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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MUMA Resource Report Resource Website 10+ mentions |
MUMA (RRID:SCR_002412) | MUMA | software application, standalone software, software resource | Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY). | standalone software, mac os x, unix/linux, windows, r, metabolomics, univariate, multivariate, data analysis |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_03370 | SCR_002412 | Metabolomics Univariate and Multivariate Analysis (MUMA), Metabolomic Univariate and Multivariate Analysis | 2026-08-15 11:29:38 | 28 | |||||||
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RFT FDR Resource Report Resource Website |
RFT FDR (RRID:SCR_002533) | RFT_FDR | software application, software resource | So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171). | console (text based), gnome, kde, matlab, mgh/mgz, modeling, magnetic resonance, os independent, rendering, statistical operation, surface analysis, surface rendering, thickness, visualization, random field theory |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155938 | SCR_002533 | RFT-FDR, RFT FDR | 2026-08-15 11:29:40 | 0 | |||||||
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NIH Toolbox Oral Reading Recognition Test Resource Report Resource Website |
NIH Toolbox Oral Reading Recognition Test (RRID:SCR_003622) | assessment test provider, material resource | Assessment test that measures the ability of patients to identify words and letters. The participant is asked to read and pronounce letters and words as accurately as possible. The test administrator scores them as right or wrong. For the youngest children, the initial items require them to identify letters (as opposed to symbols) and to identify a specific letter in an array of 4 symbols. The test is given in a computerized adaptive format and requires approximately 3 minutes. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested. Separate but parallel reading tests have been developed in English and in Spanish. | cognition, language | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157774 | SCR_003622 | Oral Reading Recognition Test | 2026-08-15 11:29:41 | 0 | |||||||||
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Source BioScience LifeSciences Resource Report Resource Website 50+ mentions |
Source BioScience LifeSciences (RRID:SCR_003344) | RZPD | biomaterial supply resource, material resource | Source BioScience LifeSciences are European leaders in DNA sequencing, genomic services, bioinformatic analyses and offers a comprehensive portfolio of genomic reagents and antibodies. Source BioScience LifeScience is a CPA, GLP/GCP accredited and Illumina NGS CSPro certified genomic service provider and distributes a comprehensive range of biological products to companies and institutions worldwide. Source BioScience is proud to announce that Source BioScience imaGenes has joined it's LifeSciences group. This will enable us to bring our customers one unified website with our complete range of Products, Clones and Services. We have merged our clone libraries together so that can now offer you over 20 million clones! Add to this our excellent sequencing service and our range of over 100,000 antibodies and Source BioScience LifeSciences is your ideal outsourcing partner. | clones, libraries, microarray, dna sequencing, rna interference, next generation sequencing, proteomics | is listed by: One Mind Biospecimen Bank Listing | Free, Freely available | nif-0000-31984 | https://sourcebioscience.com/ | SCR_003344 | imaGenes, Source BioScience imaGenes | 2026-08-15 11:29:39 | 72 | ||||||
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Mount Sinai Allograft Technologies Resource Report Resource Website |
Mount Sinai Allograft Technologies (RRID:SCR_003586) | biomaterial supply resource, material resource | Mount Sinai Allograft Technologies, a department of Mount Sinai Hospital formerly known as the The Rubinoff Bone Bank, has been a leader in advanced tissue innovations since 1972. We are committed to providing the highest quality bone and tissue allograft products as well as continued innovation in the development of allograft implants for transplantation. We are dedicated to meeting all surgical needs and to exceed all client expectations. We work closely with the Trillium Gift of Life Network to promote their mission of increasing donor awareness and to ensure that the wishes of Ontario donor families' are carried out with the utmost care and respect. Our allograft implants are 100% Ontario produced, human allograft tissues. To produce the safest and highest quality Canadian produced allograft implants, Mount Sinai Allograft Technologies leverages the expertise of a variety of medical experts, state-of-the art laboratory testing, proven bio-processing techniques, validated irradiation methods and preferred packaging systems. | is listed by: One Mind Biospecimen Bank Listing | nlx_12054 | SCR_003586 | The Rubinoff Bone Bank, Rubinoff Bone Bank | 2026-08-15 11:29:39 | 0 | ||||||||||
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NIRx2nirs: A NIRx to .nirs data converter Resource Report Resource Website 1+ mentions |
NIRx2nirs: A NIRx to .nirs data converter (RRID:SCR_002492) | NIRx2nirs | software application, software resource | A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge. | hardware, nirs, fnir, optical imaging, optical imaging, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Homer2 |
Free, Available for download, Freely available | nlx_155887 | SCR_002492 | 2026-08-15 11:29:28 | 1 | ||||||||
