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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DIAMOND Resource Report Resource Website 1000+ mentions |
DIAMOND (RRID:SCR_009457) | DIAMOND | software resource | Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans. | reusable library, analyze, database application, dicom, format conversion, image display, image reconstruction, magnetic resonance, nifti, python, software, visualization, workflow, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Davis; California; USA |
nlx_155603 | SCR_009457 | UC Davis IDeA Lab Applications for Management Of Neuroimaging Data | 2026-07-25 12:06:55 | 4152 | ||||||||
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CBS High-Res Brain Processing Tools Resource Report Resource Website 10+ mentions |
CBS High-Res Brain Processing Tools (RRID:SCR_009452) | CBS High-Res Brain Processing Tools | software resource | A fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400������m, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness. The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit is related to: MIPAV: Medical Image Processing and Visualization |
Free | nlx_155596 | SCR_009452 | 2026-07-25 12:06:53 | 20 | ||||||||
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Fiber Optic Button Response System Resource Report Resource Website 10+ mentions |
Fiber Optic Button Response System (RRID:SCR_009577) | instrument resource | Instrument that accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact, chemical resistant, medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant?s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed. | eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, response monitoring, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | https://drive.google.com/file/d/1vvm02GkPgAG6LnRzWE9FEQZD6JSqtngA/view?usp=drivesdk | nlx_155759 | http://www.nitrc.org/projects/fobrs, https://pstnet.com/wp-content/uploads/2021/04/Celeritas-Operator-Manual.pdf | SCR_009577 | Celeritas Fiber Optic Response System | 2026-07-25 12:06:54 | 22 | |||||||
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NordicNeuroLab Resource Report Resource Website 50+ mentions |
NordicNeuroLab (RRID:SCR_009632) | NNL | commercial organization | From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike. | analyze, ascii, dicom, diffusion mr fiber tracking, experiment control, eye tracking, fiber tracking, haemodynamic response, hardware, microsoft, magnetic resonance, nifti, perfusion, physiological recording, scanner, stimulus presentation, temporal curve fitting, temporal transformation, tractography, windows, windows vista, windows xp, fmri, post-processing, visualization, bold, diffusion, dti, perfusion, dce, audio stimulation, visual stimulation, eye tracking, patient response, clinical, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial | nlx_155905 | http://www.nitrc.org/projects/nnl | SCR_009632 | 2026-07-25 12:06:59 | 53 | |||||||
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Lumina LP- 400 Response System Resource Report Resource Website |
Lumina LP- 400 Response System (RRID:SCR_009596) | Lumina LP-400 | instrument resource | A reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields. | experiment control, hardware, magnetic resonance, response monitoring, fmri, clinical, research, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155789 | http://www.nitrc.org/projects/lumina | http://www.cedrus.com/ordering/mri/usa.htm | SCR_009596 | Lumina fMRI Input Device, Lumina LP-400 System for fMRI, Lumina fMRI Response Pad | 2026-07-25 12:06:57 | 0 | ||||||
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Multi-fiber Reconstruction from DW-MRI Resource Report Resource Website |
Multi-fiber Reconstruction from DW-MRI (RRID:SCR_009509) | Multi-fiber Reconstruction from DW-MRI | software resource | This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data. It is a subset of the code internally used in the CVGMI lab at the University of Florida. Three different reconstruction methods are currently included in this program, namely, Mixture of Wisharts (MOW), Diffusion Orientation Transform (DOT) and Q-ball Imaging (QBI). This program is mainly developed and maintained by Bing Jian, as part of his Ph.D. research, supervised by Prof. Baba Vemuri. Please note that the source code of this program is hosted at Google Code, see the Source Code link on the left. | reusable library, console (text based), diffusion mr fiber tracking, fiber tracking, magnetic resonance, os independent, python, tractography, reconstruction, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
