ezDICOM standalone activex and console applications and source 2009-10-16 5 - ProductionStableMature MRIcron September 2009 - source 2009-10-16 5 - ProductionStableMature MRIcron September 2009 - Windows 2009-10-16 5 - ProductionStableMature MRIcron September 2009 - Linux OSX PPCIntel 2009-10-16 5 - ProductionStableMature MRIcron September 2009 - Linux GTK1 32-bit 2009-10-16 5 - ProductionStableMature MRIcron September 2009 - Linux GTK2 32-bit 2009-10-16 5 - ProductionStableMature MRIcron September 2009 - Linux GTK1 64-bit 2009-10-16 5 - ProductionStableMature MRIcron September 2009 - Linux GTK2 64-bit 2009-10-14 5 - ProductionStableMature MRIcroGL 92009 Source 2009-10-14 5 - ProductionStableMature MRIcroGL 92009 Linux x86-32bit GTK2 2009-10-14 5 - ProductionStableMature MRIcroGL 92009 Wiindows 2009-10-14 5 - ProductionStableMature MRIcroGL 92009 Mac OSX 2009-9-02 5 - ProductionStableMature MRIcroGL 92009 Linux GTK2-64bit no scripting 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - Linux QT 32-bit 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - Linux GTK2 64-bit 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - Linux GTK1 64-bit 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - Linux GTK2 32-bit 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - Linux GTK1 32-bit 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - Source 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - OSX IntelPPC 2009-7-08 5 - ProductionStableMature MRIcron July 2009 - Windows 2009-6-15 5 - ProductionStableMature MRIcroGL IPodVideo beta 2009-6-15 5 - ProductionStableMature MRIcroGL 62009 Linux GTK2 2009-6-15 5 - ProductionStableMature MRIcroGL 62009 source 2009-6-15 5 - ProductionStableMature MRIcroGL 62009 Mac OSX 2009-6-15 5 - ProductionStableMature MRIcroGL 62009 Windows 2009-6-03 5 - ProductionStableMature MRIcroGL 52009 source 2009-6-03 5 - ProductionStableMature MRIcroGL 52009 Linux GTK2 2009-6-03 5 - ProductionStableMature MRIcroGL 52009 Mac OSX 2009-6-03 5 - ProductionStableMature MRIcroGL 52009 Windows 2008-11-06 5 - ProductionStableMature MRIcroGL 2008-9-26 5 - ProductionStableMature mricro 1.4 for Windows 2008-9-08 5 - ProductionStableMature mricrogl MRIcron End Users, 5 - ProductionStableMature, Pascal, BSD License, Linux, Windows, MacOS, Console Text Based, Win32 MS Windows, Gnome, KDE, Other Environment, English, Clipping, Volume Rendering, Two Dimensional Display, Regression, Center of Mass, NIfTI-1, DICOM, ANALYZE, MR http://www.nitrc.org/projects/mricron/ vendemis@mailbox.sc.edu Attribution Non-Commercial Share Alike Yes Yung-Chin Hsu, eric.ychsu@gmail.com NITRC OS Independent Yes Yung-Chin Hsu NTU-DSI-122 is a diffusion spectrum imaging DSI template constructed in the standard ICBM-152 space from 122 healthy adults. This template was built through incorporating the macroscopic anatomical information using high-resolution T1-weighted images and the microscopic structural information obtained from DSI datasets rendering it to achieve a high anatomical matching to the ICBM-152 space. Therefore this template can serve as a representative DSI dataset for a healthy adult population and will be of potential value for brain research and clinical applications. This template is released in the original DWI format so the users have the most freedom to perform their own advanced processing algorithms on NTU-DSI-122. NTU-DSI-122 is distributed under the terms of CC BY-NC-SA 4.0. Reference Hsu Y-C Lo Y-C Chen Y-J Wedeen VJ Tseng W-YI 2015 NTU-DSI-122 A diffusion spectrum imaging template with high anatomical matching to the ICBM-152 space. Hum Brain Mapp doi 10.1002hbm.22860. 2015-6-16 5 - ProductionStableMature NTU-DSI-122 NTU-DSI-122 A Diffusion Spectrum Imaging Template with High Anatomical Matching to the ICBM-152 Space End Users, 5 - ProductionStableMature, OS Independent, Data, NIfTI-1, Attribution Non-Commercial Share Alike, Diffusion Spectrum, Atlas Data, MR http://www.nitrc.org/projects/ntu-dsi-122/ eric.ychsu@gmail.com BSD License Yes Shekhar Chandra, shekhar.chandra@uq.edu.au NITRC Linux,MacOS,Windows Yes C,Python Shekhar Chandra The Simple Medical Imaging Library Interface SMILI pronounced smilie is an open-source light-weight and easy-to-use medical imaging viewer and library for all major operating systems. The main sMILX application features for viewing n-D images vector images DICOMs anonymizing shape analysis and modelssurfaces with easy drag and drop functions. It also features a number of standard processing algorithms for smoothing thresholding masking etc. images and models both with graphical user interfaces andor via the command-line. See our YouTube channel for tutorial videos via the homepage. The applications are all built out of a uniform user-interface framework that provides a very high level Qt interface to powerful image processing and scientific visualisation algorithms from the Insight Toolkit ITK and Visualisation Toolkit VTK. The framework allows one to build stand-alone medical imaging applications quickly and easily while having a multitude of processing and visualisations built-in. 2016-9-14 4 - Beta Version 1.0 Release Candidate 2 2016-3-12 4 - Beta Version 1.0 Release Candidate 2015-11-01 4 - Beta Version 1.0 Beta 2 2015-6-22 4 - Beta Version 1.0 Beta 1 2015-1-29 4 - Beta Version 1.0 Alpha 2014-11-23 4 - Beta Version 0.99 Simple Medical Imaging Library Interface SMILI End Users, Developers, 4 - Beta, C, Python, BSD