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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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DTIProcess ToolKit Resource Report Resource Website |
DTIProcess ToolKit (RRID:SCR_009561) | DTIProcess | data processing software, software resource, software application, image processing software, image analysis software, software toolkit | A DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess, et al.. | c++, console (text based), macos, microsoft, modeling, magnetic resonance, nrrd, posix/unix-like, resampling, spatial transformation, tensor metric, tractography, windows, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of Utah; Utah; USA works with: NIAG Addiction Data |
BSD License | nlx_155741 | http://www.nitrc.org/projects/dtiprocess | SCR_009561 | 2026-08-04 09:42:24 | 0 | |||||||
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Framework for Open Programmatic Access Resource Report Resource Website |
Framework for Open Programmatic Access (RRID:SCR_009479) | FOPA | narrative resource, standard specification, data or information resource | A standardized framework for communication and data exchange between medical imaging applications, with particular focus on neuroimaging technologies. FOPA is an attempt to design and implement a common protocol for network and command line communication with either file-system or imbedded data structures. Initial reference implementations will support interoperability between ITK, VTK, and Java platforms. Contributions are welcome from other neuroimaging development communities. | computed tomography, magnetic resonance, pet, spect, neuroimaging, interoperability | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License, The community can contribute to this resource | nlx_155626 | SCR_009479 | 2026-08-04 09:42:23 | 0 | ||||||||
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Non-rigid groupwise registration method Resource Report Resource Website |
Non-rigid groupwise registration method (RRID:SCR_009512) | Non-rigid groupwise registration method | data processing software, registration software, software resource, software application, image analysis software | An open source implementation of a non-rigid groupwise registration method. This project is implemented by Serdar K Balci (serdar at csail.mit.edu) and supervised by Polina Golland and William M. Wells All metrics are implementing in a multi-threaded fashion. The algorithm will run faster on computers with multiple CPU''s. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
nlx_155674 | SCR_009512 | 2026-08-04 09:42:23 | 0 | |||||||||
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NITRC Books Resource Report Resource Website |
NITRC Books (RRID:SCR_009510) | NITRC Books | narrative resource, book, data or information resource, bibliography | Bibliography of books related to neuroscience addressing the topic of functional and structural neuroimaging. | fmri, cognitive neuroscience, atlas, image analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
nlx_155671 | SCR_009510 | 2026-08-04 09:42:24 | 0 | |||||||||
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Epsilon Radial Networks Resource Report Resource Website |
Epsilon Radial Networks (RRID:SCR_009470) | ERNs | data processing software, software resource, software application, image processing software, image analysis software | An efficient framework for building and analyzing graphs called epsilon radial networks (ERNs) using tractography data in a normalized space. Currently there is no agreed-upon method for constructing the brain anatomical connectivity graphs out of large number of white matter tracts. The key challenge in defining brain networks is node delineation and their method defines nodes in the graph using tract-end points clustered in a sphere of a given radius (epsilon). Using a kd-tree based search algorithm they can identify the nodes computationally efficiently and in a fully automatic way. These networks can be used not only to analyze topo-physical properties of the structural brain networks but also to perform classical region-of-interest (ROI) analyses in a very efficient way. Thus ERNs can be used as a novel image processing lens for statistical and machine learning based analyses. | magnetic resonance, connectivity, white matter tract | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | DTI-TK license, Http://www.nitrc.org/include/glossary.php#540 | nlx_155617 | SCR_009470 | 2026-08-04 09:42:24 | 0 | ||||||||
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LIBEEP Resource Report Resource Website 1+ mentions |
LIBEEP (RRID:SCR_009591) | LIBEEP | software toolkit, software resource, software library | Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions. | eeg, meg, electrocorticography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Libeep EEGLAB plugin has parent organization: SourceForge |
GNU Lesser General Public License, Plus Addendum | nlx_155781 | http://www.nitrc.org/projects/libeep | SCR_009591 | LIBEEP library | 2026-08-04 09:42:24 | 1 | ||||||
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Local Label Learning Segmentation Resource Report Resource Website 1+ mentions |
Local Label Learning Segmentation (RRID:SCR_009504) | LLL Segmentation | segmentation software, data processing software, software resource, software application, image analysis software | Software using a novel local label learning strategy to estimate the target image?s segmentation label using statistical machine learning techniques. They used a support vector machine (SVM) with a K nearest neighbor (KNN) based training sample selection strategy to learn a classifier for each of the target image voxel based on a training dataset consisting of its neighboring voxels in the atlases. Validation experiments on hippocampus segmentation of 117 MR images demonstrated that the method can produce segmentation results consistently better than state-of-the-art label fusion methods. | magnetic resonance, svm, segmentation, local label learning, multi-atlas based segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24151008 | BSD License | nlx_155653 | SCR_009504 | Local Label Learning (LLL) Segmentation | 2026-08-04 09:42:23 | 1 | ||||||
