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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Vervet Probabilistic Atlas Resource Report Resource Website |
Vervet Probabilistic Atlas (RRID:SCR_000426) | Vervet Probabilistic Atlas | reference atlas, atlas, data or information resource | Vervet (Chlorocebus aethiops sabaeus) probabilistic atlas that 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 Biased directory contains the average template and probabilistic atlases for selected tissue classes constructed by registering the training population to one subject. The Unbiased 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. | atlas data, magnetic resonance, adult, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Normal | Free, Available for download, Freely available | nlx_156015 | SCR_000426 | 2026-08-04 09:40:07 | 0 | |||||||
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MPScope Resource Report Resource Website 10+ mentions |
MPScope (RRID:SCR_000065) | MPScope | software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, analysis program MPView and several software utilities. | custom built multiphoton microscopes suite, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at San Diego; California; USA |
PMID:16621010 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155796 | http://www.nitrc.org/projects/mpscope | SCR_000065 | 2026-08-04 09:40:03 | 10 | ||||||
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3DSlicerLupusLesionModule Resource Report Resource Website |
3DSlicerLupusLesionModule (RRID:SCR_000853) | 3DSlicerLupusLesionModule | data processing software, software application, software resource | Slicer3 module to provide a capability for performing white matter lesion classification and summary. | clinical neuroinformatics, magnetic resonance |
is used by: 3D Slicer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: INCF Software Center |
Free, Available for download, Freely available | nlx_155579 | SCR_000853 | 2026-08-04 09:40:15 | 0 | ||||||||
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Center for Computational Biology at UCLA Resource Report Resource Website |
Center for Computational Biology at UCLA (RRID:SCR_000334) | CCB, UCLA CCB, USC CCB | portal, organization portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. This area has a long tradition of sophisticated mathematical and computational techniques. Nevertheless, new developments in related areas of mathematics and computational science have emerged in recent years, some from related application areas such as Computer Graphics, Computer Vision, and Image Processing, as well as from Computational Mathematics and the Computational Sciences. We are confident that many of these ideas can be applied beneficially to neuroimaging. | functional, genetic, biological system, brain, clinical, computational, computational mathematic, disease, health, image processing, physiological, population, structural, neuroimaging, computational neuroscience, imaging genomics, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NCRR U54 RR021813 | PMID:22081221 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10492 | http://ccb.loni.ucla.edu/ | http://www.nitrc.org/projects/ccb, http://cms.loni.ucla.edu/CCB/ | SCR_000334 | CCB at UCLA, Center for Computational Biology | 2026-08-04 09:40:06 | 0 | |||
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SOCK Resource Report Resource Website 1+ mentions |
SOCK (RRID:SCR_002544) | SOCK | data processing software, software application, software resource | 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. | matlab, magnetic resonance, independent component analysis, fmri, artifact, automated classification, automatic, independent component labeling, resting-state fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Brain Research Institute |
National Health and MRC of Australia project grant 368650; National Health and MRC of Australia project grant 318900; National Health and MRC of Australia project grant 628952; National Health and MRC of Australia practitioner fellowship 527800; Austin Hospital Medical Research Foundation ; State Government of Victoria Australia ; Operational Infrastructure Support Program |
PMID:23847511 | Free, Available for download, Freely available | nlx_155951 | SCR_002544 | Spatially Organized Component Klassifikator | 2026-08-04 09:40:41 | 2 | |||||
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Hierarchical Attribute Matching Mechanism for Elastic Registration Resource Report Resource Website 50+ mentions |
Hierarchical Attribute Matching Mechanism for Elastic Registration (RRID:SCR_001960) | HAMMER | data processing software, software application, software resource | Software package that 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. In order to make HAMMER as robust as possible to different acquisition protocols and conditions, they provide a distribution that assumes that images have been skull-stripped and segmented into gray matter, white matter, and ventricular CSF. We have other software tools that can perform these steps, including skull stripping, reorientation and reslicing, and segmentation tools. Importantly, they use 250 for WM, 150 for GM, 50 for Ventricles and 10 for CSF in the tissue-segmented brain images. Current modules used for group analysis: Labeling subject brain using a manually-labeled brain Model; Generating RAVENS map for each tissue (WM, GM, VN); Normalizing subject brain images | magnetic resonance, software package, data processing, high dimensional warping |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