License, Linux, Windows, MacOS, Platform or Development Environment, Algorithm or Reusable Library, Shape Analysis, Animation, Image Display, Surface Rendering, Volume Rendering, NIfTI-1, DICOM, ANALYZE, Nrrd, Domain Independent http://www.nitrc.org/projects/smili/ shekhar.chandra@uq.edu.au Yes David Grayson, grayson@ohsu.edu NITRC David Grayson Age-specific rhesus monkey brain templates from T1-weighted structural MRI 3T Scanner. Templates created from 24 rhesus macaques using deformable image registration ANTS at 1week 4weeks 8weeks 13weeks 26weeks 39weeks 52weeks 104weeks and 260 weeks of age. Tissue segmentations and lobar parcellations are also provided. Longitudinal Rhesus Monkey Brain Templates NIfTI-1, MR http://www.nitrc.org/projects/ama24/ grayson@ohsu.edu Apache License 2.0 Yes Juan Prieto, jprieto@med.unc.edu NITRC Linux Yes C,Python Juan Prieto This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates an subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then we run a single atlas method with this atlas and obtain some good results especially for in subcortical midbrain structure. A quick demo on how to use the tool can be seen here httpswww.youtube.comwatchv=yTr3NJZaMos NeoSegPipeline End Users, 5 - ProductionStableMature, C, Python, Linux, X11 Applications, Segmentation, Apache License 2.0, MR http://www.nitrc.org/projects/neosegpipeline/ jprieto@med.unc.edu GNU GPL v2 Yes Anderson Winkler, andersonwinkler@gmail.com NITRC Yes Anderson Winkler PALM — Permutation Analysis of Linear Models — is a tool that allows inference using permutation methods offering a number of features not available in other analysis software. For complete details including documentation and User Guide please visit httpfsl.fmrib.ox.ac.ukfslfslwikiPALM PALM - Permutation Analysis of Linear Models Domain Independent, GNU GPL v2 http://www.nitrc.org/projects/palm/ andersonwinkler@gmail.com SchizConnect Yes Jose-Luis Ambite, ambite@isi.edu NITRC Jose-Luis Ambite Large-scale data sharing and integration is needed to further the state-of-the-art schizophrenia research but is presently not possible due to practical limitations in the way in which data are being shared. SchizConnect is a data mediation and integration resource to overcome these limitations in a low-cost manner and deliver a web portal to interact with the federated databases. Access SchizConnect at httpschizconnect.org. SchizConnect Large-Scale Schizophrenia Neuroimaging Data Mediation amp; Federation End Users, Web Environment, Database, Other Data Resource, Websites, Data, Database Application, MR, Clinical Neuroinformatics, Bipolar Disorder, Schizophrenia, SchizConnect http://www.nitrc.org/projects/schizconnect/ ambite@isi.edu Creative Commons License Yes David Kennedy, dave@dnkc.net NITRC OS Independent David Kennedy The Monthly Morphometry Report MMR is designed to be a quick high-level synopsis of the volumetric literature compiled on a monthly basis. We seek to represent the corpus of published findings in a suscinct and common format to ease human interpretation of ths vast set of measures that are being reported. To start monthly PUBMED reports of potential volumetric publications in humans are identified and human curators then summarise these abstracts into a standard report format. In the future we hope to add automation to the curation process and index more complete full-text content. This project is HIGHLY alpha in its design and should be considered only a work in progress. Enter at your own risk or volunteer to help Monthly Morphometry Report End Users, Developers, 3 - Alpha, OS Independent, Web Environment, English, Web Resource, Knowledge Environment, Creative Commons License, MR, Clinical Neuroinformatics http://www.nitrc.org/projects/mmr/ dave@dnkc.net GNU General Public License GPL Yes Tawfik Moher Alsady, tofeeq.ms@gmail.com NITRC Linux,MacOS Yes TclTk,Python Tawfik Moher Alsady mICA Toolbox is a user-friendly toolbox to perform masked independent component analysis i.e. ICA within a spatially restricted subregion of the brain. It is based on command line tools from FSL suite to perform the ICA and related analyses e.g. specific data preprocessing atlas-based mask generation mICA-based parcellation dual-regression and direct back reconstruction. Various options provide flexible control of the analysis. mICA Toolbox is a helpful utility for researchers in the field of neuroimaging. It facillitates the study of intrinsic connectivity of brain sub-regions and the reconstruction of their extrinsic connectivity i.e. connectivity with regions outside of the mask. The toolbox furthermore offers an easy way to calculate ICA reproducibility over a range of decomposition dimensions which can be used to overcome the common problem of dimensionality estimation. 2016-11-08 5 - ProductionStableMature V 1.14 2016-7-14 5 - ProductionStableMature V 1.13 2016-3-27 5 - ProductionStableMature V 1.12 2015-12-28 5 - ProductionStableMature V 1.11 2015-12-02 5 - ProductionStableMature V1.10 2015-11-17 5 - ProductionStableMature V1.09 2015-11-12 5 - ProductionStableMature V1.08 2015-7-15 5 - ProductionStableMature V1.05 2015-3-20 5 - ProductionStableMature V1.04 masked ICA mICA Toolbox End Users, 5 - ProductionStableMature, GNU General Public License GPL, Python, TclTk, Linux, MacOS, English, Independent Component Analysis, NIfTI-1, MR, Computational Neuroscience http://www.nitrc.org/projects/mica/ tofeeq.ms@gmail.com 3D Slicer License Yes Antonio Tristán-Vega, atriveg@lpi.tel.uva.es NITRC Yes Antonio Tristán-Vega This tool provides a way to trace fiber tracts based on Riemannian geodesics the local cost function being defined as the adjugate as opposed to the commonly used inverse of the diffusion tensor. The minimization of the cost function is globally not just locally attained via dynamic programming using the amp;quot;Fast sweepingamp;quot; algorithm for the sake of efficiency. 