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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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COMPARE Resource Report Resource Website 1+ mentions |
COMPARE (RRID:SCR_000855) | COMPARE | data processing software, software application, software resource, image processing software | Generic classification tool for 3D images | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155598 | SCR_000855 | 2026-08-05 10:43:16 | 1 | ||||||||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | data processing software, software application, workflow software, software resource | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-08-05 10:43:19 | 11 | |||
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Insight Segmentation and Registration Toolkit Resource Report Resource Website 50+ mentions |
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) | ITK | data or information resource, topical portal, portal, software resource | Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk |
uses: Laplace Beltrami Filter on QuadEdge Meshes uses: VTK is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is used by: Displacement Field Viewer is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Vaa3D is related to: elastix is related to: VMTK in 3D Slicer is related to: NA-MIC Kit is related to: SimpleITK |
NIBIB EB006733; NIBIB EB008374; NIBIB EB009634; NCRR P41RR013218 |
Free, Available for download, Freely available | nif-0000-00319 | http://www.nitrc.org/projects/insighttoolkit | SCR_001149 | Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit | 2026-08-05 10:43:19 | 83 | |||||
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RT Image Resource Report Resource Website 10+ mentions |
RT Image (RRID:SCR_002535) | RT_Image | software application, software resource | Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data. | computed tomography, magnetic resonance, optical imaging, pet, spect, mri, dicom |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford University School of Medicine; California; USA |
PMID:17375973 | Free, Available for download, Freely available | nlx_155940 | http://www.nitrc.org/projects/rt_image | SCR_002535 | 2026-08-04 09:40:40 | 10 | ||||||
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XCEDE Schema Resource Report Resource Website 1+ mentions |
XCEDE Schema (RRID:SCR_002571) | XCEDE | software application, software resource, data management software | Data management software that provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels: a complete project, studies within a project, subjects involved in the studies, visits for each of the subjects, the full description of the subject's participation during each visit. | computed tomography, eeg, meg, electrocorticography, magnetic resonance, pet, spect, schema, metadata, neuroimaging, clinical neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Imaging Database |
PMID:21479735 | Free, Available for download, Freely available | nlx_155974 | http://www.xcede.org/XCEDE.html, http://www.nitrc.org/projects/qa_procedure, http://www.nitrc.org/projects/xcede | SCR_002571 | XML-Based Clinical Experiment Data Exchange Schema | 2026-08-04 09:40:41 | 2 | |||||
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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 application, software resource | 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 | 2026-08-04 09:40:07 | 0 | |||||||
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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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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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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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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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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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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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JIST: Java Image Science Toolkit Resource Report Resource Website 10+ mentions |
JIST: Java Image Science Toolkit (RRID:SCR_008887) | JIST | data processing software, software application, software resource | A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University). | experimental control, modeling, quantification, segmentation, shape analysis, spatial transformation, workflow, macos, windows, os independent, bsd, linux, sunos/solaris, java, afni brik, analyze, cor, dicom, gifti, mgh/mgz, minc, minc2, nifti-1, nrrd, philips par/rec, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Maps4Mipav (Exploratory JIST) is related to: MR Connectome Automated Pipeline is related to: Multi-Modal MRI Reproducibility Resource is related to: TOADS-CRUISE Brain Segmentation Tools is related to: CBS High-Res Brain Processing Tools is related to: JHU Proj. in Applied Medical Imaging is related to: DOTS WM tract segmentation has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Vanderbilt University; Tennessee; USA |
NINDS 5R01NS037747; NINDS 1R01NS056307; NIA N01-AG-4-0012 |
PMID:20077162 | GNU Lesser General Public License | nlx_151344 | https://sources.debian.org/src/jist/ | SCR_008887 | Java Image Science Toolkit | 2026-08-04 09:42:16 | 20 | ||||
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EPILAB Resource Report Resource Website 1+ mentions |
EPILAB (RRID:SCR_009573) | EPILAB | data processing software, software application, software resource | A Matlab-based software package developed for supporting researchers in performing studies on the prediction of epileptic seizures. It provides an intuitive and convenient graphical user interface. Fundamental concepts that are crucial for epileptic seizure prediction studies were implemented.This includes, for example, the development and statistical validation of prediction methodologies in long-term continuous recordings. Seizure prediction is usually based on electroencephalography (EEG) and electrocardiography (ECG) signals. EPILAB is able to process both EEG and ECG data stored in different formats. More than 35 time and frequency domain measures (features) can be extracted based on univariate and multivariate data analysis. These features can be post-processed and used for prediction purposes. The predictions may be conducted based on optimized thresholds or by applying classifications methods such as artificial neural networks, cellular neuronal networks, and support vector machines. | eeg, meg, electrocorticography, seizure, prediction |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Coimbra; Coimbra; Portugal |
Epilepsy | PMID:21763347 | GNU General Public License | nlx_155752 | http://www.nitrc.org/projects/epilab | SCR_009573 | EPILAB Software | 2026-08-04 09:42:24 | 3 | ||||
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ImageVis3D Resource Report Resource Website 10+ mentions |
ImageVis3D (RRID:SCR_009566) | ImageVis3D | data processing software, software application, software resource | A new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core, for instance, is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with their collaborators. | magnetic resonance, rendering |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: University of Utah; Utah; USA |
NCRR P41-RR12553-15; DOE DEFC0206ER25781 |
Free, Available for download, Freely available | nlx_155776 | http://www.nitrc.org/projects/imagevis3d, https://sources.debian.org/src/imagevis3d/ | SCR_009566 | 2026-08-04 09:42:24 | 10 | ||||||
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Draw3D and Meshinator Resource Report Resource Website |
Draw3D and Meshinator (RRID:SCR_009444) | Draw3D and Meshinator | data processing software, software application, software resource | Draw3D is a 3D rendering tool written entirely in VTK-TCL script. It is intended for fast command line rendering and visual inspection of datasets commonly found in medical imaging. It also allows the generation of images for reports or videos. As it is based on pure VTK, it can render whatever VTK can render, and runs wherever VTK can run. Meshinator is a simpler tool that uses VTKs isosurface functions to generate meshes from volumetric data. Please see the wiki for documentation | magnetic resonance, tcl/tk, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Apache License, v2 | nlx_155615 | SCR_009444 | 2026-08-04 09:42:22 | 0 | ||||||||
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NICE-SIGN Resource Report Resource Website |
NICE-SIGN (RRID:SCR_009629) | NICE-SIGN | data processing software, software application, software resource | A nice sign of bias field correction (nonuniformity) in medical images. This tool is fast and efficient. Technical details can be found at http://zheng.vision.googlepages.com/biasCorrection_miccai09_Zheng.pdf | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
nlx_155881 | SCR_009629 | 2026-08-04 09:42:26 | 0 |
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