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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MultiTracer Resource Report Resource Website 10+ mentions |
MultiTracer (RRID:SCR_002445) | MultiTracer | data processing software, data visualization software, software application, software resource | A Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. It supports NIfTI-1.1 format float, double and signed and unsigned byte, short, and integer formats and provides legacy support for Analyze 7.5 8 and 16 bit images. It provides image display, editing, delineation of structure boundaries, export of traced contours and generation of masked volumes. Images are displayed in 3 orthogonal views. Time series can be displayed as averaged or contrast images and time courses can be visualized graphically. Version 2 provides enhancements to the original MultiTracer feature set. | analyze, computed tomography, image display, java, manual, magnetic resonance, nifti, os independent, pet, spect, region growing, segmentation, three dimensional display, two dimensional display, visualization, volumetric analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Los Angeles; California; USA has parent organization: Laboratory of Neuro Imaging |
PMID:12948737 | Free, Available for download, Freely available | nlx_155819 | http://www.nitrc.org/projects/multitracer2 | SCR_002445 | MultiTracer version 2 | 2026-09-03 04:45:33 | 11 | |||||
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Multi-Modal MRI Reproducibility Resource Resource Report Resource Website 10+ mentions |
Multi-Modal MRI Reproducibility Resource (RRID:SCR_002442) | Multi-Modal MRI Reproducibility Resource | data or information resource, image collection | Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047 | java image science toolkit, magnetic resonance, nifti, neuroimaging, reproducibility, mprage, flair, dti, resting state fmri, b0 field map, b1 field map, asl, vaso, quantitative t1 mapping, quantitative t2 mapping, magnetization transfer imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit |
Healthy | PMID:21094686 | Free, Available for download, Freely available | nlx_155818 | SCR_002442 | 2026-09-03 04:45:29 | 12 | ||||||
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Medical Image Visualization and Analysis Resource Report Resource Website 1+ mentions |
Medical Image Visualization and Analysis (RRID:SCR_002315) | MIVA | atlas, data or information resource, data processing software, image analysis software, software application, software resource | Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator. | magnetic resonance, fmri, graphical interface, display, segment, align, manipulate, blend, registration, alignment, region of interst, volume of interest, 3d geometry tool, 3d |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Worcester Polytechnic Institute; Massachusetts; USA |
BSD License | nlx_155664 | SCR_002315 | 2026-09-03 04:45:26 | 8 | ||||||||
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MriWatcher Resource Report Resource Website 1+ mentions |
MriWatcher (RRID:SCR_002318) | MriWatcher | data processing software, data visualization software, software application, software resource | This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. Very useful for quality control, image comparison. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155667 | SCR_002318 | 2026-09-03 04:45:25 | 2 | ||||||||
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MGDM: Multi Geometric Deformable Model Resource Report Resource Website |
MGDM: Multi Geometric Deformable Model (RRID:SCR_002311) | MGDM | data processing software, image analysis software, segmentation software, software application, software resource | An efficient level set framework for multi-object segmentation. Its representation inherently prevents overlaps and gaps and it readily preserves object topology and object relationships. MGDM is efficient, storing only a fixed number of functions for any number of objects, and therefore scales well to segmentation problems with many classes and large images. It's representation also avoids some instabilities in other multi-class level set methods. MGDM is cross-platform; MATLAB wrappers, Java source and API are provided, with MIPAV plugins forthcoming. | algorithm, reusable library, computed tomography, java, matlab, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155658 | SCR_002311 | Multi Geometric Deformable Model | 2026-09-03 04:45:25 | 0 | |||||||
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GLIRT Resource Report Resource Website |
GLIRT (RRID:SCR_002390) | GLIRT | data processing software, image analysis software, registration software, software application, software resource | Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously. | analyze, application, c++, image-to-image, intersubject, linux, microsoft, motion analysis, magnetic resonance, posix/unix-like, registration, software, spatial transformation, temporal transformation, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
Free | nlx_155763 | http://www.nitrc.org/projects/glirt | SCR_002390 | Groupwise and Longitudinal Image Registration Toolbox | 2026-09-03 04:45:24 | 0 | ||||||
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MS lesion segmentation challenge 2008 Resource Report Resource Website 1+ mentions |
