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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Multi-Modal MRI Reproducibility Resource Resource Report Resource Website 10+ mentions |
Multi-Modal MRI Reproducibility Resource (RRID:SCR_002442) | Multi-Modal MRI Reproducibility Resource | image collection, data or information resource | Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047 | java image science toolkit, magnetic resonance, nifti, neuroimaging, reproducibility, mprage, flair, dti, resting state fmri, b0 field map, b1 field map, asl, vaso, quantitative t1 mapping, quantitative t2 mapping, magnetization transfer imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit |
Healthy | PMID:21094686 | Free, Available for download, Freely available | nlx_155818 | SCR_002442 | 2026-08-01 12:02:10 | 11 | ||||||
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Multicomponent T2 estimation with stimulated echo correction Resource Report Resource Website |
Multicomponent T2 estimation with stimulated echo correction (RRID:SCR_002446) | Multicomponent T2 estimation with stimulated echo correction | software resource | Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches. | algorithm, matlab, magnetic resonance, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:23629849 | Free, Available for download, Freely available | nlx_155820 | SCR_002446 | 2026-08-01 12:02:10 | 0 | |||||||
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COGNISION Resource Report Resource Website 1+ mentions |
COGNISION (RRID:SCR_002362) | COGNISION | software resource | A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker). | eeg, eeg, meg, electrocorticography, event-related potentials, hardware, physiological recording, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | nlx_155724 | http://www.nitrc.org/projects/neuronetrix | SCR_002362 | COGNISION (TM) System | 2026-08-01 12:02:05 | 2 | ||||||
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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 | 2026-08-01 12:03:42 | 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 | 2026-08-01 12:03:59 | 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 | 2026-08-01 12:04:02 | 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 | 2026-08-01 12:04:10 | 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 | 2026-08-01 12:03:44 | 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 | 2026-08-01 12:04:00 | 0 | ||||||||
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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 | 2026-08-01 12:04:09 | 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 | 2026-08-01 12:03:45 | 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 | 2026-08-01 12:03:43 | 3 | ||||||||
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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 | 2026-08-01 12:04:00 | 0 | |||||||
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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 | 2026-08-01 12:03:43 | 0 | ||||||||
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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 | 2026-08-01 12:03:45 | 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 | 2026-08-01 12:04:10 | 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) | 2026-08-01 12:03:43 | 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 | 2026-08-01 12:04:01 | 0 | ||||||
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Scribe Resource Report Resource Website |
Scribe (RRID:SCR_000423) | Scribe | software resource | Scribe encodes papers to populate the BrainMap Database | magnetic resonance, pet, spect |
is used by: brainmap.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Freely available | nlx_155958 | SCR_000423 | 2026-08-01 12:01:20 | 0 | ||||||||
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Faceted Search Based Ontology Visualizer Resource Report Resource Website |
Faceted Search Based Ontology Visualizer (RRID:SCR_000124) | ontologyviz | software resource | Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy. | computational neuroscience, magnetic resonance, ontology, functional neuroanatomy, facet, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | nlx_155874 | SCR_000124 | 2026-08-01 12:01:10 | 0 |
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