2015-7-16 Source code OSX binaries Tractography based on Riemannian geodesics and tensor adjugates 3D Slicer License, MR, Computational Neuroscience http://www.nitrc.org/projects/riemantract/ atriveg@lpi.tel.uva.es MIT Yes Nima Bigdely-Shamlo, nima.bigdely@syntrogi.com NITRC Yes Nima Bigdely-Shamlo EEG Study Schema ESS makes it easier for researchers in the field of EEGBCI to package share and automatize the analysis workflow of their study data. You can think of ESS as a amp;quot;shipping containeramp;quot; for your EEG study data. Using other people’s EEG data could be painful as often one has to do detective work to find out What happened in the experiment Which files are for which subjectssessions What do these event codes mean To remove ‘EEG data sharing pain we have created a set of standards HED and ESS and tools ESS is designed from a user-centered viewpoint that emphasizes simplicity and ease of use. It is created to contain all the information a researcher unfamiliar with a particular EEG or MEG Study needs to further analyze the data. It is An XML-based specification Holds all the information necessary to analyze an EEG study. Please visit www.eegstudy.org for more information. EEG Study Schema ESS EEGMEGECoG, MIT http://www.nitrc.org/projects/ess/ nima.bigdely@syntrogi.com MIT Yes Nima Bigdely-Shamlo, nima.bigdely@syntrogi.com NITRC Yes Nima Bigdely-Shamlo HED tags are assigned to event codes also known as triggers or event numbers in EEG recordings and allow humans and computers to better understand what these codes represent e.g. code 5 -amp;gt; Target detection in an RSVP paradigm. Why tags In the same way that we tag a picture on Flicker or a video clip on Youtube e.g. cat cute funny we can tag EEG experimental event types used in event-related EEG research. Hierarchical Event Descriptors HED is a set of descriptor tags partially adopted from BrainMapNeuroLex ontologies and organized hierarchically. HED tags can be used to describe many types of EEG experiment events in a uniform extensible and machine-readable manner. Visit www.hedtags.org for more information. Hierarchical Event Descriptor HED Tags EEGMEGECoG, Domain Independent, MIT http://www.nitrc.org/projects/hed/ nima.bigdely@syntrogi.com GNU GPL v2 Yes Rong Chen, rong.chen.mail@gmail.com NITRC Rong Chen Using resting-state functional magnetic resonance imaging rs-fMRI to study functional connectivity is of great importance to understand normal development and function as well as a host of neurological and psychiatric disorders. Seed-based analysis is one of the most widely used rs-fMRI analysis methods. Here we describe a freely available large scale functional connectivity data mining software package called Advanced Connectivity Analysis ACA. ACA enables large-scale seed-based analysis and brain-behavior analysis. It can seamlessly examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables. 2015-10-20 ACA v1.1 2015-7-22 aca_v1.0 Advanced Connectivity Analysis ACA a large scale functional connectivity data mining environment MR, GNU GPL v2 http://www.nitrc.org/projects/aca_rc/ rong.chen.mail@gmail.com GNU Lesser General Public License LGPL Yes Neal Morton, mortonne@gmail.com NITRC MacOS,POSIXUNIX-like,Windows MATLAB Neal Morton APERTURE Analysis of Patterns in Electrophysiological Recordings Toolbox with Utilities for REsearch is a MATLAB-based toolbox for analysis of EEG MEG and ECoG data. It is designed to organize entire analysis pipelines with large datasets from preprocessing to hypothesis testing and figure generation. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity. It also supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large high-dimensional datasets is made simple through data visualization tools including advanced plotting routines and generation of PDF reports with many figures. APERTURE is designed to be flexible and highly extensible to allow the user to easily implement new analysis protocols. APERTURE End Users, Developers, 4 - Beta, GNU Lesser General Public License LGPL, POSIXUNIX-like, Windows, MacOS, Console Text Based, English, Image Display, Multivariate Analysis, Spectral Analysis, MATLAB, EEGMEGECoG, Event Related Potential http://www.nitrc.org/projects/aperture/ mortonne@gmail.com Yes Andreas Hoefler, andreas.hoefler@uni-graz.at NITRC Andreas Hoefler The content includes the fMRI data of all of the 46 participants of the study mentioned above. You will be able to download the raw data for preprocessing and analysing by yourself. Please be aware of the different conditions which are mentioned in the connected paper and attached as logfiles in the repository. Self-threat and self-concept data English, DICOM, MR http://www.nitrc.org/projects/self01/ andreas.hoefler@uni-graz.at FSL License Yes Matthew Webster, mwebster@fmrib.ox.ac.uk NITRC SunOSSolaris,Windows NT2000,Linux,MacOS 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 5 - ProductionStableMature Current 2011-5-15 5 - ProductionStableMature 4.1.8 2010-7-01 5 - ProductionStableMature fsl 4.1.6 2010-2-04 5 - ProductionStableMature 4.1.5 2009-6-09 5 - ProductionStableMature 4.1.4 2008-8-13 5 - ProductionStableMature 4.1.0 2007-7-31 5 - ProductionStableMature 4.0.4 FSL End Users, 5 - ProductionStableMature, C, C, Linux, SunOSSolaris, Windows NT2000, MacOS, Console Text Based, X11 Applications, English, Tensor Metric, Segmentation, Temporal Transformation, Tractography, Image Display, Independent Component Analysis, Registration, Affine Warp, Volumetric Analysis, NIfTI-1, ANALYZE, FSL License, MR http://www.nitrc.org/projects/fsl/ mwebster@fmrib.ox.ac.uk Creative Commons License Yes Nima Bigdely-Shamlo, nima.bigdely@syntrogi.com NITRC Nima Bigdely-Shamlo Rapid Serial Visual Presentation 12Hz Target airplane detection without immediate response. The purpose of this study was to explore the neural basis of target detection in human brain and to compare the performance of brain-computer interface BCI methods in classification of target vs. non-target images. The data was acquired during a rapid serial visual presentation task which was composed of a sequential presentation of image clips in rapid succession 12s in 4.1-s bursts to which subjects were to indicate whether or not the satellite image clips of London presented included a small target airplane image by making one of two button presses. This study was collected at UCSDSwartz Center and placed into ESS version 2.02 levels 1amp;amp;2 by Syntrogi Inc. 2015-7-22 Main EEG Study data of Rapid Serial Visual Presentation RSVP in ESS format Creative Commons License, EEGMEGECoG http://www.nitrc.org/projects/eeg_rsvp/ nima.bigdely@syntrogi.com Yes ahmet omurtag, aomurtag@gmail.com NITRC ahmet omurtag To be filled after registering EEG-FNIRS hybrid SMR BCI data EEGMEGECoG, Optical Imaging http://www.nitrc.org/projects/eegfnirshbci/ aomurtag@gmail.com Apache License 2.0 Yes Juan Prieto, jprieto@med.unc.edu NITRC Linux,MacOS Yes C,Python Juan Prieto AutoTract is an automatic tractography tool featuring advanced processing tools to clean tracts after the initial tractography. It uses the Slicer TractographyLabelMapSeeding with tracts from a reference DTI atlas as label maps. The 3 main steps of the tool are -Registration between the DTI image that we want to tract and the reference DTI atlas. -Tractography of the DTI image using the TractographyLabelMapSeeding Slicer module. -Process of each tract individually to clean and remove any unwanted fiber. The processing includes for each tract -cutting every fiber ends that are in the gray matter cutting them until the fiber ends is in the white matter based on a white matter mask created by the tool. -ensuring every fiber is not in the CSF removes them from the tract otherwise -several image comparisons with the reference tracts such as fiber length matching use of a distance map to ensure that the tract is close to the reference tract and potentially to be added later on shape comparison. 2015-6-30 5 - ProductionStableMature AutoTract_v1.1 AutoTract End Users, 5 - ProductionStableMature, C, Python, Linux, MacOS, X11 Applications, English, Diffusion MR Fiber Tracking, Nrrd, Apache License 2.0, MR, Computational Neuroscience http://www.nitrc.org/projects/autotract/ jprieto@med.unc.edu VANDPIRE software license agreement Yes Dan Arteaga, darteaga08@gmail.com NITRC MacOS,POSIXUNIX-like,Microsoft Yes Python Dan Arteaga VANDPIRE is intuitive and comprehensive software for quantifying cerebral blood flow CBF and calculating CBF territories using arterial spin labeling ASL MRI data. CBF analysis particularly CBF territory analysis is time-consuming and requires advanced knowledge of scripting and up-to-date mathematical models. This toolbox addresses these concerns and is available on multiple platforms as a graphical user interface. Features - Available on Windows Mac and Linux platforms - Runs from single folder and thus capable of being run online in scanning environment - Comes with complete help tutorial in HTML format and example data - Numerous customizable options that are responsive to user input - Output data formats Nifti Dicom - Includes modifiable motion correction and coregistration options using FSL or Elastix - Currently tested with Philips ParRec and Philips Dicom pseudocontinuous ASL input data; however support available for other data formats upon request Created by Daniel F. Arteaga. VANDPIRE End Users, 5 - ProductionStableMature, Python, POSIXUNIX-like, Microsoft, MacOS, Quantification, Visualization, NIfTI-1, DICOM, Philips PARREC, NiPyPe, MR, VANDPIRE software license agreement http://www.nitrc.org/projects/vandpire/ darteaga08@gmail.com BSD License Yes Leonardo Bonilha, bonilha@musc.edu NITRC MATLAB Leonardo Bonilha When performing computational neuroscience-based analysis it is often beneficial to view the data. Also as Matlab is a common tool for such analysis it is beneficial to visualize the data without having to open an external application that does not run in the Matlab environment. MRIcroS a Matlab-based tool provides 1 surface mesh visualization PLY PIAL NV STLVTK GIFTI formats 2 Convert NIfTI voxel images to surface meshes and save as PLY or VTK 3 track TRK files visualization 4 connectome data BrainNet Viewer .node and .edge files visualization 5 intuitive GUI 6 all functions available in the GUI are available through scripting. Therefore automated scripts can be created 7 can export rendered image as bitmap 2015-9-11 MRIcroS 9-Sept-2015 