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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NiBabel Resource Report Resource Website 100+ mentions |
NiBabel (RRID:SCR_002498) | NiBabel | software resource | A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI. | magnetic resonance, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PyNIfTI is related to: MNE software has parent organization: Neuroimaging in Python |
Free, Available for download, Freely available | nlx_155896 | http://www.nitrc.org/projects/nibabel | SCR_002498 | NIPY File IO | 2026-02-14 02:00:25 | 122 | ||||||
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Pythagorean Displacement and Motion Regressors Resource Report Resource Website 1+ mentions |
Pythagorean Displacement and Motion Regressors (RRID:SCR_002525) | Pythagorean Displacement and Motion Regressors | software resource | Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment. | algorithm, magnetic resonance, matlab, pythagorean theorem, head, motion, position, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155931 | SCR_002525 | 2026-02-14 02:00:26 | 5 | ||||||||
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Signed Differential Mapping Resource Report Resource Website 100+ mentions |
Signed Differential Mapping (RRID:SCR_002554) | SDM | software resource | Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera). | magnetic resonance, pet, spect, fmri, vbm, meta-analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155962 | http://www.nitrc.org/projects/sdm | SCR_002554 | 2026-02-14 02:00:27 | 150 | |||||||
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Triangle BioSystems Resource Report Resource Website 10+ mentions |
Triangle BioSystems (RRID:SCR_002603) | TBSI | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software | computational neuroscience, eeg, eeg, meg, electrocorticography, hardware, other software resource, physiological recording, software | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156006 | http://www.nitrc.org/projects/tbsi | SCR_002603 | Triangle BioSystems International | 2026-02-14 02:00:28 | 11 | ||||||
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TetraMetrix Resource Report Resource Website 1+ mentions |
TetraMetrix (RRID:SCR_002601) | TetraMetrix | software resource | An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left. | magnetic resonance, 3d, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
Free, Available for download, Freely available | nlx_156004 | SCR_002601 | 2026-02-14 02:00:27 | 1 | ||||||||
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PennCNV Resource Report Resource Website 100+ mentions |
PennCNV (RRID:SCR_002518) | PennCNV | software resource | A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm. | imaging genomics, copy number variation, snp, genotyping array, array, oligonucleotide, hidden markov model, genotype, genome |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VegaMC is related to: OpenBioinformatics.org has parent organization: University of Pennsylvania; Philadelphia; USA |
NIMH MH604687 | PMID:17921354 | Free | OMICS_00729, nlx_155921 | http://www.openbioinformatics.org/penncnv/ |
http://www.neurogenome.org/cnv/penncnv | SCR_002518 | PennCNV: copy number variation detection | 2026-02-14 02:00:26 | 349 | |||
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Web Interfaces for Multiscale Images Resource Report Resource Website |
Web Interfaces for Multiscale Images (RRID:SCR_002589) | Web Interfaces for Multiscale Images | knowledge environment | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web. | magnetic resonance, interoperability, microscopy, standard specification, forum | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156020 | SCR_002589 | 2026-02-14 02:00:27 | 0 | ||||||||
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OEI fMRI compatible olfactometer Resource Report Resource Website 1+ mentions |
OEI fMRI compatible olfactometer (RRID:SCR_002507) | OEI fMRI compatible olfactometer | instrument resource | A computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive / learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory. | experiment control, hardware, magnetic resonance, stimulus presentation, odor, olfactory, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | nlx_155907 | http://www.nitrc.org/projects/oei http://www.osmicenterprises.com/docs/OsmicFMRIOlfactomterManual%207-1-13.pdf |
SCR_002507 | 2026-02-14 02:00:26 | 4 | |||||||
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Corpus Callosum Thickness Profile Analysis Pipeline Resource Report Resource Website |
Corpus Callosum Thickness Profile Analysis Pipeline (RRID:SCR_003575) | ccsegthickness | software resource | An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation. Groupwise analysis is facilitated by permutation testing with FWER and FDR multiple comparison correction. Results display is facilitated by a display script that shows p-values on a 3D pipe representation of a CC. This pipeline is implemented in MATLAB and requires the Image Processing Toolbox. There are plans to implement it completely in Python. | linux, matlab, mr, nifti-1, posix/unix-like, corpus callosum | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:24968872 | GNU General Public License | nlx_157716 | SCR_003575 | 2026-02-14 02:00:50 | 0 | |||||||
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Scribe Resource Report Resource Website |
Scribe (RRID:SCR_000423) | Scribe | software resource | Scribe encodes papers to populate the BrainMap Database | magnetic resonance, pet, spect |
is used by: brainmap.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Freely available | nlx_155958 | SCR_000423 | 2026-02-14 01:59:43 | 0 | ||||||||
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CIGAL Resource Report Resource Website 1+ mentions |
