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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Numerical Fibre Generator Resource Report Resource Website 50+ mentions |
Numerical Fibre Generator (RRID:SCR_002457) | NFG | software resource | A collection of tools that generate numerical fiber structures with the complexity of human white matter and simulate Diffusion-Weighted MR images that would arise from them. Its primary use is to enable the testing of tracking algorithms | analyze, c, console (text based), macos, microsoft, magnetic resonance, posix/unix-like, tractography, windows, dw-mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Brain Research Institute |
Free, Available for download, Freely available | nlx_155832 | http://www.nitrc.org/projects/nfg | SCR_002457 | Numerical Fibre Generator (NFG) | 2026-08-01 12:01:48 | 58 | ||||||
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MRI Digital Projection System Resource Report Resource Website |
MRI Digital Projection System (RRID:SCR_002486) | Hyperion | instrument resource | MRI Digital Projection System that uses Digital Light Processing (DLP) technology providing microsecond pixel rise times, outstanding contrast with all-digital fiber optic control that allows you to project crystal clear, sharp images. Includes: * High resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, internal thermal sensor * Control room device to perform DVI to Fiber conversion, remotely power down the projector, and allow use of projector remote control from control room * 30 meter fiber optic cable that runs between the projector and projector control station * Heavy duty, magnet compatible, projector stand (assembly required) * Heavy duty, magnet compatible mirror stand with mirror (assembly required) * High resolution, lenticular pitch rear projection screen for high quality image reproduction * Optional VGA to DVI converter (native DVI video cards on Windows or Macintosh recommended) | experiment control, hardware, magnetic resonance, stimulus presentation, mri, projector, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Restricted | https://drive.google.com/file/d/1OPZZ054sMCqq-z1Fiuof2gEoLkK8Knp6/view?usp=drivesdk | nlx_155879 | http://www.nitrc.org/projects/projector, https://pstnet.com/wp-content/uploads/2018/08/2018ProductSheetHyperion.pdf | SCR_002486 | Hyperion MRI Digital Projection System | 2026-08-01 12:02:08 | 0 | |||||
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ASL spm8 Resource Report Resource Website 1+ mentions |
ASL spm8 (RRID:SCR_008873) | ASL_spm8 | software resource | Quick ASL Wrapper for preprocessing arterial spin labeled (ASL) Data and computing blood flow measurements using UPenn ASL toolbox. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ASL data processing tool box |
GNU General Public License | nlx_155580 | SCR_008873 | 2026-08-01 12:04:06 | 1 | ||||||||
|
ANTsR Resource Report Resource Website 10+ mentions |
ANTsR (RRID:SCR_008891) | ANTsR | software resource | An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data. | neuroimaging, multivariate statistical parametric mapping, dti, t1, image processing, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ANTS - Advanced Normalization ToolS |
BSD License | nlx_151365 | SCR_008891 | 2026-08-01 12:04:06 | 47 | ||||||||
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Cerebral Blood Flow Database and Analysis Pipeline Resource Report Resource Website 1+ mentions |
Cerebral Blood Flow Database and Analysis Pipeline (RRID:SCR_009454) | CBFDAP | software resource | 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. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CBFBIRN has parent organization: University of California at San Diego; California; USA |
BIRN License | nlx_155599 | SCR_009454 | 2026-08-01 12:04:09 | 2 | ||||||||
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DentalTools Resource Report Resource Website |
DentalTools (RRID:SCR_009463) | DentalTools | software resource | Software package that provides 3D imaging resources such as multimodal imaging, volume and mesh processing or segmentation for Dental Research. DentalTools package intends to contribute to the free exchange of information and methods in the dentistry research community. | domain independent | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | 3D Slicer License | nlx_155610 | SCR_009463 | 2026-08-01 12:04:09 | 0 | ||||||||
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caGWAS Resource Report Resource Website |
caGWAS (RRID:SCR_009617) | caGWAS | software resource | Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data. | application, computational neuroscience, genetic association, genomic analysis, imaging genomics, java, snp, gene, software, web environment, microarray, genomic, immunohistochemistry, imaging, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Cancer Institute |
BSD License | nlx_155841 | http://www.nitrc.org/projects/cagwas | SCR_009617 | caGWAS (Cancer Genome-Wide Association Studies), Cancer Genome-Wide Association Studies, CGOM-caGWAS | 2026-08-01 12:04:03 | 0 | ||||||
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NeuroWeb - NeuroImaging Database Resource Report Resource Website 1+ mentions |
