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Neuroimaging Informatics Tools and Resources Clearinghouse


Funded by the National Institutes of Health Blueprint for Neuroscience Research in 2006, the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses—including popular tools as well as those that once might have been hidden in another researcher's laboratory or some obscure corner of cyberspace. NITRC collects and points to standardized information about tools, making the task of finding and comparing them easier than before. Awarded 'Best Overall' for Excellence.Gov 2009, this site can help you find the right functional or structural neuroimaging tool or resource and help you decide whether it can help in your research.




  • Age Related Atrophy Dataset ( Database )

    The Age Related Atrophy dataset contains structural MR images of 70 subjects collected during 2008-2010 across a wide range of ages. The dataset also contains resting state fMRI for most subjects. The structural images are T1 weighted T2 weighted-FLAIR 25 direction DTI and the T1 mapping DESPOT 1 sequence. Reconstructed T1 maps for each subject are also available.

    The aquisition protocol was designed to study structural differences between young and older adults including both shape and intensity changes. Anonymized DICOM image sessions and processed images for each subject are available. The data is licensed under the Creative Commons Attribution License. It may be used freely for commercial academic or other use as long as the original source is properly cited.


  • BrainLiner.jp ( Database )

    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.

  • Diffusion MRI - In-vivo and Phantom Data ( Database )

    This projects is an open-data initiative for the distributation of common datasets for the evaluation and validation of diffusion MRI processing methods.

  • NIH Pediatric MRI Data Repository ( Database )

    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.


  • AFNI ( Software )

    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.

    Keywords: Surface Analysis, Response Monitoring, DICOM, AFNI BRIK, NIfTI-1, GIfTI, MINC, ANALYZE, X11 Applications, English, Haemodynamic Response, Image Display, Rendering, Resampling, Tensor Metric, Linux, Nonlinear, Freeware, Temporal Convolution - Deconvolution, 6 - Mature, End Users, Developers, MacOS, C, Python, Region of Interest, Registration, Volumetric Analysis, Uncategorized Domain

  • Automatic Registration Toolbox ( Software )

    ART `acpcdetect program for automatic detection of the AC and PC landmarks and the mid-sagittal plane on 3D structural MRI scans.

    ART `brainwash program for automatic multi-atlas skull-stripping of 3D structural MRI scans.

    ART `3dwarper program of non-linear inter-subject registration of 3D structural MRI scans.

    Software art2 for linear rigid-body intra-subject inter-modality MRI-PET image registration.

    Data resource The ART projects makes available corpus callosum segmentations of 316 normal subjects from the OASIS cross-sectional database. Keywords: C, NIfTI-1, Artifact Removal, Nearest Neighbor, Spline Interpolation, Tri-linear, Image Display, Affine Warp, Nonlinear Warp, Image-to-Template, Intermodal, Intersubject, Intramodal, Intrasubject, 3 - Alpha, MR, PETSPECT, Console Text Based, Developers, End Users, Free For Non-Commercial Use Only, English, Linux

  • BrainVision Analyzer ( Software )

    "Since 1997 BrainVision Analyzer has made its way into thousands of research labs helping scientists to manage their daily work of analyzing various neurophysiological data.
    Thanks to its ease of use the handling of an amazing number of powerful features is just a snap. The editable History Tree® lets you organize explore and trace evaluation steps.

    Automated analysis with drag and drop functions speeds up recurring tasks.

    Various data format readers recognize files from different EEG manufacturers automatically and guarantee compatibility and exchangeability with other research labs.

    Analyzer includes all necessary pre-processing functions enhanced time-frequency analysis options ICA LORETA MRI correction and a direct interface to MATLAB®.

    Various views create unlimited output possibilities to publish your results.

    PLEASE NOTE Running Analyzer requires a dongle that has to be purchased through Brain Products or one of its distributors httpwww.brainproducts.comdistributors.php.