CIGAL (RRID:SCR_002232) | CIGAL | software resource | Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables). | magnetic resonance, stimulus control, behavioral recording, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Duke University; North Carolina; USA |
Free, Available for download, Freely available | nlx_155528 | http://www.nitrc.org/projects/cigal | http://fourier.biac.duke.edu/wiki/doku.php/jvs:cigal | SCR_002232 | Compilable Imaging Graphics and Analytical Language | 2026-02-14 02:00:15 | 6 | |||||
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4D Atlases Construction Resource Report Resource Website 1+ mentions |
4D Atlases Construction (RRID:SCR_002227) | software resource | Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications. | magnetic resonance, altas, brain, software package |
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:34891818 PMID:31115143 |
Free, Available for download, Freely available | nlx_155688 | http://www.nitrc.org/projects/atlas4d | http://www.med.unc.edu/bric/ideagroup/free-softwares/4d-atlases-construction | SCR_002227 | 4D Atlas Construction Toolbox, 4D Atlas Construction | 2026-02-14 02:00:20 | 1 | |||||
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Multicomponent T2 estimation with stimulated echo correction Resource Report Resource Website |
Multicomponent T2 estimation with stimulated echo correction (RRID:SCR_002446) | Multicomponent T2 estimation with stimulated echo correction | software resource | Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches. | algorithm, matlab, magnetic resonance, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:23629849 | Free, Available for download, Freely available | nlx_155820 | SCR_002446 | 2026-02-14 02:00:16 | 0 | |||||||
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COGNISION Resource Report Resource Website 1+ mentions |
COGNISION (RRID:SCR_002362) | COGNISION | software resource | A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker). | eeg, eeg, meg, electrocorticography, event-related potentials, hardware, physiological recording, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | nlx_155724 | http://www.nitrc.org/projects/neuronetrix | SCR_002362 | COGNISION (TM) System | 2026-02-14 02:00:23 | 2 | ||||||
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Faceted Search Based Ontology Visualizer Resource Report Resource Website |
Faceted Search Based Ontology Visualizer (RRID:SCR_000124) | ontologyviz | software resource | Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy. | computational neuroscience, magnetic resonance, ontology, functional neuroanatomy, facet, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | nlx_155874 | SCR_000124 | 2026-02-14 01:59:37 | 0 | ||||||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 10+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-02-14 02:02:58 | 47 | |||||||
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EYE-EEG (combined eye-tracking & EEG) Resource Report Resource Website 10+ mentions |
EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) | EYE-EEG | software resource | A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line. | eeg, meg, electrocorticography, matlab, os independent, eye, electrophysiology, oculomotor, eye tracking device |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Humboldt University of Berlin; Berlin; Germany |
DFG | PMID:21744985 | GNU General Public License | nlx_155755 | http://www.nitrc.org/projects/eye-eeg | SCR_012903 | EYE-EEG: Eye tracking & EEG | 2026-02-14 02:02:18 | 13 | ||||
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BRAINSTracer Resource Report Resource Website 1+ mentions |
BRAINSTracer (RRID:SCR_012894) | BRAINSTracer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155705 | http://www.nitrc.org/projects/brainstracer | SCR_012894 | 2026-02-14 02:02:44 | 5 | |||||||
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BrainVisa Morphology extensions Resource Report Resource Website 1+ mentions |
BrainVisa Morphology extensions (RRID:SCR_013248) | BrainVisa Morphology extensions | software resource | An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa | analyze, c++, image display, linux, macos, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, shape analysis, software, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVISA / Anatomist is related to: INCF Software Center |
Artistic License | nlx_155716 | http://www.nitrc.org/projects/brainvisa_ext | SCR_013248 | 2026-02-14 02:02:28 | 1 | |||||||
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Internet Brain Volume Database Resource Report Resource Website 1+ mentions |
Internet Brain Volume Database (RRID:SCR_002060) | IBVD | data or information resource, database | A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group. | anatomy, volume, dsm-iv, normal, schizophrenia, autistic disorder, bipolar disorder, major depressive disorder, alzheimer's disease, attention deficit-hyperactivity disorder, alcohol dependence, dementia, traumatic brain injury, borderline personality disorder, obsessive-compulsive disorder, asperger syndrome, brain, brain structure, in vivo, ex vivo, male, female, gorilla beringei beringei, pongo pygmaeus, volumetric analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIF Data Federation is related to: Integrated Manually Extracted Annotation has parent organization: Harvard Medical School; Massachusetts; USA |
Normal, Alzheimers disease, Seizure, Complex febrile seizure, Holoprosencephaly, Alcohol dependence, Bipolar Disorder, Traumatic brain injury, Schizophrenia | The Human Brain Project ; NINDS NS034189 |
PMID:21931990 | Free, Available for download, Freely available | nif-0000-00033 | http://www.nitrc.org/projects/ibvd | http://www.cma.mgh.harvard.edu/ibvd/ | SCR_002060 | 2026-02-14 02:05:37 | 4 |
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