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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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elastix Resource Report Resource Website 100+ mentions |
elastix (RRID:SCR_009619) | elastix | software toolkit, image analysis software, data processing software, registration software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | reusable library, analyze, c++, console (text based), domain independent, nifti, nrrd, os independent, philips par/rec, registration, resampling, spatial transformation, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is related to: Insight Segmentation and Registration Toolkit has parent organization: Utrecht University; Utrecht; Netherlands |
PMID:19923044 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155845, biotools:elastix | http://www.nitrc.org/projects/elastix, https://bio.tools/elastix, https://sources.debian.org/src/elastix/ | SCR_009619 | 2026-08-15 11:23:56 | 175 | ||||||
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BrainBrowser Resource Report Resource Website 1+ mentions |
BrainBrowser (RRID:SCR_009535) | BrainBrowser | production service resource, data analysis service, data or information resource, data set, service resource, analysis service resource | A web-enabled brain surface viewer that allows the user to explore in real time a 3D brain map expressed on a base surface. BrainBrowser has two modes of operation, exploring either a pre-calculated database of structural correlation maps or working with user-defined data. In this mode, the user may choose to explore the correlation structure for cortical thickness, cortical area or cortical volume, or any other pre-calculated metric. In the second mode, the user is prompted for the local filenames of the statistical map and the base surface. BrainBrowser can also be used to manipulate 3D fibre pathways derived from DTI, using the same simple file format (.obj) as for surface data. BrainBrowser on Youtube: http://www.youtube.com/watch?v=HlRTUYUf1Ew NOTE: BrainBrowser requires a WebGL-enabled browser such as Google Chrome to support its 3D graphics capability. | image display, javascript, minc2, magnetic resonance, nifti, os independent, rendering, ruby, surface rendering, three dimensional display, two dimensional display, visualization, volume rendering, 3d visualization, neuroimaging, fmri, web application, web resource, data visualization service |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Free | nlx_155710 | http://www.nitrc.org/projects/brainbrowser | SCR_009535 | 2026-08-15 11:23:58 | 3 | |||||||
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Wisconsin White Matter Hyperintensities Segmentation Toolbox Resource Report Resource Website 1+ mentions |
Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) | W2MHS | software toolkit, image analysis software, data processing software, software application, software resource, segmentation software, software library | An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis. | computational neuroscience, matlab, nifti, white matter hyperintensity, c++, matlab, ms windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM is related to: SourceForge has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Alzheimer's disease, Aging, Neurological disorder | Academic Free License | nlx_156021 | SCR_009652 | WM Hyperintensities Segmentation Toolbox | 2026-08-15 11:23:50 | 2 | ||||||
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BVQXtools Resource Report Resource Website 10+ mentions |
BVQXtools (RRID:SCR_009532) | BVQXtools | software toolkit, image processing software, data processing software, software application, software resource | A Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab. The toolbox is freely available. | analyze, format conversion, linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, statistical operation, time domain analysis, windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVoyager |
Free, Other/Commercial license License | nlx_155707 | SCR_009532 | 2026-08-15 11:23:55 | 11 | ||||||||
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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 | 2026-08-15 11:23:55 | 1811 | |||||
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BRAINSDemonWarp Resource Report Resource Website 1+ mentions |
BRAINSDemonWarp (RRID:SCR_009524) | BRAINSDemonWarp | image analysis software, data processing software, registration software, software application, software resource | A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: University of Iowa; Iowa; USA |
NINDS NS050568; NINDS NS40068; NIMH MH31593; NIMH MH40856 |
nlx_155700 | http://www.nitrc.org/projects/brainsdemonwarp | SCR_009524 | 2026-08-15 11:23:48 | 1 | |||||||
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SPM SS - fMRI functional localizers Resource Report Resource Website 1+ mentions |
SPM SS - fMRI functional localizers (RRID:SCR_009644) | spm_ss | software toolkit, image analysis software, data processing software, software application, software resource | Spm-toolbox that performs region of interest (ROI)-level and voxel-level between-subjects analyses of functional MRI data, restricting the analyses to those areas identified using subject-specific functional localizers. Methods: The toolbox implements ROI-level and voxel-level analyses, and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics) This toolbox requires Matlab and SPM5/SPM8. | analyze, linear, matlab, modeling, magnetic resonance, nifti, os independent, regression, statistical operation, win32 (ms windows), statistical parametric mapping, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
