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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Distributome Resource Report Resource Website |
Distributome (RRID:SCR_009564) | Distributome | software resource | An open-source, open content-development project for exploring, discovering, navigating, learning, and computational utilization of diverse probability distributions. | computational neuroscience, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155746 | http://www.nitrc.org/projects/distributome | SCR_009564 | 2026-09-19 12:51:50 | 0 | |||||||
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DTIProcess ToolKit Resource Report Resource Website |
DTIProcess ToolKit (RRID:SCR_009561) | DTIProcess | data processing software, image analysis software, image processing software, software application, software resource, 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 | 2026-09-19 12:51:50 | 0 | |||||||
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ProbabilisticBiasCorrection Resource Report Resource Website |
ProbabilisticBiasCorrection (RRID:SCR_009638) | ProbabilisticBiasCorrection | software resource | A multichannel capable tool for probabilistic inhomogeneity correction implemented as both a standalone command line tool and a Slicer3 module. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
3D Slicer License | nlx_155926 | SCR_009638 | 2026-09-19 12:51:51 | 0 | ||||||||
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Program for optimal design of blocked fMRI experiments Resource Report Resource Website |
Program for optimal design of blocked fMRI experiments (RRID:SCR_009639) | POBE | software resource | Computer program that provides a graphical user interface for fMRI researchers to easily and efficiently design their blocked experiments. The computer program POBE calculates the optimal number of subjects and the optimal scanning time for user specified experimental factors and model parameters so that the statistical efficiency is maximised for a given study budget. POBE can also be used to determine the minimum budget for a given power. Furthermore, a maximin design can be determined as efficient design for a possible range of values for the unknown model parameters. | magnetic resonance, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155927 | SCR_009639 | Program for optimal design of blocked experiments | 2026-09-19 12:51:51 | 0 | |||||||
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Rockland Download Link Script Resource Report Resource Website 1+ mentions |
Rockland Download Link Script (RRID:SCR_009513) | Rockland Download Link Script | software resource | Script which points browser to Nathan Kline Institute (NKI) Rockland Sample. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI/Rockland Sample |
Creative Commons License | nlx_155675 | SCR_009513 | 2026-09-19 12:51:49 | 1 | ||||||||
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Subject Order-Independent Group ICA Resource Report Resource Website 10+ mentions |
Subject Order-Independent Group ICA (RRID:SCR_009514) | SOI-GICA | software resource | While the traditional temporally concatenated Group ICA (TC-GICA) adopting three steps of PCA reduction, it could result in inconsistent and variable components when different subject orders were used, both for the group- and individual-level results. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA (SOI-GICA) aims to fix this problem by producing stable and reliable GICA results. For details please see the paper Subject Order-Independent Group ICA (SOI-GICA) for Functional MRI Data Analysis (Zhang et al., 2010, NeuroImage)(http://dx.doi.org/10.1016/j.neuroimage.2010.03.039). MICA is the toolbox inplemented SOI-GICA for convenience of usage. | analyze, gnome, independent component analysis, kde, linux, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, software, statistical operation, win32 (ms windows), windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20338245 | GNU General Public License | nlx_155676 | SCR_009514 | 2026-09-19 12:51:49 | 18 | |||||||
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Pipeline Neuroimaging VirtualEnvironment Resource Report Resource Website |
Pipeline Neuroimaging VirtualEnvironment (RRID:SCR_009635) | PNVE | software resource | A self-contained virtual machine that can be executed on a common laptop or desktop, enabling the Pipeline to run virtually anywhere. Neophytes to the Pipeline can have their own private server running in minutes, software engineers and workflow designers can use the PNVE as a sandbox, and those without access to grid computing facilities can now take full advantage of the Pipeline processing environment. | domain independent |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
LONI Software License | nlx_155923 | SCR_009635 | LONI Pipeline Neuroimaging Virtual Environment | 2026-09-19 12:51:50 | 0 | |||||||
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Network Modification Tool Lite Resource Report Resource Website |
Network Modification Tool Lite (RRID:SCR_009511) | NeMo Tool | software resource | Tool that associates localized white matter (WM) lesions with disruptions in gray matter connectivity as a step toward understanding the lesions? functional implications. A Tractogram Reference Set (TRS), i.e. collections of white matter fibers, is constructed from 73 normal healthy individuals and coregistered to a common space (MNI). The NeMo Tool uses the TRS to assess structural network disruption due to a particular WM lesion mask on a region and network-wise level. This tool is an easy way for researchers and clinicians to investigate changes in the structural brain network without having to perform tractography on their own normal data or on diseased/injured brains where the results may not represent the underlying physiology. | computational neuroscience | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155673 | SCR_009511 | Network Modification (NeMo) Tool Lite | 2026-09-19 12:51:49 | 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, image analysis software, registration software, software application, software resource | 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 | 2026-09-19 12:51:49 | 0 | |||||||||