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Landman NeuroImaging Tools Resource Report Resource Website |
Landman NeuroImaging Tools (RRID:SCR_009503) | Landman NeuroImaging Tools | data processing software, software resource, software repository, software application, image analysis software | Project to provide long-term hosting and release for small tools related to medical image analysis. Source repository contains highly experimental code intended for collaborative development. However, any interested parties are welcome to browse/reuse code. Stable/evolved projects will be moved to independent projects. | application, java, matlab, magnetic resonance, statistical operation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155650 | SCR_009503 | 2026-08-04 09:42:24 | 0 | ||||||||
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JIST Resources for Algorithm Development Resource Report Resource Website |
JIST Resources for Algorithm Development (RRID:SCR_009500) | JIST Resources for Algorithm Development | software resource, software repository, training material, narrative resource, data or information resource | This repository stores plugins, tutorial code, and examples demonstrating MRI manipulation within the MIPAV plugin environment. This project is separate from JIST so that we can provide WRITE access to any interested party without overly exposing the infrastructure to unplanned modification. Please contact the administrators if you would like to join this project - open use is encouraged. | afni brik, analyze, bshort/bfloat, cor, dicom, gifti, java, loni pipeline, macos, mgh/mgz, microsoft, minc, minc2, magnetic resonance, nifti, no input/output (daemon), nrrd, development environment, posix/unix-like, win32 (ms windows), mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center is related to: MIPAV: Medical Image Processing and Visualization |
GNU Lesser General Public License | nlx_155648 | SCR_009500 | 2026-08-04 09:42:23 | 0 | ||||||||
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Diffusion MRI at DKFZ Heidelberg Resource Report Resource Website |
Diffusion MRI at DKFZ Heidelberg (RRID:SCR_009465) | Diffusion MRI at DKFZ Heidelberg | topical portal, portal, data or information resource | This central project points to all open-source and open-data initiatives provided by the German Cancer Research Center in the field of diffusion MRI. | magnetic resonance, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: German Cancer Research Center |
BSD/MIT-Style Open unspecified license License | nlx_155612 | SCR_009465 | 2026-08-04 09:42:23 | 0 | ||||||||
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Diffusion Warp Resource Report Resource Website |
Diffusion Warp (RRID:SCR_009466) | Diffusion Warp | data processing software, alignment software, registration software, software resource, software application, image analysis software | Software tools appropriate for the registration of diffusion tensor images to an average coordinate system. The tools include image registration methods and algorithms for the correct alignment of the diffusion tensor when applying the resulting transformation. The program uses the Slicer3 execution model framework to define the command line arguments, and can be fully integrated using the module discovery capabilities of Slicer3. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155613 | SCR_009466 | 2026-08-04 09:42:24 | 0 | |||||||||
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BrainMask Volume Processing Tool Resource Report Resource Website |
BrainMask Volume Processing Tool (RRID:SCR_009538) | BrainMask | segmentation software, data processing software, software resource, software application, image analysis software, data visualization software | Segmentation of the brain from three-dimensional MR images is a crucial pre-processing step in morphological and volumetric brain studies. BrainMask implements a fully automatic brain segmentation algorithm that uses advanced thresholding with morphology and 3D edge detection algorithms. BrainMask demonstrates high segmentation accuracy. For a representative 26 datasets, the segmentation error averaged 3.4% ������ 1.3% (Mikheev A et al. J Magn Reson Imag 27(6):1235-41;2008). BrainMask includes NNN - a tool based on the algorithm developed by John Sled for correcting the intensity non-uniformity in MR data (Sled JG et al. IEEE Trans Med Imag 17(1):87-97;1998). BrainMask also includes a versatile DICOM wiewer and allows to selectively load and organize DICOM images into 3D and 4D datasets. | analyze, application, bshort/bfloat, c++, constrained region growing, dicom, image display, microsoft, magnetic resonance, region of interest, segmentation, visualization, volume measurement, volumetric analysis, win32 (ms windows), windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
NYUMC FireVoxel-BrainMask Software License Agreement | nlx_155715 | SCR_009538 | 2026-08-04 09:42:24 | 0 | ||||||||
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BrainBrowser Resource Report Resource Website 1+ mentions |
BrainBrowser (RRID:SCR_009535) | BrainBrowser | data analysis service, analysis service resource, data set, production service resource, service resource, data or information resource | A web-enabled brain surface viewer that allows the user to explore in real time a 3D brain map expressed on a base surface. BrainBrowser has two modes of operation, exploring either a pre-calculated database of structural correlation maps or working with user-defined data. In this mode, the user may choose to explore the correlation structure for cortical thickness, cortical area or cortical volume, or any other pre-calculated metric. In the second mode, the user is prompted for the local filenames of the statistical map and the base surface. BrainBrowser can also be used to manipulate 3D fibre pathways derived from DTI, using the same simple file format (.obj) as for surface data. BrainBrowser on Youtube: http://www.youtube.com/watch?v=HlRTUYUf1Ew NOTE: BrainBrowser requires a WebGL-enabled browser such as Google Chrome to support its 3D graphics capability. | image display, javascript, minc2, magnetic resonance, nifti, os independent, rendering, ruby, surface rendering, three dimensional display, two dimensional display, visualization, volume rendering, 3d visualization, neuroimaging, fmri, web application, web resource, data visualization service |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Free | nlx_155710 | http://www.nitrc.org/projects/brainbrowser | SCR_009535 | 2026-08-04 09:42:24 | 3 | |||||||