2014-10-30 MRIcroS 30-Oct-2014 MRIcroS BSD License, Surface Rendering, Three Dimensional Display, NIfTI-1, ANALYZE, MATLAB, Other Format, GIfTI, MR, Computational Neuroscience, Clinical Neuroinformatics http://www.nitrc.org/projects/mricros/ bonilha@musc.edu BSD License Yes Mikhail Milchenko, mmilch01@gmail.com NITRC Mikhail Milchenko MGA is an MRI preprocessing pipeline built with HOF Heterogeneous Optimization Framework methodology. MGA prepares neuro-oncology clinical imaging studies for scientific analysis such as multispectral ROI analysis in both longitudinal and cross-sectional studies. MGA works on DICOM images from a single MRI study. Includes perfusion DSC sequence based analysis and DTI analysis and spatially co-registers all study images to an atlas template and to a template image within the study. MGA is designed to reasonably minimize user configuration steps and to accept a broad range of MRI submodalities including support for clinical image quality. The distribution is available as a stand-alone docker.io virtual appliance for 64-bit Linux environments see detailed instructions in the installation package httpsbitbucket.orgmmilch01mga_docker_install MGA - Multimodal Glioma Analysis BSD License, MR http://www.nitrc.org/projects/hof/ mmilch01@gmail.com Yes Li Shen, shenli@iu.edu NITRC Li Shen The Single Nucleotide Polymorphism Database dbSNP is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information NCBI in collaboration with the National Human Genome Research Institute NHGRI. dbSNP Other Web Resource, Imaging Genomics, SNPs amp;amp; Genes http://www.nitrc.org/projects/dbsnp/ shenli@iu.edu MRBrainS license Yes Adrienne Mendrik, a.m.mendrik@umcutrecht.nl NITRC Yes Adrienne Mendrik The aim of the MRBrainS online evaluation framework is to compare automatic algorithms that segment gray matter GM white matter WM and cerebrospinal fluid CSF on 3T MRI scans. Participants apply their algorithms to the provided data after which their results are evaluated and ranked. Full manual segmentations of GM WM and CSF are available for all 20 scans and used as the reference standard trainingset 5 testset 15. The evaluated methods are ranked based on their overall performance to segment GM WM and CSF and evaluated using three evaluation metrics Dice 95th percentile Hausdorff distance and absolute volume difference. The results are published on the MRBrainS13 website. If you would like to join the MRBrainS challenge please register a team on the MRBrainS website httpmrbrains13.isi.uu.nlregister.php and sign the confidentiality agreement. You will be granted access to the data and can submit your automatic segmentation results for evaluation. Visit httpmrbrains13.isi.uu.nl MRBrainS Evaluation Framework Challenge MR, Clinical Neuroinformatics, MRBrainS license http://www.nitrc.org/projects/mrbrains/ a.m.mendrik@umcutrecht.nl GNU General Public License GPL Yes Hadi Hosseini, hadi.hosseini@gmail.com NITRC Hadi Hosseini GAT is a Matlab-based software that provides a GUI framework for conducting graph analysis with MR data. It integrates the Brain Connectivity Toolbox REX toolbox BrainNet Viewer with original code for additional graph analyses and comparing networks between groups. Using GAT you can analyze structuralfunctional networks constructed from VBM Free Surfer data resting statetask fMRI DTI MRS and behavioral data. GAT provides non-parametric statistics for comparing small-world parameters regional topology hubs network resilience and modularity between groups. Please cite the following paper if you are using GAT Hosseini et al 2012. GAT a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks. PLoS ONE 77 e40709. Please subscribe to GAT mailing list at httpsmailman.stanford.edumailmanlistinfogat_user_forum to get updates and share questions. Contact Hadi Hosseini hosseiny at stanford.edu GAT Graph Analysis Toolbox GNU General Public License GPL, Multivariate Analysis, MR, Domain Independent, Computational Neuroscience, Connectivity Analysis http://www.nitrc.org/projects/gat/ hadi.hosseini@gmail.com BSD License Yes Yangming Ou, ouymcn@gmail.com NITRC Yangming Ou Unbiased atlas construction by group-wise dramms registration. Can be used to construct a normal atlas from either a normal population or an abnormal population. The tool will find a virtual space that represents the mean geometry mean anatomy and voxel-wise mean intensity of the input population hence unbiased. If the input images are from an abnormality-bearing population the above happens to normal regions only and will create an unbiased normal-appearing atlas. The software can either take as input the manually annotated abnormality masks or automatically detect and exclude abnormalities from atlas construction. 2016-7-05 popdramms_1.0.0 Unbiased Atlas Construction via Population group-wise DRAMMS Registration BSD License, Domain Independent http://www.nitrc.org/projects/popdramms/ ouymcn@gmail.com BSD License Yes Tao Chen, andrewchentao9@gmail.com NITRC Tao Chen The Augmented Reality Mirror is an open source rendering software to provide users with a virtual reality experience. With the provisions of a projection display a laptop with multi-core GPU and XBOX kinect users can stand in front of the mirror and representative anatomical images will overlay the body. The images implemented are adapted to approximate the actual anatomy. The open source software will have an application programming interface API to allow users to develop additional content within the Augmented Reality Mirror. 