Copyright 1999-2000 VA Linux Systems, Inc. Mon, 12 May 2008 2:57:50 GMT Full Tool/Resource Listing http://www.nitrc.org webmaster@www.nitrc.org en-us http://www.nitrc.org/projects/fit/ FIT is a MATLAB toolbox which uses Independent Component Analysis (ICA) to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. http://www.nitrc.org/projects/artifact_detect/ Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well. http://www.nitrc.org/projects/birn/ BIRN is a geographically distributed virtual community of shared resources to advance the diagnosis and treatment of disease. http://www.nitrc.org/projects/diffusionwarp/ This project contains tools appropriate for the registration of diffusion tensor images to an average coordinate system. The tools include image registration methods and algorithms for the correct alignment of the fiber architecture after applying th http://www.nitrc.org/projects/dtic/ Software tool (excecutable and source code in C and C++) to correct distortions in diffusion MR images that are generated by main magnetic field inhomogeneities and eddy current induced fields generated from the direction-dependent diffusion encoding http://www.nitrc.org/projects/mango/ Mango is a multi-platform viewer for medical image volumes. It provides tools to analyze images and an interface to navigate the image volume. It supports plugin development and many kinds of feature customization. Homepage: http://ric.uthscsa.edu/mango http://www.nitrc.org/projects/lumina/ The Lumina LP-400 is a reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields. http://www.nitrc.org/projects/pediatric_mri/ The NIH Pediatric MRI Data Repository contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult. http://www.nitrc.org/projects/braincsi/ BrainCSI is a tool for partial volume correction in CSI data. http://www.nitrc.org/projects/brainstestdata/ The BRAINS suite of tools (BRAINSFit, GTRACT, BRAINS, BRAINSTracer... and others) use a common set of anonymized data for nightly regression testing. This data is about 1.2GB of anonymized imaging data of many different file formats used to ensure t http://www.nitrc.org/projects/mri_studio/ MRI and DTI imaging software tool. http://www.nitrc.org/projects/grad_unwarp/ The Brain Morphometry testbed of the BIRN provides a tool to correct gradient non-linearity distortions in MR structural images. This correction improves test-retest reproducibility crucial for multi-site studies. http://www.nitrc.org/projects/idea_lab/ Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. Database management. Other packages to be added. http://www.nitrc.org/projects/func_connect/ The purpose of this project is to provide a community for the discussion of functional connectivity and all related topics. This includes discussion of related tools, data sets, methodological discussion, related websites and publications, etc. http://www.nitrc.org/projects/art/ Linear and non-linear registration algorithms for matching brain images between and within subjects and imaging modalities. Applications include inter-subject registration of 3D MRI, MRI-PET/SPECT registration, and EPI spatial distortion correction. http://www.nitrc.org/projects/lddmm-volume/ LDDMM assigns a metric distances on the space of anatomical images http://www.nitrc.org/projects/miview/ 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, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images. http://www.nitrc.org/projects/braingrpheditor/ The BrainGraph Editor 1.0 Beta is a JAVA application designed to create taxonomies or hierarchies in order to classify and organize information. http://www.nitrc.org/projects/mbat/ The Mouse BIRN Atlasing Toolkit (MBAT) 2.0 BETA is a JAVA application designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types. http://www.nitrc.org/projects/fluctuations/ The methodology and applications of task independent fluctuation measures including: connectivity maps of fMRI resting state scans, research using EEG/MEG/PET etc, methods to remove non-neural fluctuations, and applications to clinical populations. http://www.nitrc.org/projects/slicer3examples/ Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. http://www.nitrc.org/projects/mpscope/ MPScope is a comprehensive software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, the analysis program MPView and several software utilities http://www.nitrc.org/projects/hid/ The Human Imaging Database(HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. http://www.nitrc.org/projects/nptk/ NPTK provides non-rigid registration/distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI. http://www.nitrc.org/projects/threedicsi/ 3D Interactive Chemical Shift Imaging (3DiCSI) is a user-friendly and comprehensive software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis. http://www.nitrc.org/projects/vmagnotta/ GTRACT is a Diffusion Tensor fiber tracking suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. http://www.nitrc.org/projects/gifti/ Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). http://www.nitrc.org/projects/brains/ The BRAINS (Brain Research: Analysis of Images, Networks, and Systems) image analysis software has been developed to study the brain thus providing a better understand of psychiatric and neurological disorders. http://www.nitrc.org/projects/voxbo/ VoxBo is a highly modular and interoperable collection of tools for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo is useful either as a self-contained package or as a supplement to other software. http://www.nitrc.org/projects/stfilter/ Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images. This project provides tools which can perform Stochastic Tractography and related analysis on DWMRI data. http://www.nitrc.org/projects/mipav/ The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. http://www.nitrc.org/projects/dtiricianrem/ Two Slicer3 modules removing rician noise in diffusion tensor MRI http://www.nitrc.org/projects/bvqxtools/ BVQXtools is a Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab. In the publicly (for-free) available toolbox, all major file formats are supported next to a bundle of functions and methods to simplif http://www.nitrc.org/projects/hammer/ 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. http://www.nitrc.org/projects/fsl_extensions/ FSL extensions is a reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL). http://www.nitrc.org/projects/nvm/ NVM is an open-source software tool for locating and measuring neuroanatomy in structural volumetric image data. It is used to draw regions of interest for subsequent fMRI analysis. http://www.nitrc.org/projects/fbirn/ The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. http://www.nitrc.org/projects/nldo/ NeuroLens is an integrated environment for the analysis and visualization of functional neuroimages. http://www.nitrc.org/projects/freesurfer/ FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface. http://www.nitrc.org/projects/xnat/ The Extensible Neuroimaging Archive Toolkit (XNAT) is a suite of tools for managing neuroimaging studies from data acquisition and analysis to publication and public data sharing. http://www.nitrc.org/projects/mbirn/ BIRN’s Morphometry Test Bed focuses on pooling and analyzing data across neuroimaging sites for potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer’s disease. http://www.nitrc.org/projects/rex/ REX is a stand-alone MATLAB-based toolkit for the rapid and flexible exploration of ROI response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial. http://www.nitrc.org/projects/gift/ Group ICA Toolbox is a MATLAB toolbox which implements multiple algorithms for independent component analysis of group magneto resonance imaging data (GIFT) and electro encephalogram data (EEGIFT) to group studies. http://www.nitrc.org/projects/tal-daemon/ The Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach atlas. http://www.nitrc.org/projects/brainmap/ BrainMap is a community database of published functional neuroimaging studies (mainly PET and fMRI). BrainMap contains both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates. http://www.nitrc.org/projects/multimodereg/ A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. http://www.nitrc.org/projects/bioimagesuite/ BioImage Suite is a general purpose registration/segmentation/visualization suite. It also has facilities for DTI and fMRI processing. http://www.nitrc.org/projects/slicer/ An extensible, cross-platform, totally open research platform for image computing. http://www.nitrc.org/projects/iatr/ The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community. http://www.nitrc.org/projects/ibsr/ The Internet Brain Segmentation Repository (IBSR) provides manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the evaluation and development of segmentation methods. http://www.nitrc.org/projects/wfu_bpm/ The WFU Biological Parametric Mapping (WFU_BPM) toolbox performs SPM analysis with voxel-wise imaging covariates. http://www.nitrc.org/projects/wfu_pickatlas/ 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. http://www.nitrc.org/projects/rapid/ A matlab toolbox for statistical analysis of multi-subject functional data extracted using individually defined region-of-interest masks. http://www.nitrc.org/projects/inspector/ The LONI Inspector is an application for examining medical image files. The Inspector focuses on reading, displaying, searching, comparing, and exporting "metadata" (e.g., patient name, the model of scanner). http://www.nitrc.org/projects/did/ The LONI de-identification Debablet is an application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner. http://www.nitrc.org/projects/debabeler/ The LONI Debabeler manages the conversion of imaging data from one file format and convention to another. It consists of a GUI to visually program the translations, and a data translation engine to read, sort and translate the input files. http://www.nitrc.org/projects/brainfx/ A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA's and Brainwaver's User interface. http://www.nitrc.org/projects/brainwaver/ Characterisation of small-world networks constructed from wavelet analysis of resting fMRI. This package is currently available as an R library. Futrure development will take place within the CamBA software repository http://www.nitrc.org/projects/camba/ 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. http://www.nitrc.org/projects/meg-tools/ MEG Localization using FOCUSS and MR-FOCUSS http://www.nitrc.org/projects/fmripower/ A common question investigators ask statisticians when working on grants is how to calculate power. FMRIpower is an easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data. http://www.nitrc.org/projects/snpm/ The Statistical nonParametric Mapping toolbox provides an extensible framework for voxel level non-parametric permutation/randomisation tests of functional Neuroimaging experiments with independent observations. http://www.nitrc.org/projects/caret/ Caret is your surface swiss army knife. http://www.nitrc.org/projects/mindboggle/ Mindboggle automates anatomical labeling of human brain MR data. The present beta version is written in Matlab; a new version is under development... http://www.nitrc.org/projects/pipeline/ The LONI Pipeline is a free workflow application primarily aimed at Neuroimaging Researchers, but is useful for many other fields of science. Visit http://pipeline.loni.ucla.edu for more info. http://www.nitrc.org/projects/fiv/ The Functional Image Viewer, also known as FIV, is a tool for visualizing functional and anatomic MRI data. http://www.nitrc.org/projects/nifti/ The Neuroimaging Informatics Technology Initiative (NIfTI) and NIfTI Data Format Working Group, creator and maintainer of the NIfTI-1 data format. http://www.nitrc.org/projects/spm/ The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. http://www.nitrc.org/projects/afni/ AFNI is a set of C programs for processing, analyzing, and displaying FMRI data. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free for research purposes. http://www.nitrc.org/projects/ontology/ This project will discuss, debate, develop and deploy ontological practices for the fMRI community. http://www.nitrc.org/projects/fsltest/ 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. FSL runs on Apple, PCs (Linux and Windows) and Sun. http://www.nitrc.org/projects/dave1/ This project is a simple Surface and Volumetric Visualization application that has been designed to facilitate rapid and flexible visualization from neuroanatomically segmented results. http://www.nitrc.org/projects/nitrc/ This resource provides NITRC-wide facilities: Forums, Wiki, Tracker, and News.