PMID:12575879 PMID:12507441 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00310 | http://www.nitrc.org/projects/hammerwml | SCR_001960 | HAMMER: Deformable Registration | 2026-08-04 09:40:31 | 50 | |||||
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FMRISTAT - A general statistical analysis for fMRI data Resource Report Resource Website 1+ mentions |
FMRISTAT - A general statistical analysis for fMRI data (RRID:SCR_001830) | FMRISTAT | data processing software, software application, software resource, image analysis software | A Matlab toolbox for the statistical analysis of fMRI data. The fMRI data was first converted to percentage of whole volume. The statistical analysis of the percentages was based on a linear model with correlated errors. The design matrix of the linear model was first convolved with a hemodynamic response function modelled as a difference of two gamma functions timed to coincide with the acquisition of each slice. Temporal drift was removed by adding a cubic spline in the frame times to the design matrix (one covariate per 2 minutes of scan time), and spatial drift was removed by adding a covariate in the whole volume average. The correlation structure was modelled as an autoregressive process of degree 1. At each voxel, the autocorrelation parameter was estimated from the least squares residuals using the Yule-Walker equations, after a bias correction for correlations induced by the linear model. The autocorrelation parameter was first regularized by spatial smoothing, then used to "whiten" the data and the design matrix. The linear model was then re-estimated using least squares on the whitened data to produce estimates of effects and their standard errors. In a second step, runs, sessions and subjects were combined using a mixed effects linear model for the effects (as data) with fixed effects standard deviations taken from the previous analysis. This was fitted using ReML implemented by the EM algorithm. A random effects analysis was performed by first estimating the the ratio of the random effects variance to the fixed effects variance, then regularizing this ratio by spatial smoothing with a Gaussian filter. The variance of the effect was then estimated by the smoothed ratio multiplied by the fixed effects variance. The amount of smoothing was chosen to achieve 100 effective degrees of freedom. The resulting T statistic images were thresholded using the minimum given by a Bonferroni correction and random field theory, taking into account the non-isotropic spatial correlation of the errors. | fmri, pet, statistical analysis, afni brik, analyze, console (text based), linear, matlab, minc, modeling, magnetic resonance, nifti, os independent, principal component analysis, regression, statistical operation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
PMID:11771969 | Free, Available for download, Freely available | nif-0000-00303 | http://www.nitrc.org/projects/fmristat | http://www.bic.mni.mcgill.ca/users/keith/ | SCR_001830 | 2026-08-04 09:40:29 | 2 | |||||
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Quantitative Diffusion Tools Resource Report Resource Website |
Quantitative Diffusion Tools (RRID:SCR_002527) | Quantitative Diffusion Tools | data processing software, software application, software resource | Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts, summarizing measures over tract clusters, etc. | c++, magnetic resonance, os independent, quantification, segmentation, tractography | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155933 | SCR_002527 | 2026-08-04 09:40:40 | 0 | ||||||||
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MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | data processing software, software application, software resource, image analysis software | A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. | reusable library, c, file format, fortran, information specification, minc, minc2, magnetic resonance, os independent, perl, sh/bash, unix shell |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite is related to: MINC Example files is related to: Extensible MATLAB Medical image Analysis has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155794 | http://www.nitrc.org/projects/minc | SCR_002391 | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2026-08-04 09:40:39 | 122 | ||||||
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3D Interactive Chemical Shift Imaging Resource Report Resource Website 1+ mentions |