    Keywords:Event Related Potential, Segmentation, Fourier Time-domain Analysis, 5 - ProductionStable, EEGMEGECoG, End User, English"

  • CANDI Neuroimaging Access Point ( Software )

    The Child and Adolescent NeuroDevelopment Initiative CANDI at UMass Medical School is making available a series of structural brain images as well as their anatomic segmentations demographic and behavioral data and a set of related morphometric resources static and dynamic atlases.

    Schiz Bull 2008 data is now available on NITRC-IR. Please register for access httpwww.nitrc.orgprojectrequest.phpgroup_id=377

    Keywords: MR, Web Environment, End Users, Attribution, English, NIfTI-1, Segmentation, 4 - Beta, Volumetric Analysis, Data, Knowledge Environment, Web Resource, Atlas Data

  • CBS High-Res Brain Processing Tools ( Software )

    "With 7 Tesla MRI neuroscientists can investigate the structure of the human brain with enhanced resolution currently up to 350µm isotropic in vivo. Quantitative MR contrasts and increased level of detail within tissues reveal many fine anatomical structures but require efficient computational methods that handle various contrasts and scale well with data complexity.

    The CBS High-Res Brain Processing Tools provide a fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400µm including skull stripping whole brain segmentation cortical extraction surface inflation and mapping as well as dedicated tools for profile estimation across the cortical thickness.

    The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats."

  • CleanLine ( Software )

    Sinusoidal noise can be a prominent artifact in recorded electrophysiological data. This can stem from AC power line fluctuations e.g. 5060 Hz line noise harmonics power suppliers e.g. in medical equipment fluorescent lights etc. Notch filtering is generally undesirable due to creation of band-holes and significant distortion of frequencies around the notch frequency as well as phase distortion at other frequencies and Gibbs rippling in the time-domain. CleanLine is an EEGLAB plugin which adaptively estimates and removes sinusoidal artifacts from ICA components or scalp channels using a frequency-domain multi-taper regression technique with a Thompson F-statistic for identifying significant sinusoidal artifacts. This approach has been advocated by Partha Mitra and Hemant Bokil Observed Brain Dynamics Chapter 7.3.4. 2007 and CleanLine utilizes modified routines from the Mitra Labs Chronux Toolbox www.chronux.org.

    Keywords: Spectral Analysis, GNU General Public License GPL, Uncategorized Domain

  • COGNISION TM System ( Software )

    COGNISION TM with auditory or visual event-related potential ERP technology provides a direct physiologic measure of patients cognitive processing i.e. a cognitive biomarker and COGNISION is a portable highly integrated internet-enabled hardwaresoftware platform and patient management system which includes an online Patient Manager module which complies with the HIPAA Final Security Rule an ERP Viewer module to view and analyze raw and average ERP waves and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel and is designed to be used in an out-patient setting.

    Keywords: Event-Related Potentials, Other Software Resource, EEGMEGECoG

  • Curry 7 ( Software )

    Throughout the world Curry has the well deserved reputation as the most advanced and comprehensive tool for Multimodal Neuroimaging. Curry's strength has always been centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. Now we are combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition data analysis source localization and source imaging package.

    Keywords: Segmentation, Spatial Transformation, Position, Volumetric Analysis, 5 - ProductionStable, EEGMEGECoG, MR, CT, PETSPECT, End Users, Commercial License, English, Windows, Atlas Application, Connectivity Analysis, Database Application, Format Conversion, Image Reconstruction, Finite Element Analysis, EEG Modeling, MEG Modeling, Mesh Generation, Model Generation, Simulation

  • DATAPixx ( Software )

    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.

    Keywords: Other Audience, End Users, Stimulus Presentation, EEG, Response Monitoring, Commercial License VPixx, Uncategorized Domain

  • DentalTools ( Software )

    This package provides 3Dimaging resources such as multimodal imaging volume and mesh processing or segmentation for Dental Research. DentalTools package intends to contribute to the free exchange of information and methods in the dentistry research community.

  • Diffusion MRI DKFZ Heidelberg ( Software )

    This central project points to all open-source and open-data initiatives provide by the German Cancer Research Center in the field of diffusion MRI.

