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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Automated Image Registration Resource Report Resource Website 10+ mentions |
Automated Image Registration (RRID:SCR_005944) | AIR | alignment software, software application, data processing software, registration software, software resource, software toolkit, software library, image analysis software | A tool for automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs. | registration, alignment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps |
GNU General Public License | nif-0000-00260 | http://www.nitrc.org/projects/air | SCR_005944 | 2026-02-17 10:00:42 | 29 | |||||||
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Human Imaging Database Resource Report Resource Website 1+ mentions |
Human Imaging Database (RRID:SCR_006126) | HID | data management software, software application, storage service resource, data or information resource, database, software resource, service resource, source code, data repository, image repository |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented October 5, 2017. Database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. The HID can be extended to contain relevant information concerning experimental subjects, assessments of subjects, the experimental data collected, the experimental protocols, and other metadata normally included with experiments. |
imaging, fmri, clinical, behavior, biomedical imaging data, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cognitive Paradigm Ontology is related to: XCEDE Schema has parent organization: Biomedical Informatics Research Network |
Schizophrenia | PMID:19826494 PMID:18348946 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00269 | http://www.nitrc.org/projects/hid | http://fbirnbdr.nbirn.net:8080/BDR/ | SCR_006126 | fBIRN Data Repository, Human Imaging Database (HID) System, Function BIRN Data Repository | 2026-02-17 10:00:45 | 3 | |||
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BrainImage Software Resource Report Resource Website 1+ mentions |
BrainImage Software (RRID:SCR_006139) | BrainImage | software application, image processing software, data processing software, software resource, image analysis software | A multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers. BrainImageJava can: * Delineate ROIs in slices along X, Y, or Z axes, with 3D feedback in the other axes. * Create and display triangular mesh surfaces from MRI volumes. * Draw Surfaces-of-Interest (SOIs) in 3D, and edit them in a planar display. * Set Talairach grid on a volume, export an AC/PC stack, and measure the values within each grid unit. This 3D image processing and analysis program for the Apple Macintosh PowerPC is based on the public domain application, NIH Image. It includes interactive procedures for 3D MRI quantification including semi-automated procedures for removing non-brain tissues from images, fuzzy segmentation of tissue compartments, global or local parcellation (based on the Talairach atlas), region-growing, etc. The last version of the software included multiplatform capability, volume visualization and advanced image analysis tools. | mri, segmentation, visualization, volume, neuroimaging, analyze, anatomic, application, artifact removal, image display, java, labeling, macos, mesh generation, microsoft, modeling, magnetic resonance, quantification, region of interest, rendering, spatial transformation, three dimensional display, volume measurement, volumetric analysis, volumetric analysis, windows, platform |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: NIH Image has parent organization: Stanford University School of Medicine; California; USA |
Human Brain Project | GNU General Public License | nif-0000-00272 | http://spnl.stanford.edu/tools/brainimage.htm | SCR_006139 | Brain Image, BrainImageJ, BrainImageJava | 2026-02-17 10:00:45 | 8 | |||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | software application, image processing software, data processing software, software resource, image analysis software | A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. | ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Database is related to: Brede Wiki has parent organization: THOR Center for Neuroinformatics |
Free for academic use, Acknowledgement requested | nif-0000-00275 | SCR_006204 | 2026-02-17 10:00:47 | 1 | ||||||||
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Segmentation of Hippocampus Subfields Resource Report Resource Website 1+ mentions |
Segmentation of Hippocampus Subfields (RRID:SCR_005996) | ASHS | software application, data processing software, software resource, segmentation software, image analysis software | A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL | hippocampus, mri, t1-weighted image, t2-weighted image, ca1, ca2, ca3, statistical modeling, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ANTS - Advanced Normalization ToolS is related to: FSL has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:19405131 PMID:20600984 |
GNU General Public License | nlx_151370 | http://www.nitrc.org/projects/ashs | SCR_005996 | Automatic Segmentation of Hippocampal Subfields, HippocampalSubfieldSegmentation | 2026-02-17 10:00:51 | 7 | |||||
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Artifact Detection Tools Resource Report Resource Website 100+ mentions |
Artifact Detection Tools (RRID:SCR_005994) | ART | software application, image processing software, data processing software, software resource, software toolkit, image analysis software | Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well. * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE | artifact removal, quality metrics, registration, motion analysis, neuroimaging, fmri, spike, motion, artifact, timeseries, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: RapidArt has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Free, Available for download | nlx_151369 | http://www.nitrc.org/projects/artifact_detect | SCR_005994 | 2026-02-17 10:01:03 | 204 | |||||||
