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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Slicer3 Example Modules Resource Report Resource Website |
Slicer3 Example Modules (RRID:SCR_002559) | Slicer3 Example Modules | software development tool, software resource, software application | Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. Note: these are for 3D Slicer version 3. There is now a version 4 of 3D Slicer available. Information about extensions for version 4 can be found at the following links: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ExtensionsManager http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions | analyze, c++, console (text based), computed tomography, dicom, linux, macos, microsoft, magnetic resonance, nifti, pet, spect, platform or development environment, posix/unix-like, win32 (ms windows), windows, windows nt/2000, windows vista |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: INCF Software Center |
BSD License | nlx_155965 | SCR_002559 | 2025-04-03 11:01:46 | 0 | ||||||||
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SPHARM-MAT Resource Report Resource Website 1+ mentions |
SPHARM-MAT (RRID:SCR_002545) | SPHARM-MAT | software toolkit, software resource, software application | A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics. | analyze, c, matlab, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows, parametric surface model, spherical harmonics, 3d, shape modeling, analysis, morphometry |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University School of Medicine; Indiana; USA |
NIBIB R03EB008674-01 | GNU General Public License | nlx_155952 | http://www.nitrc.org/projects/spharm-mat | SCR_002545 | 2025-04-03 11:01:45 | 2 | ||||||
|
cortex Resource Report Resource Website 100+ mentions |
cortex (RRID:SCR_002467) | cortex | software resource, software application | Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package. | clinical neuroinformatics, mgh/mgz, magnetic resonance, r, surface analysis, thickness, mri, cortical thickness, morphometry, neuroimaging, power analysis, study design, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: bio.tools is listed by: Debian has parent organization: Brain Research Institute |
PMID:22807270 | GNU General Public License, Acknowledgement requested | nlx_155842, biotools:cortex | http://brain.org.au/software/cortex/power http://www.nitrc.org/projects/cortex https://bio.tools/cortex |
SCR_002467 | Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies | 2025-04-03 11:01:37 | 352 | |||||
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Diffusion Tractography with Kalman Filter Resource Report Resource Website |
Diffusion Tractography with Kalman Filter (RRID:SCR_002585) | Diffusion Tractography with Kalman Filter | software resource, software application | Software framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation. The project is written in C++. It could be used both as a Slicer3 module and as a standalone commandline application. | c++, diffusion mr fiber tracking, fiber tracking, microsoft, magnetic resonance, nrrd, posix/unix-like, tractography, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:19694258 | GNU Lesser General Public License | nlx_155990 | SCR_002585 | Tractography with Unscented Kalman Filter | 2025-04-03 11:01:48 | 0 | ||||||
|
shapeAnalysisMANCOVA - SPHARM tools Resource Report Resource Website |
shapeAnalysisMANCOVA - SPHARM tools (RRID:SCR_002578) | shapeAnalysisMANCOVA | software resource, software application | shapeAnalysisMANCOVA offers statistical shape analysis based on a parametric boundary description (SPHARM) as the point-based model computing method. The point-based models will be analyzed with the methods here proposed using multivariate analysis of covariance (MANCOVA). Here, the number of variates being tested is the dimensionality of our observations. Each point of these observations is a three dimensional displacement vector from the mean. The number of contrasts is the number of equations involved in the null-hypothesis. In order to encompass varying numbers of variates and contrasts, and to account for independent variables, a matrix computation is performed. This matrix represents the multidimensional aspects of the correlation significance and it can be transformed into a scalar measure by manipulation of its eigenvalues. Details of the methods can be found in its Insight Journal publication: http://hdl.handle.net/10380/3124 | c++, console (text based), macos, magnetic resonance, posix/unix-like, shape analysis, shape decomposition, spherical harmonics, statistical operation, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
3D Slicer License | nlx_155980 | SCR_002578 | 2025-04-03 11:01:48 | 0 | ||||||||
|