  • DTI Atlas Builder ( Software )

    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 AtlasWerks
    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 the tool 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 without using the 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
    - AtlasWerks
    - dtiaverage
    - DTI-Reg
    - unu
    - MriWatcher

  • DW-MRI registration in FSL ( Software )

    This code registers linearly and non-linearly Diffusion Weighted Magnetic Resonance Images DW-MRIs by extending FLIRT linear registration of 3D scalar volumes and FNIRT non-linear registration of 3D scalar volumes in the FMRIB Software Library FSL to work with 4D volumes. The basis for registering DW-MRIs is the concept of Angular Interpolation Tao X. Miller J. V. 2006. A method forregistering diffusion weighted magnetic resonance images. In MICCAI. Vol. 9. pp. 594?602 which is implemented and extended to non-linear registration based on the FLIRT and FNIRT models in FSL.

    The code does not overwrite FLIRT FNIRT or any of the FSL C code. It is added as FLIRT4D FNIRT4D and supporting cost functions. The corresponding makefiles in FSL will however be overwritten to compile the new code without affecting any version of FSL. This code was tested with FSL 4.8 but should work with any previous or future version since it only depends on the basic FSL functionality.

  • False Discovery Rate Weighted ( Software )

    Simple and efficient this application performs the Weighted False Discovery Rate procedure of Benjamini and Hochberg 1997 to correct for multiple testing. The good think is that you can test virtually any number of p-values even millions obtained with any test-statistics for any data set. The bonus is that you can assign a-priori weights to give a better chance to those variables that you deem important. In practice this procedure is powerful only with a relatively small number of p-values.

  • Graphtools ( Software )

    Graphtools is a set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original while some are adapted or just copied from the Brain Connectivity Toolbox.

    The source code is available via git:
    git clone ssh{user}www.nitrc.orghomegroupsgraphtoolsgit

  • Group Level Imputation of Statistic Maps ( Algorithmic software suite )

    Group Level Imputation of Statistic Maps version 1.0 is a toolkit that performs multiple imputation for group level single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts bounding box acquisition parameters and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images calculate spatial neighborhood averages that help impute values perform conventional and multiple imputed t-statistics save the results to brain maps and create result tables. The toolkit contains an instruction manual pdf two Matlab scripts and one R-Statistics script which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for R.

  • ImageVis3D ( Software )

    Note ImageVis3D development is hosted elsewhere -- see httpwww.imagevis3d.org

    ImageVis3D is a new volume rendering program developed by the NIHNCRR Center for Integrative Biomedical Computing CIBC. The main design goals of ImageVis3D are simplicity scalability and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility as shown in the images. Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation the user can interactively explore terabyte sized data sets. Finally the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it such as the rendering core. This rendering core for instance is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with our collaborators.

  • Lumina LP- 400 Response System ( Software )

    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.

    Keywords: English, 6 - Mature, Response Monitoring

  • Measure Projection Toolbox MPT ( Software )

    This toolbox is an EEGLAB plugin for performing Measure Projection Analysis.

    Measure Projection Analysis MPA is a novel probabilistic multi-subject inference method that overcomes EEG Independent Component IC clustering issues by abandoning the notion of distinct IC clusters. Instead it searches voxel by voxel for brain regions having event-related IC process dynamics that exhibit statistically significant consistency across subjects andor sessions as quantified by the values of various EEG measures.

    Local-mean EEG measure values are then assigned to all such locations based on a probabilistic model of IC localization error and inter-subject anatomical and functional differences.

  • MEG Tools ( Software )

    MEG Localization using FOCUSS and MR-FOCUSS

  • MRI_CVPR ( Software )

    Tools processing MRI data with a number of techniques from cvpr conference including segmentation matching features and classification.

  • NeuroScope ( Software )

    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.

