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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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AutoSeg Resource Report Resource Website 10+ mentions |
AutoSeg (RRID:SCR_009438) | AutoSeg | data processing software, software application, software resource, image analysis software | A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes. | analyze, c++, expectation minimization, image-to-image, image-to-template, labeling, linux, macos, microsoft, magnetic resonance, nonlinear warp, nrrd, posix/unix-like, region of interest, registration, resampling, segmentation, spatial transformation, spline interpolation, volumetric analysis, warping, win32 (ms windows), windows, workflow, pediatric, adolescent, adult, young |
is used by: UNC-Wisconsin Neurodevelopment Rhesus MRI Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
BSD License | nlx_155582 | SCR_009438 | 2026-08-04 09:42:22 | 23 | ||||||||
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BXH/XCEDE Tools Resource Report Resource Website 1+ mentions |
BXH/XCEDE Tools (RRID:SCR_009439) | BXH/XCEDE Tools | data processing software, software application, software resource, image analysis software | A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, 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. | analyze, c, c++, console (text based), dicom, format conversion, linux, macos, mgh/mgz, microsoft, minc, magnetic resonance, nifti, perl, posix/unix-like, quantification, sh/bash, statistical operation, unix shell, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Function BIRN |
BIRN License | nlx_155583 | SCR_009439 | 2026-08-04 09:42:23 | 4 | ||||||||
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DSI Studio Resource Report Resource Website 500+ mentions |
DSI Studio (RRID:SCR_009557) | DSI Studio | data processing software, software application, software resource, image analysis software | A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. | analyze, c++, console (text based), dicom, diffusion mr fiber tracking, diffusion spectrum, fiber tracking, image reconstruction, linux, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, q-ball, quantification, super tensor, tensor metric, tractography, visualization, win32 (ms windows), windows, coregistration, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Carnegie Mellon University; Pennsylvania; USA |
BSD License | nlx_155737 | http://www.nitrc.org/projects/dsistudio | SCR_009557 | 2026-08-04 09:42:25 | 558 | |||||||
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cmrep Resource Report Resource Website |
cmrep (RRID:SCR_009434) | cmrep | data processing software, software application, software resource, image analysis software | A set of deformable modeling algorithms for shape analysis and structure-specific normalization. Applications of cm-reps include structure-specific fMRI analysis, DTI analysis, and structural brain mor | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155535 | SCR_009434 | cm-reps, continuous medial representation | 2026-08-04 09:42:23 | 0 | ||||||||
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BrainVoyager Resource Report Resource Website 100+ mentions |
BrainVoyager (RRID:SCR_013057) | data processing software, software application, software resource, image analysis software | Commercial neuroimaging software package for multi-modal data analysis and management. It has been programmed in C++ with efficient statistical, numerical, and image processing routines. It supports parallelized basic math routines on all platforms and uses modern multi-core, multi-processor hardware for demanding computational routines. | image analysis, neuroimaging, software, multi modal data, data analysis, data management, fmri, eeg, dti, meg |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is affiliated with: Turbo-BrainVoyager is related to: BrainVoyager Brain Tutor is related to: BVQXtools is related to: NeuroElf has parent organization: Brain Innovation: Home of the BrainVoyager Product Family is parent organization of: BrainVoyager: Talairach Brain Atlas |
Commercial, License varies by geographic region | SCR_014267, nif-0000-00274 | SCR_013057 | BrainVoyager QX, Brain Voyager | 2026-08-04 09:43:07 | 180 | ||||||||
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BiofilmQuant Resource Report Resource Website |
BiofilmQuant (RRID:SCR_014088) | data processing software, software application, software resource, image analysis software | A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence (QLF) images. | image analysis software, volumetric analysis, biofilm, dental plaque, quantification, qlf image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download, Acknowledgement requested | SCR_014088 | 2026-08-04 09:43:20 | 0 | ||||||||||
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7T Structural MRI scans ATAG Resource Report Resource Website 1+ mentions |
7T Structural MRI scans ATAG (RRID:SCR_014084) | data set, atlas, data or information resource | Data sets 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. They 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. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases. | 7t mri, data set, atlas, basal ganglia, structural mri scan, brain, human brain, probabilistic atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Available for download | SCR_014084 | 2026-08-04 09:43:20 | 7 | ||||||||||
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CAWorks Resource Report Resource Website 1+ mentions |