Net Station EEG Software Resource Report Resource Website 10+ mentions |
Net Station EEG Software (RRID:SCR_002453) | Net Station | commercial organization, software resource, software application | A complete software package for working with electroencephalography (EEG) and event-related potential (ERP) data. You can acquire, review, analyze, and now ?see? your participant with synchronized video. Net Station also offers specialized tools and workflow options for both clinical and research applications, allows you to save different combinations of view settings (called workspaces) and helps with your reporting requirements by letting you set up and print custom cover pages. For more specialized work, Net Station also provides an optional electrical source estimation module (GeoSource) and an optional sensor location digitizer (Geodesic Photogrammetry System). | animation, eeg, meg, electrocorticography, event related potential, format conversion, spectral analysis, temporal transformation, time domain analysis, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: Net Station API |
Commercial License | nlx_155825 | SCR_002453 | Netstation | 2025-04-03 11:01:36 | 13 | |||||||
|
Automatic Segmentation Tool Adapter Resource Report Resource Website 1+ mentions |
Automatic Segmentation Tool Adapter (RRID:SCR_002481) | Automatic Segmentation Tool Adapter | software resource, software application | An open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the user's manual segmentation using the image data and manual segmentation provided by the user. The motivation of this project is to bridge the gap between the segmentation tool developer and the tool users such that the existing segmentation tools can more effectively serve the community. More and more automatic segmentation tools are publicly available to today's researchers. However, when applied by their end-users, these segmentation tools usually can not achieve the performance that the tool developer reported. Discrepancies between the tool developer and its users in manual segmentation protocols and imaging modalities are the main reasons for such inconsistency. | algorithm, analyze, c, console (text based), magnetic resonance, nifti, posix/unix-like, segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
GNU General Public License | nlx_155871 | SCR_002481 | 2025-04-03 11:01:38 | 5 | ||||||||
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PESTICA fMRI Physio Detection/Correction Resource Report Resource Website 1+ mentions |
PESTICA fMRI Physio Detection/Correction (RRID:SCR_002513) | PESTICA | software resource, software application | Tool to detect physiologic signals from the data itself as well as an adaptive physiologic noise removal tool (Impulse Response Function or IRF-RETROICOR) that zooms in on noise with only 6 regressors, getting all the noise that 5th order RETROICOR gets. These tools will allow you to correct your data for physiologic noise with what you currently have. These signals are equivalent to a parallel monitored pulse signal and a respiratory chest-bellows signal. Do you have 3D+time EPI data (BOLD or perfusion) but no usable physio signals for pulse and respiration? Are you concerned about the effect of physio noise on your data but don't know what to do but regress data-derived signals that mix unknown functional signal with possible physio noise signal? Are you concerned about the number of regressors you're incorporating once you add 5th order RETROICOR (20 more regressors!)? This is for you. | algorithm, analyze, console (text based), hardware, independent component analysis, linux, macos, matlab, magnetic resonance, multivariate analysis, physiological recording, posix/unix-like, sh/bash, statistical operation, unix shell, workflow, fmri, detection, correction | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Creative Commons Attribution-NonCommercial License | nlx_155912 | SCR_002513 | Physiologic EStimation by Temporal ICA | 2025-04-03 11:01:41 | 5 | |||||||
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OpenMEEG Resource Report Resource Website 50+ mentions |
OpenMEEG (RRID:SCR_002510) | OpenMEEG | software resource, software application | A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy. | algorithm, c++, eeg, meg, electrocorticography, eeg modeling, forward - inverse, macos, meg modeling, microsoft, modeling, posix/unix-like, windows, bioelectromagnetic |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Brainstorm has parent organization: National Institute for Research in Computer Science and Control; Brittany; France |
PMID:20819204 PMID:15638183 |
CeCILL license v2 | nlx_155910 | http://www.nitrc.org/projects/openmeeg https://sources.debian.org/src/libopenmeeg-dev/ |
SCR_002510 | 2025-04-03 11:01:41 | 90 | ||||||