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Allen Brain Atlas API Resource Report Resource Website 10+ mentions |
Allen Brain Atlas API (RRID:SCR_005984) | Allen Brain Atlas API | software application, data or information resource, topical portal, source code, software resource, portal | API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service | atlas application, expression data, 3d volume, 3d coordinate, gene, reference atlas, connectivity, histology, microarray, brain, rna sequencing, mri, dti, api, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics, ish, high resolution image, nissl, annotation, atlas, image, web service, neuroblast, gene expression, gene, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Mouse Brain Reference Atlas is related to: Allen Developing Mouse Brain Atlas is related to: International Neuroinformatics Coordinating Facility is related to: Brain Explorer Atlas and Teaching Tool is related to: CellTax vignette is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science |
Other/Commercial license License | nlx_151358 | http://www.nitrc.org/projects/incf_allen-brai | SCR_005984 | 2026-02-17 10:00:50 | 13 | |||||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | data management software, software application, collaboration tool, data processing software, software resource | A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications. | annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC has parent organization: University of Utah; Utah; USA |
Research to Prevent Blindness ; University of Utah; Utah; USA ; Graduate Research Fellowship ; Utah Science Technology and Research Initiative ; NEI R01 EY02576; NEI R01 EY015128; NEI P01 EY014800; NSF 0941717; NIDCD T32DC008553; NIBIB EB005832 |
PMID:21118201 | Open source | nlx_151360 | http://www.nitrc.org/projects/viking_viewer | SCR_005986 | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-02-17 10:00:59 | 14 | |||||
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Hammer And WML Modules for 3D Slicer Resource Report Resource Website 1+ mentions |
Hammer And WML Modules for 3D Slicer (RRID:SCR_005980) | HAMMER, hammerwml | software application, data processing software, registration software, software resource, segmentation software, image analysis software | A software plugin for 3D Slicer that matches morphological signatures of medical images automatically. HAMMER is an acronym for Hierarchical Attribute Matching Mechanism for Elastic Registration (Dinggang Shen, Christos Davatzikos, HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002) - an elastic registration algorithm for medical images, matching morphological signatures of images in a hierarchical multi-scale regime. White matter lesion (WML) segmentation is a novel multi-spectral WML segmentation protocol via incorporating information from T1-w, T2-w, PD-w and FLAIR MR brain images. (Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008). | mri, registration, white matter lesion, segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:12575879 PMID:18280928 |
3D Slicer License | nlx_151352 | http://www.nitrc.org/projects/hammerwml | SCR_005980 | HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, Hierarchical Attribute Matching Mechanism for Elastic Registration and White matter lesion Modules for 3D Slicer | 2026-02-17 10:00:59 | 1 | |||||
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ABC (Atlas Based Classification) Resource Report Resource Website 1+ mentions |
ABC (Atlas Based Classification) (RRID:SCR_005981) | ABC | software application, workflow software, data processing software, software resource, image analysis software | A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput. | brain, image, image registration, filter, segmentation, inhomogeneity correction, beta, c++, linux, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: INCF Software Center has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of Utah; Utah; USA |
3D Slicer License | nlx_151362 | SCR_005981 | 2026-02-17 10:00:42 | 3 | ||||||||
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Computerized Anatomical Reconstruction and Editing Toolkit Resource Report Resource Website 50+ mentions |
Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) | CARET | software application, image processing software, data processing software, software resource, data visualization software | Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems. | reconstruction, visualization, cerebral cortex, surface, brain, dataset, cerebellar cortex, atlas application, mesh generation, quantitative shape analysis, segmentation, shape analysis, intersubject, image-to-template, gaussian curvature, mean curvature, animation, three dimensional display, two dimensional display, surface rendering, cortical flat map, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SumsDB has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIMH R01 MH60974; NEI EY02091 |
PMID:11522765 | Free, Available for download, Freely available | nif-0000-00279 | http://www.nitrc.org/projects/caret https://sources.debian.org/src/caret/ |
SCR_006260 | Computerized Anatomical Reconstruction Editing Toolkit | 2026-02-17 10:01:05 | 57 | ||||
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Federal Interagency Traumatic Brain Injury Research Informatics System Resource Report Resource Website 50+ mentions |
Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) | FITBIR | narrative resource, storage service resource, data or information resource, topical portal, database, service resource, standard specification, portal, data repository | Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories. | Traumatic, brain, injury, platform, common, data, element, medical, imaging, clinical, assessment, environment, behavior, brain, magnetic, resonance |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: NIH Data Sharing Repositories is related to: NIH Data Sharing Repositories has parent organization: Center for Information Technology |