CAWorks (RRID:SCR_014185) | data processing software, software application, software resource, image analysis software | A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit. | image analysis software, computational anatomy, shape analysis, plugin, subcortex, landmark placement |
is used by: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
NIMH 1R01 MH084803; NIBIB R01 EB008171; NIA 5U01AG033655; NCRR P41 RR015241; NIBIB R01 EB000975 |
Available to the research community | http://www.cis.jhu.edu/software/caworks/ | SCR_014185 | Computational Anatomy Works | 2026-08-04 09:43:22 | 1 | |||||||
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ERP PCA Toolkit Resource Report Resource Website 1+ mentions |
ERP PCA Toolkit (RRID:SCR_013105) | ERP PCA Toolkit | data processing software, software application, software resource, software toolkit | This Matlab toolkit is a general purpose tool for editing, visualizing, and analyzing EEG data (both Event Related Potential - ERP and spectral) whose most recent version has been downloaded over 1000 times. Its three chief highlights are: 1) an optimized automatic artifact correction function that includes ICA correction for eye blinks and saccades. 2) Extensive support for easily conducting PCA and ICA through all stages of the procedure, including inspection of reconstituted waveforms and batch ANOVAs. 3) Implementation of robust ANOVAs, including McCarthy-Wood vector test. It has a graphical user interface for point and click usage and comes with an extensive illustrated tutorial. A description of the toolkit was published in Dien (2010) in Journal of Neuroscience Methods. It relies on both internal functions as well as borrowed functions from both EEGlab and FieldTrip. | eeg, meg, electrocorticography, matlab, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License v2 | nlx_155753 | http://www.nitrc.org/projects/erppcatoolkit | SCR_013105 | 2026-08-04 09:43:08 | 5 | |||||||
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GSA-SNP Resource Report Resource Website 10+ mentions |
GSA-SNP (RRID:SCR_013109) | GSA-SNP | data processing software, software application, software resource | 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. | clinical neuroinformatics, computational neuroscience, imaging genomics, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Soongsil University; Seoul; South Korea |
PMID:20501604 | GNU General Public License v2 | nlx_155765, biotools:gsa-snp | https://bio.tools/gsa-snp | SCR_013109 | 2026-08-04 09:43:08 | 18 | ||||||
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ShapePopulationViewer Resource Report Resource Website 1+ mentions |
ShapePopulationViewer (RRID:SCR_014167) | data processing software, software application, software resource, image analysis software | Software that allows users to dynamically interact with multiple surfaces simultaneously. It is very useful for visualisation and comparison of 3D surfaces by also displaying their scalars or vectors attributes stored in the points, and allowing the user to simply modify the colormap. ShapePopulationViewer is available as an extension of 3D Slicer. | 3d surface, colormap, vector, interaction |
is used by: 3D Slicer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Available to the research community | SCR_014167 | 2026-08-04 09:43:21 | 3 | ||||||||||
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Rhesus Macaque Brain Atlases Resource Report Resource Website |
Rhesus Macaque Brain Atlases (RRID:SCR_017533) | data set, atlas, data or information resource | Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque. | Collection, atlas, data, scan, functional, structural, imaging, rhesus macaque | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | http://brainmap.wisc.edu/monkey.html | SCR_017533 | 2026-08-04 09:44:14 | 0 | |||||||||
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COBRE Resource Report Resource Website 100+ mentions |
COBRE (RRID:SCR_010482) | COBRE | data set, data or information resource | Data set of raw anatomical and functional MR data from 72 patients with Schizophrenia and 75 healthy controls (ages ranging from 18 to 65 in each group). All subjects were screened and excluded if they had: history of neurological disorder, history of mental retardation, history of severe head trauma with more than 5 minutes loss of consciousness, history of substance abuse or dependence within the last 12 months. Diagnostic information was collected using the Structured Clinical Interview used for DSM Disorders (SCID). A multi-echo MPRAGE (MEMPR) sequence was used with the following parameters: TR/TE/TI = 2530/(1.64, 3.5, 5.36, 7.22, 9.08)/900 ms, flip angle = 7��, FOV = 256x256 mm, Slab thickness = 176 mm, Matrix = 256x256x176, Voxel size =1x1x1 mm, Number of echos = 5, Pixel bandwidth =650 Hz, Total scan time = 6 min. With 5 echoes, the TR, TI and time to encode partitions for the MEMPR are similar to that of a conventional MPRAGE, resulting in similar GM/WM/CSF contrast. Rest data was collected with single-shot full k-space echo-planar imaging (EPI) with ramp sampling correction using the intercomissural line (AC-PC) as a reference (TR: 2 s, TE: 29 ms, matrix size: 64x64, 32 slices, voxel size: 3x3x4 mm3). Slice Acquisition Order: Rest scan - collected in the Axial plane - series ascending - multi slice mode - interleaved MPRAGE - collected in the Sag plane - series interleaved - multi slice mode - single shot The following data are released for every participant: * Resting fMRI * Anatomical MRI * Phenotypic data for every participant including: gender, age, handedness and diagnostic information. | resting fmri, anatomical mri, phenotype, gender, age, handedness, diagnosis, adult human, fmri, mri, neuroimaging, mental state assessment, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Mind Research Network has parent organization: 1000 Functional Connectomes Project has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Schizophrenia, Normal control, Aging | NCRR 1P20RR021938-01A2 | Creative Commons Attribution-NonCommercial License, Account required | nlx_157762 | SCR_010482 | Center for Biomedical Research Excellence, Center for Biomedical Research Excellence (COBRE) | 2026-08-04 09:42:46 | 108 | |||||
