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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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, image analysis software, software application, registration software, software resource | 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 | 2026-08-05 10:45:13 | 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) | data or information resource, narrative resource, bibliography, catalog, database, journal | 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 | 2026-08-05 10:45:13 | 1 | ||||||||
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Functional Connectivity Community Resource Report Resource Website |
Functional Connectivity Community (RRID:SCR_009480) | Functional Connectivity Community | data or information resource, narrative resource, portal, community building portal, discussion | 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 | 2026-08-05 10:45:11 | 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, image analysis software, software application, software resource, image processing 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 | 2026-08-05 10:45:13 | 1 | ||||||||
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Level-set Segmentation for Slicer3 Resource Report Resource Website |
Level-set Segmentation for Slicer3 (RRID:SCR_009558) | Level-set Segmentation for Slicer3 | data processing software, segmentation software, image analysis software, software application, software resource | The modules in the framework support different tasks in the segmentation realization in 3DSlicer. A module called Level-set label map evolver was developed, which takes an initial label image and a feature image as input and performs a Geodesic Active Contours evolution on the label image according to the feature image and to a different terms in the level-set equation. The evolution takes place for a customizable number of iterations. The output is a label image that can be used to produce a model. Other modules were developed to accompany the main module as can be seen in http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Level-Set_Segmentation_Framework-Documentation | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 3D Slicer |
3D Slicer License | nlx_155786 | http://www.nitrc.org/projects/levelsetslicer3 | SCR_009558 | Slicer3:Module:Level-Set Segmentation Framework | 2026-08-05 10:45:13 | 0 | ||||||
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DRAMMS Resource Report Resource Website 10+ mentions |
DRAMMS (RRID:SCR_009555) | DRAMMS | data processing software, image analysis software, software application, registration software, software resource | A software designed for deformable 2D-to-2D and 3D-to-3D image registration. Some typical applications of DRAMMS include, ** Cross-subject registration of the same organ (can be brain, breast, cardiac, etc); ** Mono- and Multi-modality registration (MRI, CT, histology); Longitudinal registration (pediatric brain growth, cancer development, etc); ** Registration under partial missing correspondences (small lesions, tumors, histological cuts). DRAMMS is implemented as a Unix command-line tool. It is fully automatic and easy to use ? users input two images, and DRAMMS will output the registered image and deformation. No need for pre-segmentation of any structures, no need for any prior knowledge, and no need for human initialization or intervention. | analyze, computational neuroscience, linux, macos, magnetic resonance, nifti, posix/unix-like, brain morphometry, general registration, image registration |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
BSD License | nlx_155736 | http://www.nitrc.org/projects/dramms | SCR_009555 | Deformable Registration via Attribute Matching and Mutual-Saliency Weighting, DRAMMS: Deformable Registration via Attribute Matching and Mutual-Saliency Matching | 2026-08-05 10:45:13 | 11 | ||||||
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Connectome Viewer Resource Report Resource Website 1+ mentions |
Connectome Viewer (RRID:SCR_009552) | Connectome Viewer | data processing software, software application, data visualization software, data analysis software, software toolkit, software resource | A free, open source, cross-platform Python-based software application for visualization and analysis in connectome research. Features of the software include: Connectome File Format including metadata, networks, surfaces, volumes, track files; complex network analysis toolboxes; modular plugin architecture for extensibility; Mayavi2 for 3D Scientific Visualization and Plotting; interactive data manipulation and scripting capabilities; and Neuroimaging and Diffusion in Python libraries. | animation, atlas application, c++, format conversion, gifti, image display, linux, macos, microsoft, magnetic resonance, nifti, posix/unix-like, python, rendering, software, surface rendering, three dimensional display, tractography, two dimensional display, visualization, volume rendering, win32 (ms windows), windows, connectome, connectomics, data management, multi-modal data, network analysis, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Connectome Mapping Toolkit |
PMID:21713110 | Open Source | nlx_155732 | http://www.nitrc.org/projects/cviewer | SCR_009552 | 2026-08-05 10:45:12 | 1 | ||||||
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CONN Resource Report Resource Website 500+ mentions |
CONN (RRID:SCR_009550) | CONN | data processing software, image analysis software, software application, software toolkit, software resource | Matlab based cross platform software package for computation, display, and analysis of functional connectivity in fMRI (fcMRI). Used for resting state data (rsfMRI) as well as task related designs. Covers pipeline from raw fMRI data to hypothesis testing. | fmri functional connectivity, resting state data, seed-based correlations, ROI-to-ROI graph analyses, group ICA, masked ICA, generalized PPI, ALFF, ICC, GCOR, LCOR, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; works with: Eagle Atlas Compilation for Vestibular Research |
PMID:22642651 PMID:21889994 |
Free, Available for download, Freely available | nlx_155730 | www.nitrc.org/projects/conn | SCR_009550 | CONN toolbox, CONN - functional connectivity toolbox, Connectivity Toolbox (CONN) | 2026-08-05 10:45:13 | 995 | |||||
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CBFBIRN Resource Report Resource Website 1+ mentions |
CBFBIRN (RRID:SCR_009543) | CBFBIRN | data or information resource, data repository, data set, storage service resource, service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users. |
java, javascript, matlab, magnetic resonance, os independent, web environment, arterial spin labeling, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cerebral Blood Flow Database and Analysis Pipeline has parent organization: University of California at San Diego; California; USA |
NIH | PMID:24151465 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155722 | http://www.nitrc.org/projects/cbfbirn | SCR_009543 | Cerebral Blood Flow Biomedical Informatics Research Network | 2026-08-05 10:45:08 | 3 | ||||