2016-8-08 AR_Calc_Teaching_Tool v1.1 2016-7-18 2DImage_Overlay_20160718 2016-7-18 Sherlock_Game_07182016 2016-7-14 2016 3D Organ Rendering 1.0 Augmented Reality Mirror BSD License, CT http://www.nitrc.org/projects/ar_mirror/ andrewchentao9@gmail.com Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Boris Bernhardt, boris.bernhardt@gmail.com NITRC Yes Boris Bernhardt The MNI-HISUB25 dataset contains manual hippocampal subfield labels and associated high-resolution MRI data submillimetric T1- and T2-weighted images detailed sequence information and stereotaxic probabilistic anatomical maps based on 25 healthy subjects. Data were acquired on a 3-Tesla MRI system using a 32 phased-array head coil. The protocol divided the hippocampal formation into three subregions subicular complex Cornu Ammonis 1 2 and 3 CA1-3 and CA4-dentate gyrus CA4-DG. Segmentation was guided by consistent intensity and morphology characteristics of the densely myelinated molecular layer together with few geometry-based boundaries flexible to overall mesiotemporal anatomy and achieved excellent intra-inter-rater reliability Dice index ≥9087%. The dataset can inform neuroimaging assessments of the mesiotemporal lobe and help to develop segmentation algorithms relevant for basic and clinical neurosciences. 2015-9-29 MNI-HISUB25-1.0 Multi-contrast and submillimetric 3-Tesla hippocampal subfield segmentation protocol and dataset MNI-HISUB25 Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, MR http://www.nitrc.org/projects/mni-hisub25/ boris.bernhardt@gmail.com Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Anthony Kolasny, akolasny@jhu.edu NITRC Anthony Kolasny The purpose of this filter is to use the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. In the same way that a sound signal can be approximately characterized by a combination of its most significant frequency components so can a surface be expressed as a combination of its surface harmonics. This filter determines the requested N most significant harmonics. Laplace Beltrami Filter on QuadEdge Meshes Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, Domain Independent http://www.nitrc.org/projects/laplacebeltrami/ akolasny@jhu.edu Attribution-NonCommercial-NoDerivatives 4.0 International CC BY-NC-ND 4.0 Yes Chase Figley, cfigley@gmail.com NITRC OS Independent Yes Chase Figley This is a probabilistic atlas of human white matter tractsregions underlying various functionally-connected brain networks including the dorsal and ventral Default Mode Networks left and right Executive Control Networks and anterior and posterior Salience Networks. These regions were derived by performing fMRI-guided DTI tractography on 32 neurologically-healthy adult control subjects. The atlas comprises group probability maps for each network as well as each individual tract i.e. 1-mm isotropic NIFTI images that are aligned to both the SPM and MRIStudio ICBM templates. In accordance with the CC BY-NC-ND 4.0 License this atlas may be used for academic purposes but users should cite the following paper in all resulting presentations or publications Figley TD Bhullar N Courtney SM and Figley CR 2015. Probabilistic atlases of default mode executive control and salience network white matter tracts An fMRI-guided diffusion tensor imaging and tractography study. Front. Hum. Neurosci. 9585. 2015-7-26 5 - ProductionStableMature UManitoba – JHU Functionally-Defined Human White Matter Atlas Version 1.0 UManitoba-JHU Functionally-Defined Human White Matter Atlas End Users, 5 - ProductionStableMature, OS Independent, English, NIfTI-1, Atlas Data, MR, Clinical Neuroinformatics, Attribution-NonCommercial-NoDerivatives 4.0 International CC BY-NC-ND 4.0 http://www.nitrc.org/projects/uofm_jhu_atlas/ cfigley@gmail.com Cerebellar White Matter Atlas Yes Kirsten van Baarsen, kirsten.vanbaarsen@radboudumc.nl NITRC Yes Kirsten van Baarsen The Cerebellar White Matter Atlas is based on probabilistic tractography of high resolution high quality diffusion MR data of 90 healthy subjects from the Human Connectome Project database. The atlas comes as a 3D probabilistic map as well as binary parcellations at different probability thresholds. MNI - as well as SUIT Spatially Unbiased Infratentorial Template - compatible versions of the atlas are provided. 2015-10-23 Parcellation maps at MNI 1mm Cerebellar White Matter Atlas Diffusion MR Fiber Tracking, MR, Cerebellar White Matter Atlas http://www.nitrc.org/projects/cer_wm_atlas/ kirsten.vanbaarsen@radboudumc.nl spatial attention in 3D license Yes Wang Aijun, psy_waj@126.com NITRC Wang Aijun Using functional MRI aimming at investigated the neural interface which integrated information between the dorsal and the ventral streams. The results showed that the parietal-occipital junction POJ and bilateral superior occipital gyrus SOG showed relative increased activity when responded to a target presented in near space than in far space which was independent of the retinotopic or perceived size of the target. Furthermore the POJ showed enhanced functional connectivity with both the dorsal and ventral streams during far space processing irrespective of the target size supporting the role of the POJ as an interface between the two streams. In contrast the SOG showed enhanced functional connectivity only with the ventral stream if retinotopic sizes of the targets in near and