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Computational Morphometry Toolkit Resource Report Resource Website 10+ mentions |
Computational Morphometry Toolkit (RRID:SCR_002234) | CMTK | software toolkit, software resource, software application | A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished. | reusable library, analyze, anatomic, artifact removal, atlas application, c, c++, console (text based), cygwin, dicom, domain independent, format conversion, image display, image reconstruction, image-to-image, labeling, linear, linux, macos, microsoft, magnetic resonance, nifti-1, nrrd, posix/unix-like, principal component analysis, region of interest, registration, regression, resampling, segmentation, sh/bash, spatial transformation, statistical operation, sunos/solaris, two dimensional display, unix shell, visualization, warping, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: neurodebian |
Available for download | nlx_155536 | http://www.nitrc.org/projects/cmtk https://sources.debian.org/src/cmtk/ |
SCR_002234 | Computational Morphometry Toolkit (CMTK) | 2025-04-03 11:01:19 | 29 | ||||||
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STAPLE Resource Report Resource Website 100+ mentions |
STAPLE (RRID:SCR_002590) | STAPLE | software resource, software application | An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion. | algorithm, analyze, c++, dicom, gifti, image display, linux, macos, microsoft, magnetic resonance, nifti, nrrd, posix/unix-like, quantification, rendering, segmentation, surface rendering, visualization, win32 (ms windows), windows, standard |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:15250643 | Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552 | nlx_155994 | http://www.nitrc.org/projects/staple | SCR_002590 | Simultaneous Truth and Performance Level Estimation, STAPLE - Simultaneous Truth and Performance Level Estimation | 2025-04-03 11:01:49 | 116 | |||||
|
Nipype Resource Report Resource Website 500+ mentions |
Nipype (RRID:SCR_002502) | Nipype | software resource, software application | A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. | magnetic resonance, python, workflow, analysis, pipeline, interface, data processing, neuroimaging |
is used by: Forward: Accurate finite element electromagnetic head models is used by: fMRIPrep is used by: NHP BIDS is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
PMID:21897815 | BSD License | nlx_155901 | http://www.nitrc.org/projects/nipype | SCR_002502 | Nipype: Neuroimaging in Python Pipeline and Interfaces, NIPY Pipeline and Interfaces | 2025-04-03 11:01:40 | 607 | |||||
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Object-Oriented Development Interface for NMR Resource Report Resource Website 10+ mentions |
Object-Oriented Development Interface for NMR (RRID:SCR_005974) | ODIN | software resource, software application | A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms. | analyze, c++, console (text based), dicom, image display, image reconstruction, modeling, magnetic resonance, nifti, os independent, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: SourceForge |
GNU General Public License | nlx_155909 | https://sources.debian.org/src/odin/ | SCR_005974 | Object Oriented Development Interface for NMR, ODIN - Object-Oriented Development Interface for NMR | 2025-04-03 11:04:50 | 15 | ||||||
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DONE: Detection of Outlier NEurons Resource Report Resource Website |
DONE: Detection of Outlier NEurons (RRID:SCR_005299) | DONE | software resource, software application | Software that performs a morphology-based approach for the automatic identification of outlier neurons based on neuronal tree structures. This tool was used by Zawadzki et al. (2012), who reported on and its application to the NeuroMorpho database. For the analysis, each neuron is represented by a feature vector composed of 20 measurements, which are projected into lower dimensional space with PCA. Bivariate kernel density estimation is then used to obtain a probability distribution for cells. Cells with high probabilities are understood as archetypes, while those with the small probabilities are classified as outliers. Further details about the method and its application in other domains can be found in Costa et al. (2009) and Echtermeyer et al. (2011). This version requires Matlab (Mathworks Inc, Natick, USA) and allows the user to apply the workflow using a graphical user interface. | neuron, feature-space, archetype, outlier, matlab, neuromorphometry, computational neuroscience |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NeuroMorpho.Org has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
FAPESP 05/00587-5; CNPq 301303/06-1; CNPq 573583/2008-0; FAPESP sponsorship 2010/01994-1; FAPESP sponsorship 2010/16310-0; EPSRC EP/G03950X/1; EPSRC EP/E002331/1; National Research Foundation of Korea R32-10142 |