  • NFT Neuroelectromag Forward Modeling ( Software )

    Neuroelectromagnetic Forward Head Modeling Toolbox NFT httpsccn.ucsd.edunft is a MATLAB Toolbox for generating realistic head models from available data MRI andor electrode locations for computing numerical solutions for the forward problem of electromagnetic source imaging and for single dipole source localization. The NFT includes tools for segmenting scalp skull cerebrospinal fluid CSF and brain tissues from T1-weighted magnetic resonance MR images. The Boundary Element Method BEM and Finite Element Method FEM are used for the numerical solution of the forward problem. When a subject MR image is not available a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB or from the MATLAB command line. The toolbox is freely available under the GNU Public License for noncommercial use and open source development.

  • NIRAL Utilities ( Software )

    NIRAL Utilities are open-source applications developped at UNC-Chapel Hill in the Neuro Image Research and Analysis Lab NIRAL. These utilities are C based command line applications that allow image analysis and processing using ITK or VTK libraries.

    Specifically the following utilities are contained thus far:

    ImageMath - the swiss army knife image modification

    ImageStat - compute stats on images

    IntensityRescaler - rescalenormalize intensities using a prior brain tissue segmentation
    convertITKformats - convert 3D images in all ITK formats NRRD NIFTI GIPL Meta etc

    DWI_NiftiNrrdConversion - convert DWI and DTI fromto NRRD and NIFTI works with UNC DTI tools and FSL

  • Open Connectome Project ( Software )

    The Open Connectome Project OCP openconnectomeproject.org provides access to high resolution neuroanatomical images that can be used to explore connectomes. We also provide programmatic access to this data for human and machine annotation with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access so collectively we can begin to unravel connectomes.

  • ParaView ( Software )

    ParaView is an open-source multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaViews batch processing capabilities.

    ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

  • PING ( Software )

    Pediatric Imaging Neurocognition and Genetics - PING for short.
    PING represents an ambitious multi-site project involving a Coordinating Center and 4 Scientific Cores. Leading pediatric researchers across the country are participating at nine universities nation-wide UC San Diego the University of Hawaii UCLA UC Davis Kennedy Krieger Institute at Johns Hopkins Sacker Institute at Cornell University the University of Massachusetts Massachusetts General Hospital at Harvard University and Yale.

    The overarching goal of the project is to create a large MRI and genetics data resource to be shared openly with the scientific community. The data resource will also include information about the developing mental and emotional functions of the children. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined.

  • POLGUI- Matlab GUI for Polhemus Fastrak ( Software )

    "POLGUI is an interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations.

    There are 5 versions all of which work under MATLAB R14 on both linux and windows platforms
    1. polgui_ver1_r14 works with 1 receiver stylus pen
    2. polgui_ver2_r14 works with 2 receivers including the pen
    3. polgui_ver3_r14 works with 3 receiversincluding the pen
    4. polgui_ver4_r14 works with 4 receivers including the pen
    5. polgui_ver5_r14 Generic version which works with 1234 receivers WARNING Ver 5 might be buggy; not fully tested

    MATLAB R14

    Keywords: 4 - Beta, EEGMEGECoG, X11 Applications, Win32 MS Windows, End Users, BSD License, English, Other Software Resource"

  • TARQUIN MRS analysis package ( Software )

    TARQUIN is an analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies in particular brain tumours both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features

    Free to use and modify under the GPL licence.

    Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis.

    Cross platform works on Windows, Linux and OSX.

    Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters.

    Includes both GUI and command line interface for one-off and batch analyses.

  • Working Memory Trainer ( Software )

    This is a stand-alone axecutable under all main Windows OS. It is a program for training the working memory. The WM Trainer looks and behaves a little bit like a video-game and has been specifically conceived for children attending the primary school. However it can be used purposefully by people of any age including adult and elderly.

    This application features highest graphic quality a powerful adaptive engine for the difficulty level a database of users and statistical tools to evaluate the progress.

    Currently English French and Italian are supported but any language can be easily supported.

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Last updated: 2013-10-01T14:57:01.385-05:00

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