GNU General Public License | nlx_155669 | SCR_009509 | 2026-07-25 12:06:54 | 0 | ||||||||
|
MASIMatlab Resource Report Resource Website 1+ mentions |
MASIMatlab (RRID:SCR_009506) | MASIMatlab | software resource | This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling. | magnetic resonance, matlab, population characterization, mri, dti, smri, qmri, shape modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
nlx_155655 | SCR_009506 | 2026-07-25 12:06:58 | 4 | |||||||||
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iView X MRI-LR - Eye Tracking for fMRI Resource Report Resource Website 1+ mentions |
iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) | iView X MRI-LR | software resource | A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output | magnetic resonance, fmri, meg, eye, eye tracking, mri, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commerical | nlx_155853 | http://www.nitrc.org/projects/iviewx_mri-lr | SCR_009627 | 2026-07-25 12:06:57 | 3 | |||||||
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MASI Label Fusion Resource Report Resource Website 1+ mentions |
MASI Label Fusion (RRID:SCR_009505) | MASI Label Fusion | software resource | Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
GNU Lesser General Public License | nlx_155654 | SCR_009505 | 2026-07-25 12:06:56 | 3 | ||||||||
|
BRAINSROIAuto Resource Report Resource Website |
BRAINSROIAuto (RRID:SCR_009501) | BRAINSROIAuto | software resource | Automatically creates a mask based on the "foreground" of an anatomical scan volume. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
BRAINS License | nlx_155703 | http://www.nitrc.org/projects/brainsroiauto | SCR_009501 | 2026-07-25 12:06:54 | 0 | |||||||
|
JHU Proj. in Applied Medical Imaging Resource Report Resource Website |
JHU Proj. in Applied Medical Imaging (RRID:SCR_009499) | JHU Proj. in Applied Medical Imaging | software resource | This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit has parent organization: Johns Hopkins University; Maryland; USA |
Free | nlx_155647 | SCR_009499 | 2026-07-25 12:06:56 | 0 | ||||||||
|
DATAPixx Resource Report Resource Website 10+ mentions |
DATAPixx (RRID:SCR_009648) | DATAPixx | commercial organization | Supplies a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor, the DATAPixx includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision. | eeg, eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, physiological recording, response monitoring, stimulus presentation, vision | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155989 | http://www.nitrc.org/projects/vpixx | SCR_009648 | 2026-07-25 12:06:57 | 15 | |||||||
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Robust Biological Parametric Mapping Resource Report Resource Website 1+ mentions |
Robust Biological Parametric Mapping (RRID:SCR_009642) | Robust Biological Parametric Mapping | software resource | To enable widespread application of the Biological parametric mapping (BPM) approach, they introduce robust regression and non-parametric regression in the neuroimaging context of application of the general linear model. Biological parametric mapping (BPM) has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects. | magnetic resonance, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155944 | SCR_009642 | 2026-07-25 12:06:59 | 3 | ||||||||
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Connectome File Format Resource Report Resource Website |
Connectome File Format (RRID:SCR_009551) | CFF | software resource | A container format for multi-modal neuroimaging data. It comprises connectome objects of type: CMetadata, CNetwork, CVolume, CSurface, CTrack, CScript, CData, CTimeseries, CImagestack. The Python library cfflib provides read/write functionality. | file format, gifti, information resource, information specification, magnetic resonance, nifti, portable document format, python, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155731 | http://www.nitrc.org/projects/cff | SCR_009551 | Connectome File Format (CFF) | 2026-07-25 12:06:56 | 0 | ||||||
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CDF-HC PointSetReg Resource Report Resource Website |