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NITRC Books Resource Report Resource Website |
NITRC Books (RRID:SCR_009510) | NITRC Books | bibliography, book, data or information resource, narrative resource | 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 | 2026-09-19 12:51:49 | 0 | |||||||||
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LIBEEP Resource Report Resource Website 1+ mentions |
LIBEEP (RRID:SCR_009591) | LIBEEP | software library, software resource, software toolkit | 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 | 2026-09-19 12:51:50 | 1 | ||||||
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map3d Resource Report Resource Website 1+ mentions |
map3d (RRID:SCR_009628) | map3d | data processing software, data visualization software, software application, software resource | A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG. | c++, eeg, meg, electrocorticography, forward - inverse, linux, macos, microsoft, modeling, posix/unix-like, visualization, win32 (ms windows), windows, windows 95/98/2000 |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Map3d License | nlx_155857 | http://www.nitrc.org/projects/map3d | SCR_009628 | 2026-09-19 12:51:50 | 3 | ||||||
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Local Label Learning Segmentation Resource Report Resource Website 1+ mentions |
Local Label Learning Segmentation (RRID:SCR_009504) | LLL Segmentation | data processing software, image analysis software, segmentation software, software application, software resource | 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 | 2026-09-19 12:51:49 | 1 | ||||||
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Landman NeuroImaging Tools Resource Report Resource Website |
Landman NeuroImaging Tools (RRID:SCR_009503) | Landman NeuroImaging Tools | data processing software, image analysis software, software application, software repository, software resource | 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 | 2026-09-19 12:51:49 | 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 | data or information resource, narrative resource, software repository, software resource, training material | 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 | 2026-09-19 12:51:49 | 0 | ||||||||
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fMRI Grocer Resource Report Resource Website 1+ mentions |
fMRI Grocer (RRID:SCR_009622) | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software toolbox containing many kinds of kits that you may be interested in during fMRI data analysis. This toolbox is a homebrew kits built during practical ASL(arterial spin labeling) based Cerebral Blood Flow (CBF) data analysis. Meanwhile, this toolbox is also compatible with BOLD data analysis. Everyone would find something useful for their own data analysis! This toolbox is run and tested on SPM8 with MATLAB 7.6.0(R2008a) under the Linux OS. Theoretically, most of the functions (except the menu1&2 which are specially designed for the Batch Editor of SPM8) of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS. Feel free to give feedback to authors if you encounter any bugs or problems. Senhua Zhu Center for functional Neuroimaging, University of Pennsylvania 3 W.Gates Bldg, 3400, Philadelphia, PA (19104), United States Email: [email protected] ; [email protected] QQ group number (QQ?): 60524357 Google group: https://groups.google.com/d/forum/fmri-grocer | magnetic resonance, cerebral blood flow, fmri, arterial spin labeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
Free, Available for download, Freely available, | nlx_155847 | http://code.google.com/p/fmrigrocer/ | SCR_009622 | 2026-09-19 12:51:50 | 1 | ||||||||
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elastix Resource Report Resource Website 100+ mentions |
elastix (RRID:SCR_009619) | elastix | data processing software, image analysis software, registration software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | reusable library, analyze, c++, console (text based), domain independent, nifti, nrrd, os independent, philips par/rec, registration, resampling, spatial transformation, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is related to: Insight Segmentation and Registration Toolkit has parent organization: Utrecht University; Utrecht; Netherlands |
PMID:19923044 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155845, biotools:elastix | http://www.nitrc.org/projects/elastix, https://bio.tools/elastix, https://sources.debian.org/src/elastix/ | SCR_009619 | 2026-09-19 12:51:50 | 175 | ||||||
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BrainMask Volume Processing Tool Resource Report Resource Website |
BrainMask Volume Processing Tool (RRID:SCR_009538) | BrainMask | data processing software, data visualization software, image analysis software, segmentation software, software application, software resource | 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 | 2026-09-19 12:51:49 | 0 | ||||||||
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BrainBrowser Resource Report Resource Website 1+ mentions |
BrainBrowser (RRID:SCR_009535) | BrainBrowser | analysis service resource, data analysis service, data or information resource, data set, production service resource, service 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 | 2026-09-19 12:51:49 | 3 | |||||||
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Wisconsin White Matter Hyperintensities Segmentation Toolbox Resource Report Resource Website 1+ mentions |
Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) | W2MHS | data processing software, image analysis software, segmentation software, software application, software library, software resource, software toolkit | An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis. | computational neuroscience, matlab, nifti, white matter hyperintensity, c++, matlab, ms windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM is related to: SourceForge has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Alzheimer's disease, Aging, Neurological disorder | Academic Free License | nlx_156021 | SCR_009652 | WM Hyperintensities Segmentation Toolbox | 2026-09-19 12:51:51 | 2 |
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