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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Generic Exome Analysis Plan Resource Report Resource Website |
Generic Exome Analysis Plan (RRID:SCR_009656) | data or information resource, narrative resource, experimental protocol | Outline of a generic plan for analysis of a whole exome sequencing project. |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
nlx_156093 | SCR_009656 | 2026-08-08 11:59:26 | 0 | |||||||||||
|
BSMac Resource Report Resource Website |
BSMac (RRID:SCR_009531) | BSMac | software toolkit, image analysis software, software resource, software application, data processing software | A statistical and graphical visualization MATLAB toolbox for the analysis of fMRI data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on MCMC methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results. | computational neuroscience, magnetic resonance, brain activation, connectivity, matlab, statistics, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Emory University; Georgia; USA |
PMID:22101143 PMID:17936016 |
Acknowledgement requested, BSD License, GNU Lesser General Public License, GNU General Public License | nlx_155706 | http://www.nitrc.org/projects/bsmac | SCR_009531 | BSMAC Software, Bayesian Spatial Model for Brain Activation and Connectivity, BSMac: Bayesian Spatial Model for Brain Activation and Connectivity | 2026-08-08 11:59:13 | 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 | 2026-08-08 11:59:13 | 0 | ||||||||
|
iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-08-08 11:59:21 | 11 | ||||||
|
SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-08-08 11:59:24 | 21 | |||||||
|
INCF Neuroimaging Data Sharing Resource Report Resource Website |
INCF Neuroimaging Data Sharing (RRID:SCR_009497) | INCF Neuroimaging Data Sharing | data or information resource, narrative resource, standard specification | Program to develop generic standards and tools to facilitate the recording, sharing, and reporting of neuroimaging metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications. | community, knowledge environment, loni pipeline, magnetic resonance, nipype |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: International Neuroinformatics Coordinating Facility |
Creative Commons License | nlx_155645 | SCR_009497 | 2026-08-08 11:59:24 | 0 | ||||||||
|
GTRACT Resource Report Resource Website 1+ mentions |
GTRACT (RRID:SCR_009651) | GTRACT | software toolkit, image processing software, image analysis software, software resource, software application, data processing software | A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools | c++, dicom, macos, microsoft, modeling, morphology, magnetic resonance, nifti, posix/unix-like, quantification, tensor metric, tractography, windows, dti, diffusion tensor fiber tracking, fiber tracking, nrrd, algorithm, connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of Iowa; Iowa; USA |
Aging | NARSAD ; NINDS R01NS050568-01A2S1; NINDS 5R01NS040068-04; NIMH 5R01MH063405-04; NIMH 5R01MH031593-23; NIMH 2R01MH040856-17A2; NIA 5K23AG020649-03; NIDCR 5R01DE014399-04 |
PMID:16631385 | BSD License | nlx_155992 | SCR_009651 | Guided Tensor Restore Anatomical Connectivity Tractography | 2026-08-08 11:59:26 | 2 | ||||
|
IDeA Lab brain image processing suite Resource Report Resource Website 1+ mentions |
IDeA Lab brain image processing suite (RRID:SCR_009495) | IDeA Lab brain image processing suite | software toolkit, image analysis software, software resource, software application, data processing software | Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added. | analyze, c++, console (text based), csh/tcsh, image display, image-to-image, image-to-template, intermodal, intersubject, linux, magnetic resonance, nifti, nonlinear warp, posix/unix-like, quantification, registration, resampling, spatial transformation, spline interpolation, tri-linear, two dimensional display, unix shell, visualization, volume measurement, volumetric analysis, warping | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155644 | SCR_009495 | 2026-08-08 11:59:13 | 1 | |||||||||
|
Groupwise Image Registration Toolbox Resource Report Resource Website |
Groupwise Image Registration Toolbox (RRID:SCR_009492) | Groupwise Image Registration | registration software, image analysis software, software resource, software application, data processing software | A method for group-wise image registration by pairwisely registering similar images identified using graph theoretic techniques. Particularly, they use sparse coding to estimate image similarity measures among images to be registered, yielding asymmetric, group-wise image similarity measures for each image to others in the group. | domain independent |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
PAMI License, Http://www.nitrc.org/include/glossary.php#690, Non-commercial | nlx_155640 | SCR_009492 | 2026-08-08 11:59:21 | 0 | ||||||||
|
HD Neuro-Informatics Resource Report Resource Website 1+ mentions |
HD Neuro-Informatics (RRID:SCR_009493) | HDNI | data or information resource, portal, topical portal | An international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in Huntington''s Disease (HD). The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Huntington''s disease | BSD License | nlx_155641 | SCR_009493 | Huntington Disease Nueroimaging Initiative | 2026-08-08 11:59:24 | 2 | ||||||
|
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 | 2026-08-08 11:59:15 | 15 | |||||||
|
REST: a toolkit for resting-state fMRI Resource Report Resource Website 1000+ mentions |