MIT License, X Consortium License | nlx_155955 | http://www.nitrc.org/projects/spm_ss | SCR_009644 | spm_ss toolbox, SPM toolbox for subject-specific analyses | 2026-08-15 11:24:00 | 5 | ||||||
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fMRI Classification in R Resource Report Resource Website 1+ mentions |
fMRI Classification in R (RRID:SCR_009519) | fMRI Classification in R | image processing software, image analysis software, data processing software, software application, software resource | They demonstrate and provide R code that can classify between groups of fMRI scans based on functional network connectivity differences, requiring only 4 lines of code to be altered. In addition, they include a detailed article explaining the methods behind and motivations of this tool. This code can also be altered to perform connectivity analysis and classification using ROI based methods by reading in distance arrays previously created. They run Independent component analysis (ICA) on fMRI data to establish functional networks, measure the functional connectivity between these networks using the temporal cross-correlations between independent component to create a distance matrix and indicating the networking. Connectivity properties are used as a feature matrix for an SVM classifier. Collectively, this project provides and explains both methods and code to perform functional network connectivity and fMRI SVM classi?cation. | magnetic resonance, connectivity, fmri, independent component analysis, functional network, classification | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155681 | SCR_009519 | 2026-08-15 11:23:58 | 1 | ||||||||
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DRAMMS Resource Report Resource Website 10+ mentions |
DRAMMS (RRID:SCR_009555) | DRAMMS | image analysis software, data processing software, registration software, software application, software resource | A software designed for deformable 2D-to-2D and 3D-to-3D image registration. Some typical applications of DRAMMS include, ** Cross-subject registration of the same organ (can be brain, breast, cardiac, etc); ** Mono- and Multi-modality registration (MRI, CT, histology); Longitudinal registration (pediatric brain growth, cancer development, etc); ** Registration under partial missing correspondences (small lesions, tumors, histological cuts). DRAMMS is implemented as a Unix command-line tool. It is fully automatic and easy to use ? users input two images, and DRAMMS will output the registered image and deformation. No need for pre-segmentation of any structures, no need for any prior knowledge, and no need for human initialization or intervention. | analyze, computational neuroscience, linux, macos, magnetic resonance, nifti, posix/unix-like, brain morphometry, general registration, image registration |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
BSD License | nlx_155736 | http://www.nitrc.org/projects/dramms | SCR_009555 | Deformable Registration via Attribute Matching and Mutual-Saliency Weighting, DRAMMS: Deformable Registration via Attribute Matching and Mutual-Saliency Matching | 2026-08-15 11:23:58 | 11 | ||||||
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Connectome Viewer Resource Report Resource Website 1+ mentions |
Connectome Viewer (RRID:SCR_009552) | Connectome Viewer | software toolkit, data processing software, software application, data analysis software, software resource, data visualization software | A free, open source, cross-platform Python-based software application for visualization and analysis in connectome research. Features of the software include: Connectome File Format including metadata, networks, surfaces, volumes, track files; complex network analysis toolboxes; modular plugin architecture for extensibility; Mayavi2 for 3D Scientific Visualization and Plotting; interactive data manipulation and scripting capabilities; and Neuroimaging and Diffusion in Python libraries. | animation, atlas application, c++, format conversion, gifti, image display, linux, macos, microsoft, magnetic resonance, nifti, posix/unix-like, python, rendering, software, surface rendering, three dimensional display, tractography, two dimensional display, visualization, volume rendering, win32 (ms windows), windows, connectome, connectomics, data management, multi-modal data, network analysis, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Connectome Mapping Toolkit |
PMID:21713110 | Open Source | nlx_155732 | http://www.nitrc.org/projects/cviewer | SCR_009552 | 2026-08-15 11:23:56 | 1 | ||||||
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CONN Resource Report Resource Website 1000+ mentions |
CONN (RRID:SCR_009550) | CONN | software toolkit, image analysis software, data processing software, software application, software resource | Matlab based cross platform software package for computation, display, and analysis of functional connectivity in fMRI (fcMRI). Used for resting state data (rsfMRI) as well as task related designs. Covers pipeline from raw fMRI data to hypothesis testing. | fmri functional connectivity, resting state data, seed-based correlations, ROI-to-ROI graph analyses, group ICA, masked ICA, generalized PPI, ALFF, ICC, GCOR, LCOR, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; works with: Eagle Atlas Compilation for Vestibular Research |