far space were matched which suggested the functional dissociation between the POJ and SOG. The role of V6 in the interaction between dorsal and ventral streams in near and far space processing MR, spatial attention in 3D license http://www.nitrc.org/projects/visuospatial/ psy_waj@126.com ANIMA Data Usage and Contributor Agreement Yes Andrew Reid, typically@yahoo.com NITRC Yes JavaScript,Java,PHP Andrew Reid ANIMA the Archive of Neuroimaging Meta-analyses is an online repository of meta-analytic neuroimaging results using methods such as activation likelihood estimation and multi-kernel density analysis. The ANIMA platform consists of an intuitive online interface for querying downloading and contributing data from published meta-analytic studies. Additionally to aid the process of organizing visualizing and working with these data we present an open-source desktop application called Volume Viewer. Volume Viewer allows users to easily arrange imaging data into composite stacks and save these sessions as individual files which can also be uploaded to the ANIMA database. The application also allows users to perform basic functions such as computing conjunctions between images or extracting regions-of-interest or peak coordinates for further analysis. ANIMA End Users, Developers, PHP, Java, JavaScript, Database, Websites, Web Service, MR, Clinical Neuroinformatics, ANIMA Data Usage and Contributor Agreement http://www.nitrc.org/projects/anima-db/ typically@yahoo.com GNU Affero General Public License v3 Yes Olivier Commowick, olivier.commowick@inria.fr NITRC MacOS,POSIXUNIX-like,Windows Yes C Olivier Commowick Anima is a set of ITKVTK based libraries and multi-platform command line tools for medical image analysis. It contains software for image registration linear and non linear block matching registration EPI distortion correction statistical analysis group comparison patient to group comparison diffusion imaging model estimation tractography etc. quantitative MRI processing quantitative relaxation times estimation MR simulation image denoising and filtering and segmentation tools Graph cut segmentation and multiple sclerosis lesion segmentation. Anima is available as a Github repository see the source code link and compiled binaries for various OS OSX Fedora Ubuntu Windows. 2017-3-22 5 - ProductionStableMature Anima v2.1 2016-10-11 5 - ProductionStableMature Anima v2.0 2016-5-27 5 - ProductionStableMature Anima v1.2 2015-11-20 5 - ProductionStableMature Anima v1.1 2015-11-02 5 - ProductionStableMature Anima v1.0 Anima End Users, Developers, 5 - ProductionStableMature, C, POSIXUNIX-like, Windows, MacOS, Console Text Based, Win32 MS Windows, Algorithm or Reusable Library, MR, Computational Neuroscience, GNU Affero General Public License v3 http://www.nitrc.org/projects/anima/ olivier.commowick@inria.fr Attribution Non-Commercial Yes Ann Choe, annschoe@gmail.com NITRC Ann Choe We have acquired a longitudinal single-subject dataset of a healthy volunteer 40 years of age at time of initial scan; male. A total of 158 sessions of MRI data was acquired on a weekly basis over a span of 185 weeks a little over 3 years. The subject was scanned on a 3T Philips Achieva scanner Philips HealthCare Best Netherlands. Rs-fMRI data of the subject was acquired using a multi-slice SENSE-EPI pulse sequence with TRTE = 200030 ms SENSE factor = 2 flip angle = 75° 37 axial slices nominal resolution = 3x3x3 mm3 1 mm gap 16 channel neuro-vascular coil number of dynamics frames per run = 200. The subject was instructed to stay as still as possible with his eyes closed during the entire scan and no other instruction was provided. This is intended to be a resource for statisticians and imaging scientists to be able to quantify the intra-subject inter-session reproducibility of their image analysis methods using data available from a 7 min session at 3T 2015-9-30 Kirby Weekly Single-subject Resting state fMRI Reproducibility Resource Attribution Non-Commercial, MR http://www.nitrc.org/projects/kirbyweekly/ annschoe@gmail.com Artistic License Yes Vladimir Fonov, vladimir.fonov@gmail.com NITRC Vladimir Fonov Whole set of MINC-based image processing tools packaged together and several ITKv4 tools Includes MINCN3BICPLEBKTSANIMALINSECTBEaSTRegisterDisplayxdispANTS Elastix ABC C3D minc-toolkit-v2 Artistic License, MR http://www.nitrc.org/projects/minc-toolkit-v2/ vladimir.fonov@gmail.com Open Data Commons Open Database License ODbL Yes LabNuero CogDevel, will.foran@gmail.com NITRC Yes LabNuero CogDevel Eyes closed 5 min rest and structural 1.5 TR 3T Siemens Trio in developmenetal sample 10-26 years of age. 192 subjects. Data used in PLOS Bio paper Contribution of Network Organization and Integration to the development of Cognitive Control Download httpdevrsfmri_2015.projects.nitrc.orgdevrsfmri_2015.tar.bz2 Developmental Resting State fMRI and Structrual Sample 10-26 yo MR, Open Data Commons Open Database License ODbL http://www.nitrc.org/projects/devrsfmri_2015/ will.foran@gmail.com Public Domain Yes Sinead Kelly, Sinead.Kelly2@loni.usc.edu NITRC Yes Sinead Kelly The ENIGMA DTI pipeline provides tools to extract whole-brain average and regional measurements from DTI images including FA AD RD and MD. The pipeline has been used successfully across sites worldwide and shown to extract reliable and heritable measures from diffusion imaging. We provide a FA-template created from multiple high resolution datasets to better