NeuroWeb - NeuroImaging Database (RRID:SCR_009610) | NeuroWeb | software resource | Infrastructure for data aggregation, processing, and management in multi-dimensional medical imaging research (i.e., MRI, CT, PET). NeuroWeb is designed for rapid deployment on a small/moderate scale with limited hardware. | computed tomography, magnetic resonance, pet, spect, mri, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155829 | http://www.nitrc.org/projects/neuroweb | SCR_009610 | 2026-08-01 12:03:44 | 1 | ||||||||
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MagVenture: MagPro Magnetic Stimulator Resource Report Resource Website 10+ mentions |
MagVenture: MagPro Magnetic Stimulator (RRID:SCR_009601) | MagPro | instrument resource | A complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry. | experiment control, hardware, magnetic resonance, response monitoring, stimulus presentation, clinical, neurophysiology, neurology, cognitive neuroscience, rehabilitation, psychiatry, instrument, equipment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is provided by: MagVenture |
Commercial license | nlx_155803 | http://www.nitrc.org/projects/magpro | SCR_009601 | MagPro Magnetic Stimulator (TMS) | 2026-08-01 12:04:02 | 10 | ||||||
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Mag Design and Engineering Resource Report Resource Website 1+ mentions |
Mag Design and Engineering (RRID:SCR_009600) | Mag Design & Engineering | commercial organization | A variety of MEG- and fMRI-compatible hardware for research use including typical response collection devices such as joysticks, response pads, mice, as well as stimulation devices such as vibrotactile stimulators, olfactometers, and pressure/force generators. The company also offers custom design and production services for many different applications. | mag, eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, optical imaging, physiological recording, response monitoring, stimulus presentation, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155802 | http://www.magconcept.com | SCR_009600 | 2026-08-01 12:04:10 | 6 | |||||||
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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 | 2026-08-01 12:04:10 | 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 | 2026-08-01 12:03:45 | 0 | ||||||||
|
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 | 2026-08-01 12:04:10 | 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 | 2026-08-01 12:03:43 | 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 | 2026-08-01 12:04:09 | 17 | |||||||
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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 | 2026-08-01 12:03:45 | 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 | 2026-08-01 12:04:09 | 0 | |||||||
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ADJUST Resource Report Resource Website 1000+ mentions |
ADJUST (RRID:SCR_009526) | ADJUST | software resource | A completely automatic algorithm for artifact identification and removal in EEG data. ADJUST is based on Independent Component Analysis (ICA), a successful but unsupervised method for isolating artifacts from EEG recordings. ADJUST identifies artifacted ICA components by combining stereotyped artifact-specific spatial and temporal features. Features are optimised to capture blinks, eye movements and generic discontinuities. Once artifacted IC are identified, they can be simply removed from the data while leaving the activity due to neural sources almost unaffected. | eeg, meg, electrocorticography, matlab, os independent |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institute of Health and Medical Research; Rennes; France |
PMID:20636297 | GNU General Public License | nlx_155689 | http://www.nitrc.org/projects/adjust | SCR_009526 | ADJUST - EEG Automatic Artifact Removal, ADJUST: automatic algorithm for EEG artifact removal | 2026-08-01 12:04:09 | 1782 | |||||
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Brainwaver Resource Report Resource Website 1+ mentions |
Brainwaver (RRID:SCR_009540) | Brainwaver | software resource | Characterization of small-world networks constructed from wavelet analysis of resting fMRI. This package is currently available as an R library. Futrure development will take place within the CamBA software repository | reusable library, linux, macos, magnetic resonance, other unix-like, posix/unix-like, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Cambridge; Cambridge; United Kingdom |
GNU General Public License | nlx_155719 | http://www.nitrc.org/projects/brainwaver | http://www.wbic.cam.ac.uk/~sa428/brainwaver/, https://cran.r-project.org/web/packages/brainwaver/index.html | SCR_009540 | 2026-08-01 12:03:43 | 8 | ||||||
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TREES toolbox Resource Report Resource Website 10+ mentions |
TREES toolbox (RRID:SCR_010457) | TREES toolbox | software resource | Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance. | neuronal branching, microscopy, neuron, matlab, visualization, rendering, reconstruction, analysis, modeling, morphology, dendrite, axon, computational neuroanatomy, tree |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Max Planck Society ; Wellcome Trust ; Gatsby Charitable Foundation ; Alexander von Humboldt-Stiftung ; European Research Council |
PMID:20700495 | GNU General Public License v3, Creative Commons Attribution-NonCommercial-ShareAlike License v3, The community can contribute to this resource | nlx_157723 | http://www.nitrc.org/projects/treestoolbox | SCR_010457 | treestoolbox - A Matlab toolbox to generate edit visualize and analyze neuronal structure | 2026-08-01 12:04:13 | 28 |
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