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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NeuroLens Resource Report Resource Website 1+ mentions |
NeuroLens (RRID:SCR_007372) | NeuroLens | data visualization software, data processing software, software application, image processing software, software resource, image analysis software | An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format | image-to-image, linear, temporal convolution - deconvolution, multivariate analysis, neuroimaging, fmri, brain structure, neural structure, brain, temporal convolution, temporal deconvolution, afni brik, analyze, cor, dicom, image display, macos, mgh/mgz, minc, magnetic resonance, objective c, registration, regression, rendering, software, spatial transformation, statistical operation, surface rendering, temporal transformation, three dimensional display, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Montreal; Quebec; Canada |
MGH CSRL License, - free for academic and non-profit research use. | nif-0000-00333 | http://www.nitrc.org/projects/nldo | SCR_007372 | 2026-02-14 02:01:31 | 9 | |||||||
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Automated Image Registration Resource Report Resource Website 10+ mentions |
Automated Image Registration (RRID:SCR_005944) | AIR | data processing software, alignment software, software library, software toolkit, software application, registration software, software resource, 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 | 2026-02-14 02:01:11 | 29 | |||||||
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BASH4RfMRI Resource Report Resource Website |
BASH4RfMRI (RRID:SCR_005970) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI. | algorithm or reusable library, information theory, spectral analysis, correlation, multivariate analysis, platform or development environment, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL is related to: Analysis of Functional NeuroImages is related to: FreeSurfer is related to: 1000 Functional Connectomes Project |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151343 | SCR_005970 | BASH Scripts, bash-rs-fcmri | 2026-02-14 02:01:01 | 0 | ||||||||
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Segmentation of Hippocampus Subfields Resource Report Resource Website 1+ mentions |
Segmentation of Hippocampus Subfields (RRID:SCR_005996) | ASHS | data processing software, software application, segmentation software, software resource, 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 | 2026-02-14 02:01:01 | 7 | |||||
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Artifact Detection Tools Resource Report Resource Website 100+ mentions |
Artifact Detection Tools (RRID:SCR_005994) | ART | data processing software, software toolkit, software application, image processing software, software resource, 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 | 2026-02-14 02:01:03 | 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 | portal, data or information resource, source code, software application, software resource, topical 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 | 2026-02-14 02:01:13 | 13 | |||||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | data processing software, data management software, software application, collaboration tool, 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 | 2026-02-14 02:01:12 | 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 | registration software, data processing software, software application, segmentation software, software resource, 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 | 2026-02-14 02:01:13 | 1 | |||||
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ABC (Atlas Based Classification) Resource Report Resource Website 1+ mentions |
ABC (Atlas Based Classification) (RRID:SCR_005981) | ABC | data processing software, workflow software, software application, 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 | 2026-02-14 02:01:01 | 3 | ||||||||
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Human Imaging Database Resource Report Resource Website 1+ mentions |
Human Imaging Database (RRID:SCR_006126) | HID | data repository, storage service resource, data management software, data or information resource, source code, service resource, software application, image repository, software resource, database |
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 | 2026-02-14 02:01:14 | 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 | data visualization software, data processing software, software application, image processing software, software resource | 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 | 2026-02-14 02:01:04 | 57 | ||||
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BrainImage Software Resource Report Resource Website 1+ mentions |
BrainImage Software (RRID:SCR_006139) | BrainImage | data processing software, software application, image 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 | 2026-02-14 02:01:03 | 8 | |||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | data processing software, software application, image 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 | 2026-02-14 02:01:14 | 1 | ||||||||
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NiftySim Resource Report Resource Website 1+ mentions |
NiftySim (RRID:SCR_006591) | NiftySim | software resource | A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages. | pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
BSD License | nlx_155900 | http://www.nitrc.org/projects/niftysim | SCR_006591 | Nifty Sim | 2026-02-14 02:01:09 | 3 | ||||||
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Web Game for Collaborative Labeling Resource Report Resource Website 1+ mentions |
Web Game for Collaborative Labeling (RRID:SCR_006685) | Web Game for Collaborative Labeling | software resource | Web game that provides an innovative infrastructure for labeling to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many, minimally-trained raters. Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system. Typically, an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive, so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function. | magnetic resonance, labeling, crowdsourcing | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_156019 | http://www.nitrc.org/projects/webmill | SCR_006685 | 2026-02-14 02:01:20 | 2 | |||||||
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S-rep Fitting Statistics and Segmentation Resource Report Resource Website |
S-rep Fitting Statistics and Segmentation (RRID:SCR_002540) | S-rep Fitting Statistics and Segmentation | data processing software, software application, segmentation software, software resource, image analysis software | Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed. | computational neuroscience, computed tomography, domain independent, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155948 | SCR_002540 | 2026-02-14 02:00:27 | 0 | ||||||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | data analysis software, software resource, data processing software, software application | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2026-02-14 02:00:25 | 17 | ||||||
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Resource Ontology Discussion Group Resource Report Resource Website |
Resource Ontology Discussion Group (RRID:SCR_002536) | Resource Ontology Discussion Group | knowledge environment, data or information resource, narrative resource, discussion | Project to discuss, debate, develop and deploy ontological practices for the fMRI community. | community, ontology, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155943 | SCR_002536 | 2026-02-14 02:00:25 | 0 | ||||||||
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Rodent Cortical Thickness Analysis Resource Report Resource Website |
Rodent Cortical Thickness Analysis (RRID:SCR_002539) | data processing software, software application, image processing software, software resource, image analysis software | An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling | microscopy, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155946 | http://www.nitrc.org/projects/rodentthickness | SCR_002539 | RodentThickness | 2026-02-14 02:00:17 | 0 | |||||||
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Rodent Brain Extraction Tool Resource Report Resource Website |
Rodent Brain Extraction Tool (RRID:SCR_002538) | rBET | image processing software, software resource, data processing software, software application | A modified version of the Brain Extraction Tool (BET) that can process rodent brains. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: King's College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_155945 | http://www.nitrc.org/projects/rbet | SCR_002538 | 2026-02-14 02:00:26 | 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.
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