accommodate registrations to a standard atlas than current existing tools. The ENIGMA-DTI analysis team is continuously working to bridge together pipelines to analyze DTI in reliable ways across multiple datasets and reduce inter-site inhomogeneities and inconsistencies between findings so stay tuned for more updates and tools. Successful global studies of genetic or disease effects underlying variability in white matter neuroanatomy have been published through ENIGMA and many more are underway. To get involved in any ENIGMA group send us a message -- enigmaini.usc.edu or support.enigmaDTIini.usc.edu. 2016-1-14 ENIGMA DTI ROI extraction protocol 2016-1-14 ENIGMA DTI diffusivity protocol 2015-11-11 ENIGMA-DTI FA Original Template 2015-11-11 ENIGMA GitHub 2015-11-11 ENIGMA-DTI FA protocols 2015.11.11.v1.1 2015-10-14 Third ENIGMA-DTI publication - a report on collaboration between ENIGMA and HCP 2015-10-14 Second ENIGMA-DTI publication Kochunov NeuroImage 2014 2015-10-14 First ENIGMA-DTI publication Jahanshad 2014 ENIGMA-DTI pipeline Public Domain, Imaging Genomics http://www.nitrc.org/projects/enigma_dti/ Sinead.Kelly2@loni.usc.edu GNU GPL v2 Yes Andreas Horn, mail@andreas-horn.de NITRC Andreas Horn The Gibbs connectome is a set of ready-processed high-dimensional structural and functional connectivity matrices and group fibertract information of 169 subjects. The data is based on the openly available NKI enhanced Rockland sample httpfcon_1000.projects.nitrc.orgindienhanced which represents a state-of-the-art community sample. To estimate a group connectome of fiber tracts the Gibbs tracking algorithm has been applied to each subjects dMRI data. Fiber tracts have been normalized into standard space using DARTEL. Explicit methodology of the data set is described here httpwww.ncbi.nlm.nih.govpubmed26327244 2016-4-06 Gibbsconnectome data Gibbsconnectome MR, GNU GPL v2 http://www.nitrc.org/projects/gibbsconnectome/ mail@andreas-horn.de Free For Non-Commercial Use Only Yes Mauricio Reyes, mauricio.reyes@istb.unibe.ch NITRC Yes Mauricio Reyes BraTumIA for Brain Tumor Image Analysis is a software dedicated to multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences currently T1 T1-contrast T2-contrast and FLAIR. Segmented tissues include Gray Matter GM White Matter WM Cerebrospinal Fluid CSF necrotic core edema non-enhancing tumor and enhancing tumor. The current version of BraTumIA is designed to work on pre-operative images. BraTumIA Brain Tumor Image Analysis Free For Non-Commercial Use Only, MR, Computational Neuroscience, Clinical Neuroinformatics http://www.nitrc.org/projects/bratumia/ mauricio.reyes@istb.unibe.ch Attribution Non-Commercial Yes Emilie McKinnon, mckinnon@musc.edu NITRC Emilie McKinnon KIN has an alternative website please go to httpkin.projects.nitrc.org Kurtosis Imaging Network KIN is an open source database for normal healthy controls as well as various pathologies in an attempt to establish a standard range of kurtosis values within each population. This database of diffusional kurtosis images will also allow for quantitative comparisons between sites vendors and various protocol parameters. Finally KIN will also help develop a strong collaborative network for researchers to troubleshoot current projects and create future projects. By downloading or uploading data from and to KIN you automatically accept the KIN data use agreement which certifies that you understand and agree to all applicable terms contained herein. Kurtosis Imaging Network - KIN Attribution Non-Commercial, MR, Computational Neuroscience http://www.nitrc.org/projects/kin/ mckinnon@musc.edu Attribution Share Alike Yes Jeffrey Young, jeffrey@unc.edu NITRC Jeffrey Young This is a set of cross-sectional structural atlases as well as cross-sectional and longitudinal DTI atlases of a cohort of 40 rhesus macaques scanned longitudinally at ages 2 weeks 3 months 6 months 12 months and 18 months. 2016-9-15 Structural atlases 2weeks 2016-9-15 DTI 2w 3m 6m 12m 18m atlases 2016-9-15 Structural atlases 12months 2016-9-15 Structural atlases 6months 2016-9-15 Structural atlases 3months Emory-UNC Developmental Macaque Structural and DTI Atlases Attribution Share Alike, MR http://www.nitrc.org/projects/macaque_atlas/ jeffrey@unc.edu BSD License Yes Yangming Ou, ouymcn@gmail.com NITRC Yangming Ou STandardized Abnormality-free Multi-Parametric STAMP atlases can help detect various lesions e.g. MS lesions stroke lesions primaryrecurrent tumors post-surgery cavity etc. STAMP atlases include 4 modalities T1 T2 T1c FLAIR and 1 artificial modality T1d=T1c-T1 highlighting pure contrast. Here T1c is T1 MRI with gadolinium contrast. Multi-modal atlases help detect lesion components. The otherwise rarely available T1cT1d atlases can help differentiate between normal vessels and enhancing tumor both enhancing upon gadolinium injection. The STAMP atlases quantify the normal intensity variations at the voxel level which adds to those at the image or tissue level. This may help abnormality detection because normal variations and hence abnormal detection may depend on anatomical locations. The STAMP atlas can also be used to standardize intensity to spatially normalize patient images or to extract alignment-based features. Publication pending. 2015-11-20 STAMP atlases 1.0.1 2015-11-20 STAMP atlases 1.0.0 STAMP Atlases for Brain Abnormality Detection BSD License, MR http://www.nitrc.org/projects/stamp_atlases/ ouymcn@gmail.com