REST: a toolkit for resting-state fMRI (RRID:SCR_009641) | REST | image processing software, software toolkit, image analysis software, software resource, software application, data processing software | A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files. | correlation, cross-correlation, fourier time-domain analysis, gnome, kde, linux, macos, matlab, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, two dimensional display, visualization, windows, resting-state functional magnetic resonance imaging, resting-state fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China |
National High Technology Program of China ; National Natural Science Foundation of China ; Program for Changjiang Scholars and Innovative Research Team in University |
PMID:21949842 | Academic Free License | nlx_155936 | http://www.nitrc.org/projects/rest | SCR_009641 | Resting-State fMRI Data Analysis Toolkit, REsting State fMRI Data analysis Toolkit | 2026-08-08 11:59:15 | 1004 | ||||
|
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 | 2026-08-08 11:59:23 | 3 | ||||||||
|
QCQP Resource Report Resource Website |
QCQP (RRID:SCR_009640) | QCQP | image processing software, segmentation software, image analysis software, software resource, software application, data processing software | Quadratically constrained quadratic programing (QCQP) technique in medical image analysis. QCQP based tools are provided for classification, segmentation, and bias field correction. | magnetic resonance, classification, segmentation, bias field correction | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155932 | SCR_009640 | Quadratically constrained quadratic programing | 2026-08-08 11:59:26 | 0 | ||||||||
|
DTI BrainImageScope Resource Report Resource Website |
DTI BrainImageScope (RRID:SCR_009559) | dtiBrainScope | image processing software, software resource, software application, data processing software | Software package for processing diffusion tensor imaging data. The following functions are included: 1. Converting imaging data in DICOME format to ANALYZE format 2. Extracting binary brain mask for quick scalp-removing 3. Correcting eddy-current induced distortion 4. Optimized tensor estimation based on noisy diffusion-weighted imaging (DWI) data 5. Scalp removal using a brain mask image 6. Corregistering imaging data and generating deformation field for mapping images from individual spaces to a template or target space 7. Spatial Normalization and Warping DTI 8. Fiber tracking 9. Clustering fiber tracts 10. Identifying brain ventricles and generating binary masks for the baseline and DW imaging data 11. Deriving diffusion anisotropy indices (DAIs) and principal directions (PD) and the corresponding color-coded PD-map. | magnetic resonance, diffusion tensor imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: Columbia University; New York; USA |
NIBIB 1R03EB008235-01A1; Shanghai CST 10440710200 |
Other/Commercial license License | nlx_155739 | SCR_009559 | 2026-08-08 11:59:22 | 0 | |||||||
|
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) | 2026-08-08 11:59:14 | 0 | ||||||
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CoCoMac-Paxinos3D viewer Resource Report Resource Website |
CoCoMac-Paxinos3D viewer (RRID:SCR_009548) | CoCoMac-Paxinos3D viewer | software resource, software application, data visualization software, data processing software | An interactive interface of macaque stereotaxic atlas with a connectivity database, allowing integrated data analysis and mapping between 3D structures with database vocabularies. These Java-based tools are capable of reading stacks of polygons described in svg vector format and arrange them in 3D space so that the corresponding structures can be viewed and manipulated individually. An additional excel (currently v. 1997-2003) file maintains the structure abbreviations and their mapping to the terminology of databases that provide supplementary information. Here in particular we have manually drawn the cortical, striatal, thalamic and amygdaloid structures of the 151 frontal sections from the Rhesus Monkey Brain in Stereotactic Coordinates authored by Paxinos and colleagues in 1999. After loading the excel file and a set of the svg files, the view can be rotated, zoomed and individual brain structures be selected for identification and simple geometric measures. A stereotaxic grid is a display option. The abbreviations of the brain structures are mapped to entities recorded in the CoCoMac database of primate brain connectivity. Thereby one can retrieve mapping and connectivity information for the selected structure as text or connecting arrows. | magnetic resonance, java, mapping, connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: CoCoMac |
PMID:19145492 | GNU General Public License | nlx_155728 | http://www.nitrc.org/projects/cp3d | SCR_009548 | 2026-08-08 11:59:14 | 0 | ||||||
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INVIZIAN Resource Report Resource Website 1+ mentions |
INVIZIAN (RRID:SCR_009549) | INVIZIAN | software resource, software application, data visualization software, data processing software | A visualization environment that enables you, via your computer, to display and interact with hundreds of neuroimaging data sets at once ?bringing together brain image data from some of the world?s best neuroscience research teams. INVIZIAN empowers both researchers and students of neuroscience to explore and understand the human brain using a simple yet powerful user interface for neuroimaging data exploration and discovery. See a beautiful example of a cloud of individual brains tumbling around in the INVIZIAN interface in Vimeo (http://vimeo.com/67984681). Visit often to see how we are making continuing progress to make Invizian even more amazing. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
LONI Software License | nlx_155775 | http://www.nitrc.org/projects/invizian | SCR_009549 | Informatics Visualization in Neuroimaging | 2026-08-08 11:59:22 | 1 | ||||||
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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 | 2026-08-08 11:59:25 | 0 | ||||||