MS lesion segmentation challenge 2008 (RRID:SCR_002425) | MS Lesion Segmentation 08 | data or information resource, data set, narrative resource, training material | Training material for the MS lesion segmentation challenge 2008 to compare different algorithms to segment the MS lesions from brain MRI scans. Data used for the workshop is composed of 54 brain MRI images and represents a range of patients and pathology which was acquired from Children's Hospital Boston and University of North Carolian. Data has initially been randomized into three groups: 20 training MRI images, 24 testing images for the qualifying and 8 for the onsite contest at the 2008 workshop. The downloadable online database consists now of the training images (including reference segmentations) and all the 32 combined testing images (without segmentations). The naming has not been changed in comparison to the workshop compeition in order to allow easy comparison between the workshop papers and the online database papers. One dataset has been removed (UNC_test1_Case02) due to considerable motion present only in its T2 image (without motion artifacts in T1 and FLAIR). Such a dataset unfairly penalizes methods that use T2 images versus methods that don't use the T2 image. Currently all cases have been segmented by expert raters at each institution. They have significant intersite variablility in segmentation. MS lesion MRI image data for this competition was acquired seperately by Children's Hospital Boston and University of North Carolina. UNC cases were acquired on Siemens 3T Allegra MRI scanner with slice thickness of 1mm and in-plane resolution of 0.5mm. To ease the segmentation process all data has been rigidly registered to a common reference frame and resliced to isotrophic voxel spacing using b-spline based interpolation. Pre-processed data is stored in NRRD format containing an ASCII readable header and a separate uncompressed raw image data file. This format is ITK compatible. If you want to join the competition, you can download data set from links here, and submit your segmentation results at http://www.ia.unc.edu/MSseg after registering your team. They require team name, password, and email address for future contact. Once experiment is completed, you can submit the segmentation data in a zip file format. Please refer submission page for uploading data format. | magnetic resonance, competition, challenge, segmentation, segment, ms lesion, brain, mri scan, mri, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
Multiple Sclerosis | NIH Roadmap for Medical Research ; NIBIB U54 EB005149-01 |
Free, Available for download, Freely available | nlx_155799 | SCR_002425 | 2008 MICCAI MS Lesion Segmentation Challenge | 2026-09-03 04:45:29 | 1 | |||||
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BRAINSFit Resource Report Resource Website 10+ mentions |
BRAINSFit (RRID:SCR_002340) | BRAINSFit | data processing software, image analysis software, registration software, software application, software resource | 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. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3 | affine warp, analyze, c++, console (text based), dicom, image-to-image, intermodal, intersubject, linear warp, macos, microsoft, magnetic resonance, nifti, os independent, posix/unix-like, registration, spatial transformation, warping, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155701 | http://www.nitrc.org/projects/multimodereg | SCR_002340 | 2026-09-03 04:45:30 | 20 | |||||||
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NeuroScope Resource Report Resource Website 50+ mentions |
NeuroScope (RRID:SCR_002455) | NeuroScope | data processing software, data visualization software, software application, software resource | 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. | eeg, meg, electrocorticography, behavior, neuronal spike, behavioral event, edit |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Buzsaki Lab |
PMID:16580733 | Free, Freely available | nlx_155828 | SCR_002455 | 2026-09-03 04:45:26 | 88 | |||||||
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Multicomponent T2 estimation with stimulated echo correction Resource Report Resource Website |
Multicomponent T2 estimation with stimulated echo correction (RRID:SCR_002446) | Multicomponent T2 estimation with stimulated echo correction | software resource | Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches. | algorithm, matlab, magnetic resonance, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:23629849 | Free, Available for download, Freely available | nlx_155820 | SCR_002446 | 2026-09-03 04:45:30 | 0 | |||||||
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MNI N3 Resource Report Resource Website 10+ mentions |
MNI N3 (RRID:SCR_002484) | N3 | data processing software, image processing software, software application, software resource | The perl script nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data, the method can be applied at an early stage in an automated data analysis, before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction. | magnetic resonance, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155878 | http://www.nitrc.org/projects/nu_correct | SCR_002484 | MNI N3 Software Package, MNI_N3, Non-parametric Non-uniform intensity Normalization, N3 - MINC B0 nonuniformity correction, MNI_N3 Software Package | 2026-09-03 04:45:30 | 11 | ||||||