3D Interactive Chemical Shift Imaging (RRID:SCR_002581) | 3DiCSI | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis. | c++, dicom, microsoft, magnetic resonance, quantification, spatial transformation, statistical operation, temporal transformation, visualization, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Columbia University; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155986 | SCR_002581 | 3D Chemical Shift Imaging | 2026-08-04 09:40:41 | 1 | |||||||
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Cluster reporter Resource Report Resource Website |
Cluster reporter (RRID:SCR_002218) | Cluster reporter | data processing software, software application, software resource | This matlab script and associated files will take resultant statistical images and essentially output everything you could ever want to know. It can work off of images that were previously corrected for multiple comparisons, but it can actually do the correction itself. This is because the cluster_correct script is incorporated within. It will iterate through atlases (borrowed from other software) to tell you the location of significant results. It outputs an extremely detailed report as well as a summary table for quick investigation. In addition, it will output statistics for each surviving cluster, and the image as a whole. Feedback would be much appreciated. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155532 | SCR_002218 | 2026-08-04 09:40:35 | 0 | ||||||||
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WFU Pipeline Resource Report Resource Website |
WFU Pipeline (RRID:SCR_002614) | WFU_Pipeline | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. A fully automated software application for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer, archiving, real-time SPM5 batch script generation with distributed grid processing, automated error-recovery procedures, full data-provenance, email notifications, optional conversion back to DICOM (Digital Imaging and Communications in Medicine), and picture archiving and communications systems (PACS) insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition. Requirements: * MATLAB 7.3 or greater with the Image Processing Toolbox * SPM5 | analyze, c++, dicom, linux, matlab, magnetic resonance, nifti, posix/unix-like, unix shell, workflow, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Wake Forest School of Medicine; North Carolina; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156017 | http://www.nitrc.org/projects/wfu_pipeline | SCR_002614 | WFU SPM5 Pipeline | 2026-08-04 09:40:41 | 0 | ||||||
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ValMap: simple statistical mapping tool Resource Report Resource Website 1+ mentions |
ValMap: simple statistical mapping tool (RRID:SCR_002610) | ValMap | data processing software, software application, software resource, image analysis software | A command line voxel-wise statistical analysis software program for images. Images can be gray matter density, jacobian images, etc. The linear model is implemented, i.e. designs that can be modeled as Y=AB, where Y is a vector or matrix of dependent variables, B is a vector or matrix of parameters to be estimated, and A is a design matrix. Why use valmap? # Do not need a Matlab license to run. # Can incorporate a spatially varying independent variable (e.g., you have a perfusion map as your dependent variable, and you want to co-vary for gray matter at each voxel, so use a gray matter map as an independent variable). # Can use spatially invariant independent variables (e.g., you can have a cognitive test score as the dependent variable, and use jacobian maps as the independent variable). # Can have multiple dependent variables and do multivariate analyses (e.g., want to know the overall effect of disease on perfusion and structure, so use perfusion maps and jacobian maps as dependent variables). | analyze, c, c++, java, linear, linux, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, regression, statistical operation, win32 (ms windows), windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free, Available for download, Freely available | nlx_156013 | SCR_002610 | 2026-08-04 09:40:41 | 2 | ||||||||
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Functional Regression Analysis of DTI Tract Statistics Resource Report Resource Website |
Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) | FRATS | data processing software, software application, software resource, image analysis software | Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. | computational neuroscience, imaging genomics, magnetic resonance, regression analysis, dti, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NSF BCS-08-26844; NCRR UL1-RR025747-01; NIMH MH086633; NIA AG033387; NIMH MH064065; NICHD HD053000; NIMH MH070890; NINDS R01NS055754; NIBIB U54 EB005149-01 |
PMID:20335089 | Academic Free License | nlx_155629 | SCR_002293 | Functional Regression Analysis of DTI | 2026-08-04 09:40:37 | 0 | |||||
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DTI-TEMPLATE-RHESUS-MACAQUES Resource Report Resource Website 1+ mentions |