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Slicer3 Module Rician noise filter Resource Report Resource Website 1+ mentions |
Slicer3 Module Rician noise filter (RRID:SCR_009614) | Slicer3:Module:Rician Noise Removal | data processing software, software application, software resource, image processing software | Two Slicer3 modules removing rician noise in diffusion tensor MRI | c++, console (text based), linux, magnetic resonance, posix/unix-like, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 3D Slicer |
NIH Roadmap for Medical Research ; NIBIB U54 EB005149; NCRR 2-P41-RR12553-07 |
PMID:17354881 | GNU General Public License | nlx_155836 | http://www.nitrc.org/projects/dtiricianrem | SCR_009614 | 2026-08-05 10:45:14 | 1 | |||||
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GIFTI Resource Report Resource Website 10+ mentions |
GIFTI (RRID:SCR_009579) | GIfTI | data or information resource, standard specification, narrative resource, software resource | Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI. | algorithm or reusable library, c, computational neuroscience, information resource, magnetic resonance, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuroimaging Informatics Technology Initiative |
nlx_155761 | SCR_009579 | 2026-08-05 10:45:12 | 28 | |||||||||
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Neuroimaging Made Easy Blog Resource Report Resource Website |
Neuroimaging Made Easy Blog (RRID:SCR_009611) | Neuroimaging Made Easy | data or information resource, blog, narrative resource, software resource | Blog presenting some scripts that can be used to facilitate and automate processing and analysis of brain data. In addition, it could be helpful explaining non clear stages and steps of brain data processing using some software such as; Freesurfer, FSL, Brainvoyager QX... At the moment, there are more than 10 applescripts in the main website http://www.easyneuroimaging.com that control different tools and commands (aparcstats2table, asegstats2table, BET, dcm2nii, FIRST, fslsplit, fslswapdim, fslview, mri_convert, Qdec, Recon-all, SIENAX, tkmedit, tksurfer) | analyze, applescript, application, ascii, dicom, linux, macos, mgh/mgz, magnetic resonance, nifti, posix/unix-like, sh/bash, unix shell, workflow, script | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Personal License | nlx_155830 | http://www.nitrc.org/projects/easy_neuroimage | SCR_009611 | 2026-08-05 10:45:12 | 0 | |||||||
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ERPLAB Resource Report Resource Website 100+ mentions |
ERPLAB (RRID:SCR_009574) | ERPLAB | software resource, data processing software, software application, data analysis software | A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH. | anova, eeg, meg, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Bioelectromagnetism Matlab Toolbox has parent organization: University of California at Davis; California; USA |
NIMH | GNU General Public License | nlx_155754 | http://www.nitrc.org/projects/erplab | SCR_009574 | ERPLAB Toolbox | 2026-08-05 10:45:08 | 428 | |||||
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EMSE Suite Resource Report Resource Website 10+ mentions |
EMSE Suite (RRID:SCR_009571) | EMSE Suite | data processing software, image analysis software, software application, software toolkit, software resource | A technically supported modular platform for space-time-frequency analyses of EEG/MEG/ECoG integrated (optionally) with structural MRI and functional hemodynamic measures (fMRI and NIRS). The Locator module uses Polhemus devices to acquire 3D sensor coordinates. Data Editor provides pipelines of spatial and temporal filters, and easy-to-use event pipelines for conditional binning of time, frequency, and time-frequency data across participants, with group results. Coherence, phase synchronication, and quasi-causal information assess connectivity. Source Estimator enables modeling of discrete overdetermined and distributed underdetermined sources, and spatial filtering for 3D brain regions of interest. Statistical nonparametric mapping (SnPM) may be performed for all measures. MR Viewer and Image Processor comprise tools for BEM and FEM volume conductor models, using cortical source space models. See http://www.sourcesignal.com/Features_EMSE_550.pdf for details and a supported free trial. | application, eeg, meg, electrocorticography, eeg modeling, forward - inverse, modeling, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155751 | http://www.nitrc.org/projects/emse | SCR_009571 | 2026-08-05 10:45:13 | 10 | |||||||
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LONI Brain Parser Resource Report Resource Website 1+ mentions |
LONI Brain Parser (RRID:SCR_009572) | Brain Parser | data processing software, segmentation software, image analysis software, software application, software resource | Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest. | analyze, anatomic, application, c++, console (text based), labeling, linux, microsoft, magnetic resonance, posix/unix-like, region of interest, segmentation, sh/bash, unix shell, windows, windows nt/2000, windows vista, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
GNU General Public License, LONI Software License | nlx_155783 | http://www.nitrc.org/projects/brainparser | SCR_009572 | BrainParser | 2026-08-05 10:45:12 | 3 | |||||
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DTIProcess ToolKit Resource Report Resource Website |
DTIProcess ToolKit (RRID:SCR_009561) | DTIProcess | data processing software, software application, image analysis software, software toolkit, software resource, image processing software | 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 | 2026-08-05 10:45:13 | 0 | |||||||
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LIBEEP Resource Report Resource Website 1+ mentions |
LIBEEP (RRID:SCR_009591) | LIBEEP | software toolkit, software library, software resource | 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 | 2026-08-05 10:45:14 | 1 | ||||||
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fMRI Grocer Resource Report Resource Website 1+ mentions |
fMRI Grocer (RRID:SCR_009622) | data processing software, image analysis software, software application, data analysis software, software toolkit, software resource | 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 | 2026-08-05 10:45:13 | 1 | ||||||||
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elastix Resource Report Resource Website 100+ mentions |
elastix (RRID:SCR_009619) | elastix | data processing software, image analysis software, software application, registration software, software toolkit, software resource | 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 | 2026-08-05 10:45:12 | 167 | ||||||
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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, software library, segmentation software, image analysis software, software application, software toolkit, software resource | 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 | 2026-08-05 10:45:14 | 1 |
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