PMID:22642651 PMID:21889994 |
Free, Available for download, Freely available | nlx_155730 | www.nitrc.org/projects/conn | SCR_009550 | CONN toolbox, CONN - functional connectivity toolbox, Connectivity Toolbox (CONN) | 2026-08-15 11:23:58 | 1127 | |||||
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CBFBIRN Resource Report Resource Website 1+ mentions |
CBFBIRN (RRID:SCR_009543) | CBFBIRN | data repository, storage service resource, data or information resource, data set, service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is 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. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users. |
java, javascript, matlab, magnetic resonance, os independent, web environment, arterial spin labeling, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cerebral Blood Flow Database and Analysis Pipeline has parent organization: University of California at San Diego; California; USA |
NIH | PMID:24151465 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155722 | http://www.nitrc.org/projects/cbfbirn | SCR_009543 | Cerebral Blood Flow Biomedical Informatics Research Network | 2026-08-15 11:23:55 | 3 | ||||
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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 | 2026-08-15 11:23:48 | 8 | ||||||
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Alzheimer's disease ontology Resource Report Resource Website 1+ mentions |
Alzheimer's disease ontology (RRID:SCR_010289) | ADO | ontology, data or information resource, controlled vocabulary | An open, public ontology representing relevant knowledge on Alzheimer's disease. | owl, ontology, alzheimer | is listed by: BioPortal | Alzheimer's disease | Public, Open unspecified license | nlx_157314 | SCR_010289 | Alzheimers disease ontology | 2026-08-15 11:23:52 | 1 | ||||||
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CLIIQ Resource Report Resource Website 1+ mentions |
CLIIQ (RRID:SCR_009972) | CLIIQ | software resource | An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01272 | SCR_009972 | 2026-08-15 11:23:50 | 1 | ||||||||||
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G Protein-Coupled Receptor BioAssays Ontology Resource Report Resource Website 1+ mentions |
G Protein-Coupled Receptor BioAssays Ontology (RRID:SCR_010324) | BAO-GPCR | ontology, data or information resource, controlled vocabulary | Ontology (http://www.bioassayontology.org/bao_gpcr) that describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies. | owl |
is listed by: BioPortal has parent organization: Bioassay Ontology |
nlx_157410 | SCR_010324 | 2026-08-15 11:24:03 | 5 | |||||||||
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Crop Ontology Resource Report Resource Website 10+ mentions |
Crop Ontology (RRID:SCR_010299) | CO | ontology, data or information resource, controlled vocabulary | Ontology that includes crop-specific trait ontologies for several economically important plants like rice, wheat, maize, potato, musa, chickpea and sorghum along with other important domains for crop research such as germplasm, passport, trait measurement scales, experimental design factors etc. | obo | is listed by: BioPortal | nlx_157378 | http://cropontology.org/ | SCR_010299 | 2026-08-15 11:24:00 | 12 | ||||||||
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Sageweb Resource Report Resource Website 1+ mentions |
Sageweb (RRID:SCR_010217) | Sageweb | database, topical portal, portal, data or information resource, community building portal | A resource center that distributes important resources to the biogerontological community and facilitates interactions and collaborative efforts amongst researchers to aid biogerontologists and enhance research into the basic biology of aging. They aim to make SAGEWEB the premier aging-related website containing a variety of different content types including: * Databases related to the basic biology of aging * Software and bioinformatic tools for aging-related science * Educational tools for teachers and students interested in aging biology * Primers on important topics in aging-related science * Videos and podcasts of aging-related topics * Aging-related discussion forums and blogs * Links to additional aging-related labs, conferences, and resources | biogerontology, video, podcast, blog, meeting resource, software resource, training material |
has parent organization: University of Washington; Seattle; USA is parent organization of: Lifespan Observations Database |
Aging | Ellison Medical Foundation ; NIA |
The community can contribute to this resource | nlx_156771 | SCR_010217 | Sageweb - Science of Aging, Sageweb.org | 2026-08-15 11:23:58 | 2 | |||||
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BRENDA Tissue and Enzyme Source Ontology Resource Report Resource Website 1+ mentions |
BRENDA Tissue and Enzyme Source Ontology (RRID:SCR_010031) | BTO | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. | obo |
is used by: TISSUES is listed by: BioPortal has parent organization: BRENDA |
nlx_157323 | SCR_010031 | 2026-08-15 11:24:01 | 1 | |||||||||
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Society for Endocrinology Resource Report Resource Website 100+ mentions |
Society for Endocrinology (RRID:SCR_010273) | organization portal, data or information resource, portal, journal article | The major British society representing scientists, clinicians and nurses who work with hormones. | nlx_156934 | SCR_010273 | 2026-08-15 11:23:59 | 102 |
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