DTI-TEMPLATE-RHESUS-MACAQUES (RRID:SCR_002482) | DTI-TEMPLATE-RHESUS-MACAQUES | reference atlas, atlas, data or information resource | A population-specific DTI template for young adolescent Rhesus Macaque (Macaca mulatta) monkeys using 271 high-quality scans. Using such a large number of animals in generating a template allows it to account for variability in the species. Their DTI template is based on the largest number of animals ever used in generating a computational brain template. It is anticipated that their DTI template will help facilitate voxel-based and tract specific WM analyses in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution. | magnetic resonance, dti, young, adolescent, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NIMH MH62015; NIMH MH084051; NIMH MH080826; NIMH MH46729; NIMH MH81884; NIMH MH018931; NIBIB R03-EB009321 |
PMID:21803162 | Free, Available for download, Freely available | nlx_155872 | SCR_002482 | 2026-08-04 09:40:39 | 3 | ||||||
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Cluster Extent Correction Resource Report Resource Website |
Cluster Extent Correction (RRID:SCR_002226) | Cluster Extent Correction | data processing software, software application, software resource | This script will take any .img file and correct it based on a cluster extent, cluster definition and voxelwise threshold. The threshold entered will be applied to positive and negative values separately, and separate pos and neg corrected images will be output. This script requires a license for the matlab image processing toolbox. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155531 | SCR_002226 | 2026-08-04 09:40:36 | 0 | ||||||||
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Knowing what you know (kwyk) - Bayesian Brain Parcellation Resource Report Resource Website |
Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) | kwyk | segmentation software, data processing software, software resource, software application, image analysis software | Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation. | Deep, neural, network, prediction, FreeSurfer, segmentation, structural, MRI, volume, brain, parcellation, uncertainty, estimation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | https://github.com/neuronets/kwyk | SCR_017470 | knowing what you know | 2026-08-04 09:44:10 | 0 | |||||||
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MonkeyCBP Resource Report Resource Website 1+ mentions |
MonkeyCBP (RRID:SCR_017640) | MonkeyCBP | software toolkit, software resource, algorithm resource | Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community. | MonkeyCBP, Atlas, Parcellation Atlas, neuroimaging pipeline, brain, | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | SCR_017675 | http://www.nitrc.org/projects/monkey-cbp/ | SCR_017640 | Monkey Connectivity Based Parcellation; MonkeyCBP: A toolbox for connectivity-based parcellation of monkey brain | 2026-08-04 09:44:12 | 1 | ||||||
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McConnell Brain Imaging Center MNI Macaque Atlas Resource Report Resource Website 1+ mentions |
McConnell Brain Imaging Center MNI Macaque Atlas (RRID:SCR_005265) | reference atlas, atlas, data or information resource | A reference atlas of standard macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual macaque monkeys and studies. We have used MRI volumes from a group of 25 normal adult macaque monkeys (18 Macaca fascicularis, 7 Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous macaque brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the MNI macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format. | macaque, brain, early adult, template, atlas application, minc, minc2, magnetic resonance, nifti, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McConnell Brain Imaging Center |
PMID:21256229 | Free | nlx_144292 | http://www.nitrc.org/projects/mniatlas | SCR_005265 | MNI Macaque Atlas, BIC MNI Macaque Atlas | 2026-08-04 09:41:19 | 2 | ||||||
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MeshValmet: Validation Metric for Meshes Resource Report Resource Website |
MeshValmet: Validation Metric for Meshes (RRID:SCR_006622) | MeshValmet | data processing software, software application, software resource | A tool that measures surface to surface distance between two triangle meshes using user-specified uniform sampling. Thus, users can choose finer sampling level to calculate errors to gain more accuracy in theerror space, or sparser sampling to gain speed and get an approximate feeling of error distribution between boundaries. Besides its pleasant visualization using the VTK library, MeshValmet also provides useful histogram and statistical information based on the sample errors, such as mean and median distance, root mean square distance, mean square distance, mean absolute distance, Hausdorff distance, 95 percentile, 68 percentile, etc. MeshValmet is based on the work of Nicolas Aspert, etc.: MESH: Measuring Errors between Surfaces using the Hausdorff distance in the proceedings of the IEEE Int. Conf. on Multimedia and Expo 2002 (ICME), vol. I, pp. 705-708. The calculation of the Dice's Coefficient is calculated by Joshua Stough using the concept of a Riemannian sum. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155811 | http://www.nitrc.org/projects/meshvalmet | SCR_006622 | 2026-08-04 09:41:40 | 0 |
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