Traumatic Brain Injury | NINDS ; U.S. Army Medical Research and Material Command ; Center for Information Technology |
Restricted | nlx_151755, r3d100012837 | https://doi.org/10.17616/R31NJMED | SCR_006856 | Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System, FITBIR Informatics System | 2026-02-17 10:01:00 | 57 | ||||
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Scalable Brain Atlas Resource Report Resource Website 10+ mentions |
Scalable Brain Atlas (RRID:SCR_006934) | SBA | software application, data or information resource, atlas, reference atlas, service resource, software resource | A web-based, interactive brain atlas viewer, containing a growing number of atlas templates for various species, including mouse, macaque and human. Standard features include fast brain region lookup, point and click to select a region and view its full 3D extent, mark a stereotaxic coordinate and view all regions in a hierarchy. Built-in extensions are the CoCoMac plugin, which provides a spatial display of Macaque connectivity, and a service to transform stereotaxic coordinates to and from the INCF Waxholm space for the mouse. Three dimensional renderings of brain regions are available through a Matlab interface (local installation of Matlab required). The SBA is designed to be customizable. External users can create plugins, hosted on their own servers, to interactively attach images or data to spatial atlas locations. This fully web-based display engine for brain atlases and topologies allows client websites to show brain region related data in a 3D interactive context. Currently available atlases are: * Macaque: The Paxinos Rhesus Monkey atlas (2000) * Macaque: Various templates available through Caret, registered to F99 space: Felleman and Van Essen (1991), Lewis and Van Essen (2000), Regional Map from K��tter and Wanke (2005), Paxinos Rhesus Monkey (2000) * Macaque: The NeuroMaps Macaque atlas (2008) * Mouse: The INCF Waxholm Space for the mouse (2011). Previous versions available. * Mouse: The Allen Mouse Brain volumetric atlas (ABA07) * Human: The LPBA40 parcellation, registered to SRI24 space A variety of services are being developed around the templates contained in the Scalable Brain Atlas. For example, you can include thumbnails of brain regions in your own webpage. Other applications include: * Analyze atlas templates in Matlab * List all regions belonging to the given template * List of supported atlas templates * Find region by coordinate * Color-coded PNG (bitmap) or SVG (vector) image of a brain atlas slice * Region thumbnail in 2D (slice) or 3D (stack of slices) The Scalable Brain Atlas is created by Rembrandt Bakker and Gleb Bezgin, under supervision of Rolf K��tter in the NeuroPhysiology and -Informatics group of the Donders Institute, Radboud UMC Nijmegen. | atlas application, atlas data, image display, javascript, magnetic resonance, os independent, php, three dimensional display, tractography, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CoCoMac is related to: 3DBar has parent organization: International Neuroinformatics Coordinating Facility |
International Neuroinformatics Coordinating Facility | GNU General Public License | nlx_98156 | http://www.nitrc.org/projects/sba | SCR_006934 | INCF Scalable Brain Atlas | 2026-02-17 10:01:10 | 21 | |||||
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NeuroPub Visualizer Resource Report Resource Website |
NeuroPub Visualizer (RRID:SCR_006797) | NeuroPub | mobile app, software application, data processing software, software resource, data visualization software | A NIfTI visualizer for statistical brain images (fMRI, VBM, etc) the iPad. The visualizer displays these images as overlay on the MNI standard brain. You can use it to store all your statistical images from your fMRI / VBM / TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. It's the perfect app to bring to meetings, conferences, etc, and show your latest results. | magnetic resonance, fmri, vbm, tbss | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155827 | http://www.nitrc.org/projects/neuropub | SCR_006797 | 2026-02-17 10:00:58 | 0 | |||||||
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Cambridge Brain Activation Resource Report Resource Website 10+ mentions |
Cambridge Brain Activation (RRID:SCR_007109) | CamBA | software application, workflow software, data processing software, software resource, software toolkit, image analysis software | Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution. | analysis, brain, anova, resampling, statistical, wavelet, fmri, pipeline, affine warp, algorithm or reusable library, application, c, image-to-template, java, linux, macos, magnetic resonance, nifti-1, posix/unix-like, registration, regression, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, unix shell, warping, wavelet transformation, web environment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Cambridge; Cambridge; United Kingdom |
GlaxoSmithKline ; Human Brain Project ; NIMH ; NIBIB |
GNU General Public License | nif-0000-00267 | http://www-bmu.psychiatry.cam.ac.uk/software/ | SCR_007109 | 2026-02-17 10:01:01 | 11 | ||||||
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ABSORB: Atlas Building by Self-Organized Registration and Bundling Resource Report Resource Website 1+ mentions |