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ProLinks Database of Functional Linkages Resource Report Resource Website |
ProLinks Database of Functional Linkages (RRID:SCR_003185) | software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage. | functional linkage, protein linkage, inference method |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:15128449 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00580 | http://prl.mbi.ucla.edu/prlbeta/prolinks.jsp http://dip.mbi.ucla.edu/dipbeta/prolinks.jsp | SCR_003185 | Prolinks | 2026-08-15 11:29:39 | 0 | ||||||
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MBF BioScience: Stereo Investigator Resource Report Resource Website 100+ mentions |
MBF BioScience: Stereo Investigator (RRID:SCR_002526) | instrument resource, software resource | Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology. | stereology, MBF Bioscience, number, length, area, volume cells, biological structures, tissue specimen |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
Restricted | SciRes_000114, SCR_024705, SCR_018948 | http://www.nitrc.org/projects/si_stereology | SCR_002526 | Stereo Investigator system | 2026-08-15 11:29:38 | 162 | |||||||
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Primate Embryo Gene Expression Resource Resource Report Resource Website 1+ mentions |
Primate Embryo Gene Expression Resource (RRID:SCR_002765) | PREGER | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods. | primate, embryo, gene, expression, embryologist, microarray, rhesus, monkey, oocyte, embryo, cdna, library, molecular, analysis, stem cell, oocyte quality, preimplantation development, transcription |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Temple University School of Medicine; Pennsylvania; USA |
NIH Office of the Director R24 OD012221; NCRR RR15253 |
PMID:14724133 PMID:17147927 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24366 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | SCR_002765 | PREGER Online, Preger.org | 2026-08-15 11:29:28 | 6 | ||||
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Advanced Neuroscience Imaging Research Laboratory Software Packages Resource Report Resource Website 10+ mentions |
Advanced Neuroscience Imaging Research Laboratory Software Packages (RRID:SCR_002926) | ANSIR Software | software toolkit, software resource | Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime. | multimodal, image, analysis, biological, parametric, mapping, voxel, linear, model, regressor, software, matlab, visualization, statistical, inference, in vivo, brain imaging, brain | has parent organization: Wake Forest School of Medicine; North Carolina; USA | NIBIB R01EB004673; NIBIB 1R03EB008670 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30033 | SCR_002926 | Advanced Neuroscience Imaging Research Software, ANSIR Laboratory Software Packages | 2026-08-15 11:29:29 | 38 | ||||||
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NIH Toolbox Picture Sequence Memory Test Resource Report Resource Website |
NIH Toolbox Picture Sequence Memory Test (RRID:SCR_003618) | Picture Sequence Memory Test | assessment test provider, material resource | A measure for the assessment of episodic memory that involves recalling increasingly lengthy series of illustrated objects and activities that are presented in a particular order on the computer screen. The participants are asked to recall the sequence of pictures that is demonstrated over two learning trials; sequence length varies from 6-18 pictures, depending on age. Participants are given credit for each adjacent pair of pictures (i.e., if pictures in locations 7 and 8 and placed in that order and adjacent to each other anywhere such as slots 1 and 2 one point is awarded) they correctly place, up to the maximum value for the sequence, which is one less than the sequence length (if there are 18 pictures in the sequence, the maximum score is 17, because that is the number of adjacent pairs of pictures that exist). The test takes approximately 7 minutes to administer. This test is recommended for ages 3-85. | cognition, episodic memory, memory |
is related to: NIH Toolbox Auditory Verbal Learning Test (Rey) has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function |
nlx_157771 | SCR_003618 | 2026-08-15 11:29:29 | 0 | |||||||||
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RightField Resource Report Resource Website 1+ mentions |
RightField (RRID:SCR_002649) | RightField | software application, software resource | An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies. | annotation, semantic, ontology, term selection, excel, java, bio.tools |
is listed by: BioPortal is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: SEEK is related to: Workflow4Ever has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:21622664 | Free, Available for download, Freely available | biotools:rightfield, nlx_156077 | https://bio.tools/rightfield | SCR_002649 | 2026-08-15 11:29:38 | 3 | ||||||
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NIH Toolbox Flanker Inhibitory Control and Attention Test Resource Report Resource Website 1+ mentions |
NIH Toolbox Flanker Inhibitory Control and Attention Test (RRID:SCR_003617) | Flanker task | assessment test provider, material resource | Assessment test that measures both a participant''s attention and inhibitory control. The test requires the participant to focus on a given stimulus while inhibiting attention to stimuli (fish for ages 3-7 or arrows for ages 8-85) flanking it. Sometimes the middle stimulus is pointing in the same direction as the flankers (congruent) and sometimes in the opposite direction (incongruent). Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 3 minutes to administer. This test is recommended for ages 3-85. | cognition, attention, executive function, inhibitory control | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157770 | SCR_003617 | Flanker Inhibitory Control and Attention Test | 2026-08-15 11:29:41 | 1 | ||||||||