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COGNISION Resource Report Resource Website 1+ mentions |
COGNISION (RRID:SCR_002362) | COGNISION | software resource | A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (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. 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). | eeg, eeg, meg, electrocorticography, event-related potentials, hardware, physiological recording, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | nlx_155724 | http://www.nitrc.org/projects/neuronetrix | SCR_002362 | COGNISION (TM) System | 2026-09-03 04:45:23 | 2 | ||||||
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NIDB - Neuroinformatics Database Resource Report Resource Website 1+ mentions |
NIDB - Neuroinformatics Database (RRID:SCR_002488) | NIDB | data management software, data or information resource, database, software application, software resource | Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data. | connectome file format, clinical neuroinformatics, computational neuroscience, computed tomography, imaging genomics, interfile, javascript, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:25888923 | Free, Available for download, Freely available | nlx_155882 | http://www.nitrc.org/projects/nidb | http://nidb.sourceforge.net/ | SCR_002488 | Neuroinformatics Database | 2026-09-03 04:45:32 | 2 | ||||
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iBEAT Resource Report Resource Website 10+ mentions |
iBEAT (RRID:SCR_002470) | iBEAT | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing. | atlas application, atlas data, data resource, image display, information resource, magnetic resonance, registration, segmentation, spatial transformation, visualization, warping, mri, infant, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:23055044 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155851 | http://www.nitrc.org/projects/ibeat | SCR_002470 | Infant Brain Extraction and Analysis Toolbox, LIBRA, iBEAT: Infant Brain Extraction and Analysis Toolbox | 2026-09-03 04:45:28 | 39 | |||||
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S-rep Fitting Statistics and Segmentation Resource Report Resource Website |
S-rep Fitting Statistics and Segmentation (RRID:SCR_002540) | S-rep Fitting Statistics and Segmentation | data processing software, image analysis software, segmentation software, software application, software resource | Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed. | computational neuroscience, computed tomography, domain independent, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155948 | SCR_002540 | 2026-09-03 04:45:27 | 0 | ||||||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | data analysis software, data processing software, software application, software resource | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2026-09-03 04:45:31 | 17 | ||||||
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Resource Ontology Discussion Group Resource Report Resource Website |
Resource Ontology Discussion Group (RRID:SCR_002536) | Resource Ontology Discussion Group | data or information resource, discussion, knowledge environment, narrative resource | Project to discuss, debate, develop and deploy ontological practices for the fMRI community. | community, ontology, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155943 | SCR_002536 | 2026-09-03 04:45:30 | 0 | ||||||||
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Rodent Cortical Thickness Analysis Resource Report Resource Website |
Rodent Cortical Thickness Analysis (RRID:SCR_002539) | data processing software, image analysis software, image processing software, software application, software resource | An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. 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 configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling | microscopy, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155946 | http://www.nitrc.org/projects/rodentthickness | SCR_002539 | RodentThickness | 2026-09-03 04:45:34 | 0 | |||||||
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Rodent Brain Extraction Tool Resource Report Resource Website |
Rodent Brain Extraction Tool (RRID:SCR_002538) | rBET | data processing software, image processing software, software application, software resource | A modified version of the Brain Extraction Tool (BET) that can process rodent brains. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: King's College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_155945 | http://www.nitrc.org/projects/rbet | SCR_002538 | 2026-09-03 04:45:38 | 0 | |||||||
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NPTK Resource Report Resource Website |
NPTK (RRID:SCR_002496) | NPTK | data processing software, image analysis software, registration software, software application, software resource | Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI. | analyze, artifact removal, c++, image-to-image, intermodal, linux, macos, microsoft, magnetic resonance, nifti, nonlinear warp, posix/unix-like, registration, spatial transformation, warping, windows, windows xp, fmri, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155893 | SCR_002496 | 2026-09-03 04:45:36 | 0 |
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