CDF-HC PointSetReg (RRID:SCR_009544) | CDF-HC PointSetReg | software resource | A Matlab demo for group wise point set registration using a novel CDF-based Havrda-Charvat Divergence, which is based on the paper: Ting Chen, Baba C. Vemuri, Anand Rangarajan and Stephan J. Eisenschenk, Group-wise Point-set registration using a novel CDF-based Havrda-Charvat Divergence. In IJCV : International Journal of Computer Vision, 86(1):111-124, January, 2010. | matlab | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20221321 | GNU General Public License | nlx_155723 | http://www.nitrc.org/projects/cdfhc2010 | SCR_009544 | 2026-07-25 12:06:54 | 0 | ||||||
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NINDS Repository Resource Report Resource Website 1+ mentions |
NINDS Repository (RRID:SCR_004520) | biomaterial supply resource, material resource | Open resource of biological samples (DNA, cell lines, and other biospecimens) and corresponding phenotypic data to promote neurological research. Samples from more than 34,000 unique individuals with cerebrovascular disease, dystonia, epilepsy, Huntington's Disease, motor neuron disease, Parkinsonism, and Tourette Syndrome, as well as controls (population control and unaffected relatives) have been collected. The mission of the NINDS Repository is to provide 1) genetics support for scientists investigating pathogenesis in the central and peripheral nervous systems through submissions and distribution; 2) information support for patients, families, and advocates concerned with the living-side of neurological disease and stroke. | nervous system disorder, neurogenetics, genetic, clinical data, cerebrovascular disease, epilepsy, motor neuron disease, parkinson's disease, parkinsonism, tourette's disorder, normal control, stroke, amyotrophic lateral sclerosis, huntington's disease, dystonia, dementia, neurologically normal, blood, dna, biomarker, plasma, urine, cell line, induced pluripotent stem cell, fibroblast, stem cell, frozen, lymphoblast, biospecimen banking, biospecimen processing, biospecimen distribution, biospecimen, genetics, phenotype, neurological disease |
is listed by: One Mind Biospecimen Bank Listing is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PD-DOC is related to: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) has parent organization: Coriell Cell Repositories |
Cerebrovascular disease, Epilepsy, Motor neuron disease, Parkinson's disease, Tourette's Disorder, Normal control, Stroke, Amyotrophic Lateral Sclerosis, Huntington's disease, Dystonia, Dementia, Neurologically normal, Neurological disorder | NINDS ; NIH Blueprint for Neuroscience Research |
Public | nlx_143800 | SCR_004520 | NINDS Human Genetics DNA Cell Line Repository, NINDS Human Genetics DNA and Cell Line Repository, The NINDS Repository, The NINDS Human Genetics Resource Center, The NINDS Human Genetics DNA and Cell Line Repository | 2026-07-25 12:12:31 | 3 | ||||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 10+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-07-25 12:08:07 | 47 | |||||||
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EYE-EEG (combined eye-tracking & EEG) Resource Report Resource Website 10+ mentions |
EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) | EYE-EEG | software resource | A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line. | eeg, meg, electrocorticography, matlab, os independent, eye, electrophysiology, oculomotor, eye tracking device |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Humboldt University of Berlin; Berlin; Germany |
DFG | PMID:21744985 | GNU General Public License | nlx_155755 | http://www.nitrc.org/projects/eye-eeg | SCR_012903 | EYE-EEG: Eye tracking & EEG | 2026-07-25 12:07:41 | 13 | ||||
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BRAINSTracer Resource Report Resource Website 1+ mentions |
BRAINSTracer (RRID:SCR_012894) | BRAINSTracer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155705 | http://www.nitrc.org/projects/brainstracer | SCR_012894 | 2026-07-25 12:07:38 | 5 | |||||||
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BrainVisa Morphology extensions Resource Report Resource Website 1+ mentions |
BrainVisa Morphology extensions (RRID:SCR_013248) | BrainVisa Morphology extensions | software resource | An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa | analyze, c++, image display, linux, macos, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, shape analysis, software, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVISA / Anatomist is related to: INCF Software Center |
Artistic License | nlx_155716 | http://www.nitrc.org/projects/brainvisa_ext | SCR_013248 | 2026-07-25 12:07:50 | 1 |
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