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Epilepsy T1 and Hippocampal Segmentation Datasets Resource Report Resource Website |
Epilepsy T1 and Hippocampal Segmentation Datasets (RRID:SCR_014926) | data set, data or information resource | Shared dataset which consists of skull-stripped T1 MRI images and segmented hippocampi of 163 Temporal Lobe Epilepsy (TLE) patients. The T1 and hippocampal segmentation data of TLE patients are uploaded in three separate datasets which can be accessed from the main site. | hippocampus, t1, dataset, skull stripped, mri, segmented hippocampus, epilepsy, temporal lobe epilepsy, tle | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_014926 | 2026-08-04 09:43:34 | 0 | ||||||||||
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Stark Cross-Sectional Aging Resource Report Resource Website |
Stark Cross-Sectional Aging (RRID:SCR_014171) | data set, data or information resource | Behavioral and imaging data from about 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, and structural MRI including segmentation of grey/white/CSF, of cortical regions and of hippocampal subfields. | data set, aging, hippocampus, behavioral, dti, mri, image |
uses: Neuroimaging Informatics Technology Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
NIA R01 AG034613 | Available to the research community | SCR_014171 | 2026-08-04 09:43:22 | 0 | |||||||||
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YMDTI: Diffusion Tensor Images of Healthy Young Males Resource Report Resource Website |
YMDTI: Diffusion Tensor Images of Healthy Young Males (RRID:SCR_014183) | YMDTI | data set, data or information resource | A dataset which contains diffusion tensor images of 93 healthy, young male subjects. | data set, diffusion tensor image, young male subject | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014183 | Diffusion Tensor Images of Healthy Young Males | 2026-08-04 09:43:21 | 0 | ||||||||
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iso2mesh Resource Report Resource Website 10+ mentions |
iso2mesh (RRID:SCR_013202) | iso2mesh | software application, software resource, software toolkit | A Matlab / Octave-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 scripts/programs, 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. | matlab, mesh generation, modeling, magnetic resonance, optical imaging, os independent, mri, computed tomography, octave |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155855 | http://www.nitrc.org/projects/iso2mesh | SCR_013202 | 2026-08-04 09:43:09 | 25 | |||||||
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E-Prime Resource Report Resource Website 100+ mentions |
E-Prime (RRID:SCR_009567) | E-Prime | software application, software resource | A suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime provides millisecond precision timing to ensure the accuracy of your data. E-Prime's flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime suite of applications includes: * E-Studio ? Drag and drop graphical interface for experiment design * E-Basic ? Underlying scripting language of E-Prime * E-Run ? Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection. * E-Merge ? Merges your single session data files for group analysis * E-DataAid ? Data management utility * E-Recovery ? Recovers data files | experimental control, microsoft, magnetic resonance, visual basic, win32 (ms windows), windows, windows vista, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
nlx_155747 | http://www.nitrc.org/projects/eprime | SCR_009567 | E-Prime 2.0 | 2026-08-04 09:42:24 | 162 | |||||||
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DWI/DTI Quality Control Tool: DTIPrep Resource Report Resource Website 1+ mentions |
DWI/DTI Quality Control Tool: DTIPrep (RRID:SCR_009562) | DTIPrep | software application, software resource | DTIPrep performs a Study-specific Protocol based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice-wise, interlace-wise and gradient-wise intensity and motion check, head motion and Eddy current artifact correction, and DTI computing. | c++, linux, microsoft, magnetic resonance, nrrd, posix/unix-like, win32 (ms windows), windows, windows xp, dti | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155742 | http://www.nitrc.org/projects/dtiprep | SCR_009562 | 2026-08-04 09:42:24 | 2 | |||||||
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Mach2dat Resource Report Resource Website 10+ mentions |
Mach2dat (RRID:SCR_009599) | software application, software resource | Software that performs logistic regression, using imputed SNP dosage data and adjusting for covariates. | genetic association, genomic analysis, imaging genomics, snp, gene, imputation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MACH 1.0 has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 |
Free, Non-commercial, Acknowledgement requested | nlx_155801 | http://www.nitrc.org/projects/mach2dat | SCR_009599 | Mach2dat: Association with MACH output | 2026-08-04 09:42:25 | 40 |
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