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Oregon Health and Science University; Oregon; USA Resource Report Resource Website 1+ mentions |
Oregon Health and Science University; Oregon; USA (RRID:SCR_009665) | OHSU | university | As the state''s only health and research university, OHSU brings together patient care, research, education of the next generation of health care providers and scientists and community service to improve the health and well-being of all Oregonians. |
is related to: Alzheimers Disease Genetics Consortium is related to: International AMD Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is parent organization of: OHSU MRI Support Core Laboratory is parent organization of: MCML and CONV is parent organization of: Neuron Registry Annotated Corpus is parent organization of: OHSU Biolibrary is parent organization of: Sterol and Isoprenoid Research Consortium is parent organization of: CTSAconnect is parent organization of: CTSA ShareCenter is parent organization of: OHSU Layton Aging and Alzheimer's Disease Center is parent organization of: Clinical Outcomes Research Initiative is parent organization of: OHSU Investigator Support and Integration Services is parent organization of: OHSU Advanced Computing Center Core Facility is parent organization of: OHSU Advanced Imaging Research Center Core Facility is parent organization of: OHSU Advanced Light Microscopy Core Facility is parent organization of: OHSU Assisted Reproductive Technologies and Embryonic Stem Cell Laboratory is parent organization of: OHSU Bioanalytical Shared Resource Pharmacokinetics Core Facility is parent organization of: OHSU Biochemical Genetics Laboratory is parent organization of: Oregon Clinical and Translational Research Institute Biomedical Informatics Program is parent organization of: OHSU Biomedical Informatics Shared Resource is parent organization of: OHSU Clinical Cytogenetics Laboratory is parent organization of: OHSU DNA Services Core Facility is parent organization of: Oregon Health and Science University Multiscale Microscopy Core Facility is parent organization of: OHSU Electronics and Instrumentation Design Core Resource is parent organization of: OHSU Endocrine Technology Support Core Laboratory is parent organization of: OHSU Flow Cytometry and Monoclonal Antibody Shared Resource Core Facility is parent organization of: OHSU Gene Profiling Shared Resource Core Facility is parent organization of: OHSU Lipid-Atherosclerosis Laboratory is parent organization of: OHSU Histopathology Shared Resource Core Facility is parent organization of: OHSU Imaging and Morphology Support Core Laboratory is parent organization of: OHSU Immuno Electron Microscopy Core is parent organization of: OHSU Immunology Support Core Cellular Immunology Unit is parent organization of: OHSU Immunology Support Core Flow Cytometry Unit is parent organization of: OHSU In Vivo Optical Imaging Center is parent organization of: OHSU Massively Parallel Sequencing Shared Resource Core Facility is parent organization of: OHSU Methamphetamine Abuse Research Center Animal Core Component is parent organization of: OHSU Molecular and Cellular Biology Core Laboratory is parent organization of: OHSU Monoclonal Antibody Core Laboratory is parent organization of: OHSU Neuropathology Core is parent organization of: OHSU Nuclear Magnetic Resonance Core Facility is parent organization of: OHSU Proteomics Shared Resource Core Facility is parent organization of: OHSU Research Cytogenetics Core Laboratory is parent organization of: OHSU Animal Model Support Core Facility is parent organization of: Oregon Clinical and Translational Research Institute Bionutrition Unit is parent organization of: OHSU Oregon Clinical and Translational Research Center Core Facility is parent organization of: Oregon Stem Cell Center Monoclonal Antibody Core is parent organization of: OSHU Gene Microarray Shared Resource is parent organization of: Oregon Health and Science University Labs and Facilities is parent organization of: OHSU DNA Services Core Facility is parent organization of: OHSU Molecular Virology Support Core is parent organization of: Oregon Health and Science University School of Medicine; Oregon; USA is parent organization of: Zebra Finch Expression Brain Atlas is parent organization of: Oregon Brain Bank is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: Eagle I is parent organization of: Oregon Health and Science University Integrated Genomics Laboratory Core Facility is parent organization of: Oregon Health and Science University Multiscale Microscopy Core Facility is parent organization of: Oregon Health and Science University Elemental Analysis Core Facility is parent organization of: Oregon Health and Science University Center for Radiochemistry Research Core Facility is parent organization of: Oregon Health and Science University Biophysics Core Facility is parent organization of: Oregon Health and Science University Small Animal Research Imaging Core Facility is parent organization of: Oregon Health and Science University Biostatistics and Design Program Core Facility is parent organization of: Oregon Health and Science University Medicinal Chemistry Core Facility is parent organization of: Oregon Health and Science University Bioinformatics and Biostatistics Core Facility is parent organization of: MONARCH Initiative is parent organization of: Oregon Health and Science University Primate Genetics Core Facility is parent organization of: OHSU Monoclonal Antibody Shared Resource Core Facility |
nlx_80843, grid.5288.7, Crossref funder ID:100006668, Wikidata:Q282097, ISNI:0000 0000 9758 5690 | https://ror.org/009avj582 | SCR_009665 | Oregon Health & Science University; Oregon; USA, Oregon Health & Science University, Oregon Health University | 2026-08-08 11:59:24 | 1 |
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