ABSORB: Atlas Building by Self-Organized Registration and Bundling (RRID:SCR_007018) | ABSORB | software application, data processing software, registration software, source code, software resource, image analysis software | This software package implements an algorithm for effective groupwise registration. The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5). The images should be pre-processed before applying ABSORB: * All brain MR images used as inputs to ABSORB should be in the same situation (e.g., skull-stripped or not, cerebellum removed or not, etc.). * The input images should be in Analyze format with paired header and image files. This software was developed in IDEA group in UNC-Chapel Hill. | image, registration, bundling, atlas, magnetic resonance, algorithm or reusable library, intermodal, intersubject, intrasubject, image-to-template, affine warp, nonlinear warp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:20226255 | Free, Public | nlx_144409 | http://www.nitrc.org/projects/absorb | SCR_007018 | ABSORB: Atlas Building by Self-Organized Registration Bundling, Atlas Building by Self-Organized Registration Bundling, Atlas Building by Self-Organized Registration and Bundling | 2026-02-17 10:01:11 | 1 | |||||
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Matlab Neuroshare Library Resource Report Resource Website |
Matlab Neuroshare Library (RRID:SCR_006957) | NeuroshareLibrary | software library, software resource, software toolkit | This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file. | console (text based), eeg, meg, electrocorticography, format conversion, japanese, linux, macos, matlab, microsoft, posix/unix-like, windows, neuroshare, data format, data sharing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ATR; Kyoto; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | GNU General Public License | nlx_155880 | http://www.nitrc.org/projects/nslib_v1_3_1 | SCR_006957 | Neuroshare Library | 2026-02-17 10:01:00 | 0 | |||||
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MRI Studio Resource Report Resource Website 100+ mentions |
MRI Studio (RRID:SCR_001398) | data visualization software, software application, image processing software, data processing software, software resource, image analysis software | An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration | tensor calculation, color mapping, fiber tracking, 3d visualization, dti, image registration, mri, diffusion mr fiber tracking, microsoft, c++, analyze |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion Tensor Imaging ToolKit has parent organization: Johns Hopkins University; Maryland; USA works with: UManitoba - JHU Functionally Defined Human White Matter Atlas |
NCRR ; Biomedical Informatics Research Network ; NIBIB |
Free, Freely Available | nif-0000-00291 | http://www.nitrc.org/projects/mri_studio | SCR_001398 | dtiStudio, DTI Studio | 2026-02-17 09:59:36 | 165 | ||||||
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Waxholm Space Resource Report Resource Website 10+ mentions |
Waxholm Space (RRID:SCR_001592) | WHS, WSA, WSS | narrative resource, data or information resource, atlas, standard specification, waxholm atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files. | mouse WHS atlas, neuroanatomy, mapping, atlas, digital, brain, reference, registration, neuroanatomical, data, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Waxholm Space is related to: Duke University; North Carolina; USA is related to: PMOD Software is related to: ITK-SNAP has parent organization: International Neuroinformatics Coordinating Facility has parent organization: University of Oslo; Oslo; Norway works with: MeshView works with: VisuAlign |
PMID:20600960 PMID:21304938 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_009594, nlx_153838, nlx_155839 | http://software.incf.org/software/waxholm-space/home, http://www.nitrc.org/projects/incf_waxholm-sp | SCR_001592 | Waxholm Space Atlas, Waxholm Space, Waxholm Standard Space, Mouse WHS atlas | 2026-02-17 09:59:38 | 16 | |||||
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NIDAG: Neuroimaging Data Access Group Resource Report Resource Website |
NIDAG: Neuroimaging Data Access Group (RRID:SCR_001674) | NIDAG | narrative resource, international standard specification, data or information resource, standard specification, knowledge environment | An international working group dedicated to improving access to neuroimaging results in a free and open-access manner. It seeks to establish a universal coordinate database, including both past papers and future studies. Their current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete, this will allow anyone to find all of the articles that report a coordinate, or set of coordinates, easily and without cost. Eventually, they hope to expand this database to include not only coordinates, but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited, and also be a very useful tool for those interested in meta-analysis, and hopefully clarify structure-function relationships. They are interested in hearing from people who might be willing to contribute to their projects, particularly those with programming experience. The number of published neuroimaging studies is increasing rapidly and it is not feasible to read them all. If a computer database could store key information from published fMRI papers and make that information easier to search or share, this would have substantial benefits for the neuroimaging community. Projects like AMAT, Brainmap, Brede and SumsDB have started to tackle this problem. NIDAG wants to formalize and improve these databases so that they meet the needs of the neuroimaging community. Formal meta-analysis of published data is a valuable way to assess the consistency and reliability of experimental results. A database of neuroimaging results would facilitate meta-analyses, in conjunction with tools like GingerALE and Multi-level Kernel Density Analysis. | fmri, database, neuroimaging, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: AMAT |
Free, Freely Available | nif-0000-10161 | http://www.nitrc.org/projects/nidag | SCR_001674 | Neuroimaging Data Access Group | 2026-02-17 09:59:41 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
Email: info_at_ dknet.org