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BVQXtools Resource Report Resource Website 10+ mentions |
BVQXtools (RRID:SCR_009532) | BVQXtools | data processing software, software resource, software application, image processing software, software toolkit | A Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab. The toolbox is freely available. | analyze, format conversion, linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, statistical operation, time domain analysis, windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVoyager |
Free, Other/Commercial license License | nlx_155707 | SCR_009532 | 2026-08-04 09:42:24 | 11 | ||||||||
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B0 and eddy current correction for DTI Resource Report Resource Website |
B0 and eddy current correction for DTI (RRID:SCR_009529) | B0 and Eddy Current Correction Code for Diffusion MRI | data processing software, software application, software resource, source code | Software tool (excecutable and source code in C and C++) to correct distortions in diffusion MR images that are generated by main magnetic field inhomogeneities and eddy current induced fields generated from the direction-dependent diffusion encoding | analyze, c, c++, microsoft, magnetic resonance, win32 (ms windows), dti, diffusion mri, magnetic field, eddy current |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
GNU General Public License | nlx_155694 | http://www.nitrc.org/projects/dtic | SCR_009529 | 2026-08-04 09:42:24 | 0 | |||||||
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BRAINSDemonWarp Resource Report Resource Website 1+ mentions |
BRAINSDemonWarp (RRID:SCR_009524) | BRAINSDemonWarp | data processing software, registration software, software resource, software application, image analysis software | A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: University of Iowa; Iowa; USA |
NINDS NS050568; NINDS NS40068; NIMH MH31593; NIMH MH40856 |
nlx_155700 | http://www.nitrc.org/projects/brainsdemonwarp | SCR_009524 | 2026-08-04 09:42:23 | 1 | |||||||
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GPU based affine registration Resource Report Resource Website |
GPU based affine registration (RRID:SCR_009486) | GPU based affine registration | data processing software, registration software, software resource, software application, image analysis software | This tool can be used as a command line module with 3D Slicer (version 3 and above) for the affine registration of image volumes. The registration toolbox has 2 options: 1) a Mutual Information based registration, 2) a Sum-of-Square differences registration method. The final output is in the same space as the fixed image. You do require to have CUDA v2.2 or greater installed on your system with atleast 256MB Nvidia GPU memmory card. All operating systems are supported, but take a look at the CMakeLists.txt file for how to compile for you system. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer |
GPL-Style Open unspecified license, Http://www.nitrc.org/include/glossary.php#573 | nlx_155633 | SCR_009486 | 2026-08-04 09:42:24 | 0 | ||||||||
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Functional and Structural Neuroimaging Journals Listing Resource Report Resource Website 1+ mentions |
Functional and Structural Neuroimaging Journals Listing (RRID:SCR_009482) | journal, catalog, narrative resource, database, data or information resource, bibliography | Journals addressing functional and structural neuroimaging topics. | journal, functional neuroimaging, structural neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | SCR_014130, nlx_155630 | SCR_009482 | , Neuroimaging Journals, Journals | 2026-08-04 09:42:23 | 1 | ||||||||
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Functional Connectivity Community Resource Report Resource Website |
Functional Connectivity Community (RRID:SCR_009480) | Functional Connectivity Community | portal, community building portal, narrative resource, discussion, data or information resource | A community for the discussion of functional connectivity and all related topics. This includes discussion of related tools, data sets, methodological discussion, related websites and publications, etc. | community, knowledge environment, magnetic resonance, os independent, web environment, functional connectivity | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155627 | SCR_009480 | 2026-08-04 09:42:24 | 0 | |||||||||
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fMRI Classification in R Resource Report Resource Website 1+ mentions |
fMRI Classification in R (RRID:SCR_009519) | fMRI Classification in R | data processing software, software resource, software application, image processing software, image analysis software | They demonstrate and provide R code that can classify between groups of fMRI scans based on functional network connectivity differences, requiring only 4 lines of code to be altered. In addition, they include a detailed article explaining the methods behind and motivations of this tool. This code can also be altered to perform connectivity analysis and classification using ROI based methods by reading in distance arrays previously created. They run Independent component analysis (ICA) on fMRI data to establish functional networks, measure the functional connectivity between these networks using the temporal cross-correlations between independent component to create a distance matrix and indicating the networking. Connectivity properties are used as a feature matrix for an SVM classifier. Collectively, this project provides and explains both methods and code to perform functional network connectivity and fMRI SVM classi?cation. | magnetic resonance, connectivity, fmri, independent component analysis, functional network, classification | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155681 | SCR_009519 | 2026-08-04 09:42:24 | 1 |
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