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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Parallel Stochastic Ion Channel Simulator Resource Report Resource Website 1+ mentions |
Parallel Stochastic Ion Channel Simulator (RRID:SCR_014159) | PSICS | simulation software, software resource, software application | Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools. | simulation software, ion channel, dendritic membrane, axonal membrane, neuronal behavior, stochastic simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Edinburgh; Scotland; United Kingdom |
BBSRC | Public, Free | http://www.psics.org | SCR_014159 | 2026-08-12 10:50:54 | 1 | |||||||
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Longitudinal MS Lesion Imaging Archive Resource Report Resource Website |
Longitudinal MS Lesion Imaging Archive (RRID:SCR_014136) | data or information resource, data set, image collection | The Longitudinal MS Lesion Imaging Archive provides Training data consisting of longitudinal images from five patients and Testing data consisting of 15 patients. Each longitudinal dataset includes T1-weighted, T2-weighted, PD-weighted, and T2-weighted FLAIR MRI with 3-5 time points acquired on a 3T MR scanner. T1-weighted images have approximately a 1mm cubic voxel resolution, while the other scans are 1mm in plane with 3mm sections. Accounting for the multiple time points, this constitutes approximately 80 individual data sets. The Training data contains manual segmentations of the MS lesions from two different raters for each of the time points provided. | data set, image collection, longitudinal image, t1 weighted, t2 weighted |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
http://www.iacl.ece.jhu.edu/MSChallenge | SCR_014136 | Longitudinal MS Lesion Segmentation Challenge | 2026-08-12 10:50:57 | 0 | |||||||||
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SOCK Resource Report Resource Website 1+ mentions |
SOCK (RRID:SCR_002544) | SOCK | data processing software, software resource, software application | 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 | 2026-08-12 10:48:37 | 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 resource, software application | 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 | 2026-08-12 10:48:30 | 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, image analysis software, software resource, software application | 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 | 2026-08-12 10:48:28 | 2 | |||||
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Connectir Resource Report Resource Website 1+ mentions |
Connectir (RRID:SCR_000863) | Connectir | data processing software, image analysis software, software resource, software application | An R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies (CWAS) using functional connectivity. | console (text based), magnetic resonance, r, connectivity, brain, connectome-wide association study, functional connectivity | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155729 | http://www.nitrc.org/projects/connectir | SCR_000863 | 2026-08-12 10:48:18 | 1 | |||||||
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Net Station API Resource Report Resource Website |
Net Station API (RRID:SCR_000867) | Net Station API | application programming interface, commercial organization, data access protocol, software resource | APIs for Net Station data files. APIs are available for C++, C#, and Java. | eeg, meg, electrocorticography, c++, java, visualization, analysis, presentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Net Station EEG Software |
Free, Available for download, Freely available | nlx_155824 | http://www.nitrc.org/projects/netstation_api | SCR_000867 | Net Station Software for EEG Acquisition and Physician and Review | 2026-08-12 10:48:18 | 0 | ||||||
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Quantitative Diffusion Tools Resource Report Resource Website |
Quantitative Diffusion Tools (RRID:SCR_002527) | Quantitative Diffusion Tools | data processing software, software resource, software application | 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 | 2026-08-12 10:48:37 | 0 | ||||||||
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HBM Hackathon Resource Report Resource Website 1+ mentions |
HBM Hackathon (RRID:SCR_014119) | meeting resource, training resource | A multi-day event hosted by the Organization for Human Brain Mapping which features collaborative and open neuroscience projects in data analysis and methods development. Locations change annually. | conference, human brain, meeting resource |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: brainhack.org |
Open to the neuroscience community (though a fee is required to attend) | http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3281, http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=1 | SCR_014119 | OHBM Annual Meeting | 2026-08-12 10:50:53 | 6 | ||||||||
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MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | data processing software, image analysis software, software resource, software application | 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 | 2026-08-12 10:48:35 | 126 | ||||||
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International Imaging Genetics Conference Resource Report Resource Website |
International Imaging Genetics Conference (RRID:SCR_014125) | meeting resource, training resource | An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics. This annual conference features presentations from investigators world-wide and places emphasis on facilitating in-depth discussions among the participants and presenters. | meeting resource, symposium, international, imaging genetics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
http://www.imaginggenetics.uci.edu | SCR_014125 | 2026-08-12 10:50:57 | 0 | ||||||||||
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Convert MNI coordinates to or from XYZ Resource Report Resource Website |
Convert MNI coordinates to or from XYZ (RRID:SCR_000406) | Convert MNI coordinates to or from XYZ | data processing software, software resource, software application | Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NINDS K23NS083741; Stiftung Charité ; Berlin Institute of Health ; Prof. Klaus Thiemann Foundation ; German Research Agency |
Free, Available for download, Freely available | nlx_155600 | SCR_000406 | 2026-08-12 10:48:13 | 0 | |||||||
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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 resource, software application | 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 | 2026-08-12 10:48:37 | 1 | |||||||
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Cluster reporter Resource Report Resource Website |
Cluster reporter (RRID:SCR_002218) | Cluster reporter | data processing software, software resource, software application | 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 | 2026-08-12 10:48:33 | 0 | ||||||||
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WFU Pipeline Resource Report Resource Website |
WFU Pipeline (RRID:SCR_002614) | WFU_Pipeline | data processing software, software resource, software application | 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 | 2026-08-12 10:48:38 | 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, image analysis software, software resource, software application | 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 | 2026-08-12 10:48:38 | 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, image analysis software, software resource, software application | 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 | 2026-08-12 10:48:34 | 0 | |||||
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3DSlicerLupusLesionModule Resource Report Resource Website |
3DSlicerLupusLesionModule (RRID:SCR_000853) | 3DSlicerLupusLesionModule | data processing software, software resource, software application | 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 | 2026-08-12 10:48:17 | 0 | ||||||||
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Cluster Extent Correction Resource Report Resource Website |
Cluster Extent Correction (RRID:SCR_002226) | Cluster Extent Correction | data processing software, software resource, software application | 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 | 2026-08-12 10:48:33 | 0 | ||||||||
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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 resource, software application | 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 | 2026-08-12 10:49:31 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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