PMID:22615032 | GNU General Public License | nlx_144348 | http://www.nitrc.org/projects/done | SCR_005299 | Detection of Outlier NEurons | 2025-04-03 11:04:06 | 0 | ||||
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Mesh-based Monte Carlo (MMC) Resource Report Resource Website |
Mesh-based Monte Carlo (MMC) (RRID:SCR_006950) | MMC | software resource, software application | A Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MMC or tMCimg), MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smooth/complex boundaries, but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores. | c, console (text based), modeling, monte carlo, optical imaging, posix/unix-like |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155810 | http://www.nitrc.org/projects/mmc | SCR_006950 | Mesh-based Monte Carlo | 2025-04-03 11:05:41 | 0 | ||||||
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Atlasing of the basal ganglia Resource Report Resource Website 1+ mentions |
Atlasing of the basal ganglia (RRID:SCR_009431) | Atlasing of the basal ganglia | data or information resource, atlas | This atlas takes advantage of ultra-high resolution 7T MRI to provide unprecedented levels of detail on structures of the basal ganglia in-vivo. The atlas includes probability maps of the Subthalamic Nucleus (STh) using T2*-imaging. For now it has been created on 13 young healthy participants with a mean age of 24.38 (range: 22-28, SD: 2.36). We recently also created atlas STh probability maps from 8 middle-aged participants with a mean age of 50.67 (range: 40-59, SD: 6.63), and 9 elderly participants with a mean age of 72.33 (range: 67-77, SD: 2.87). You can find more details about the creation of these maps in the following papers: Young: http://www.ncbi.nlm.nih.gov/pubmed/22227131 Middle-aged & Elderly: http://www.ncbi.nlm.nih.gov/pubmed/23486960 Participating institutions are the Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, and the Cognitive Science Center Amsterdam, University of Amsterdam, the Netherlands. | magnetic resonance, mri, late adult human, early adult human, middle adult human, basal ganglia |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LEAD-DBS |
Aging | PMID:22227131 PMID:23486960 |
Creative Commons License | nlx_155581 | SCR_009431 | 2025-04-03 11:08:16 | 4 | ||||||
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Mixed Effect Model of Genetic-Set and Environment Interaction Resource Report Resource Website |
Mixed Effect Model of Genetic-Set and Environment Interaction (RRID:SCR_015514) | software toolkit, software resource, data or information resource, model | MATLAB Toolbox which provides a mixed effect model for gene-environment interaction (MixGE) on neuroimaging phenotypes, such as structural volumes and tensor-based morphometry (TBM). This model incorporates both fixed and random effects of genetic-set and environment interaction in order to investigate homogeneous and heterogeneous contributions of sets of genetic variants and their interactions with environmental risks to phenotypes. | gene environment interaction, gene environment interaction model, neuroimaging phenotype |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National University of Singapore; Singapore; Singapore |
Singapore National Research Foundation Singapore-NMRC/TCR/004-NUS/2008; Singapore National Research Foundation Singapore-NMRC/TCR/012-NUHS/2014; Singapore Ministry of Health National Medical Research Council NMRC/CBRG/0039/2013; Singapore Ministry of Education Academic Research Fund Tier 2 MOE2012-T2-2-130 |
Free for non-commercial use | SCR_015514 | Mixed Effect Model of Genetic Set and Environment Interaction, Mixed Effect Model of Genetic Set and Environment Interaction Toolbox, MixGE Toolbox | 2025-04-03 11:11:46 | 0 | ||||||||
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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 | software resource, image analysis software, software application, segmentation software, data processing 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 | 2025-04-03 11:01:44 | 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 |
GNU General Public License | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2025-04-03 11:01:44 | 17 | ||||||
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Resource Ontology Discussion Group Resource Report Resource Website |
Resource Ontology Discussion Group (RRID:SCR_002536) | Resource Ontology Discussion Group | discussion, narrative resource, data or information resource, knowledge environment | 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) |
nlx_155943 | SCR_002536 | 2025-04-03 11:01:44 | 0 |
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