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NIH Toolbox Dimensional Change Card Sort Test Resource Report Resource Website 1+ mentions |
NIH Toolbox Dimensional Change Card Sort Test (RRID:SCR_003616) | DCCS | assessment test provider, material resource | Assessment test that measures the cognitive flexibility of patients. Two target pictures are presented that vary along two dimensions (e.g., shape and color). Participants are asked to match a series of bivalent test pictures (e.g., yellow balls and blue trucks) to the target pictures, first according to one dimension (e.g., color) and then, after a number of trials, according to the other dimension (e.g., shape). Switch trials are also employed, in which the participant must change the dimension being matched. For example, after 4 straight trials matching on shape, the participant may be asked to match on color on the next trial and then go back to shape, thus requiring the cognitive flexibility to quickly choose the correct stimulus. Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 4 minutes to administer. This test is recommended for ages 3-85. | cognitive flexibility, cognition, executive function | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157769 | SCR_003616 | 2026-08-15 11:29:39 | 2 | |||||||||
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CERAD - Consortium to Establish a Registry for Alzheimer's Disease Resource Report Resource Website 1000+ mentions |
CERAD - Consortium to Establish a Registry for Alzheimer's Disease (RRID:SCR_003016) | CERAD | assessment test provider, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Consortium that developed brief, standardized and reliable procedures for the evaluation and diagnosis of patients with Alzheimer's disease (AD) and other dementias of the elderly. These procedures included data forms, flipbooks, guidebooks, brochures, instruction manuals and demonstration tapes, which are now available for purchase. The CERAD assessment material can be used for research purposes as well as for patient care. CERAD has developed several basic standardized instruments, each consisting of brief forms designed to gather data on normal persons as well as on cognitively impaired or behaviorally disturbed individuals. Such data permit the identification of dementia based on clinical, neuropsychological, behavioral or neuropathological criteria. Staff at participating CERAD sites were trained and certified to administer the assessment instruments and to evaluate the subjects enrolled in the study. Cases and controls were evaluated at entry and annually thereafter including (when possible) autopsy examination of the brain to track the natural progression of AD and to obtain neuropathological confirmation of the clinical diagnosis. The CERAD database has become a major resource for research in Alzheimer's disease. It contains longitudinal data for periods as long as seven years on the natural progression of the disorder as well as information on clinical and neuropsychological changes and neuropathological manifestations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | clinical, behavior, late adult human, male, female, caucasian, african-american, autopsy, longitudinal, neuropsychology, neuropathology, FASEB list | has parent organization: Duke University; North Carolina; USA | Aging, Alzheimer's disease, Dementia, Cognitive impairment, Neurodegenerative disorder, Systemic illness, Cerebrovascular disease, Parkinson's disease, Depressive Disorder | NIA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00523 | SCR_003016 | Consortium to Establish a Registry for Alzheimer's Disease | 2026-08-15 11:29:39 | 2337 | |||||
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Slicer3 Example Modules Resource Report Resource Website |
Slicer3 Example Modules (RRID:SCR_002559) | Slicer3 Example Modules | software application, software development tool, software resource | 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 |
Free, Available for download, Freely available | nlx_155965 | SCR_002559 | 2026-08-15 11:29:40 | 0 | ||||||||
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TherMos Resource Report Resource Website 100+ mentions |
TherMos (RRID:SCR_002790) | algorithm resource, software resource | Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein dna binding energy, in vivo binding profiles, motif discovery |
uses: MATLAB is listed by: OMICtools |
PMID:23595148 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00498 | SCR_002790 | 2026-08-15 11:29:38 | 208 | ||||||||
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AltAnalyze - Alternative Splicing Analysis Tool Resource Report Resource Website 50+ mentions |
AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) | AltAnalyze | software application, software resource | Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph. | analysis, alternative splicing, microarray, calculate, pathway, ontology, domain, microrna, targeting, splicing, microarry, rna-seq, metabolomics, mac osx, windows, ubuntu, cross platform, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Cytoscape has parent organization: University of California at San Francisco; California; USA |
PMID:20513647 | Free, Available for download, Freely available | nif-0000-30083, OMICS_02250, biotools:altanalyze | https://bio.tools/altanalyze | SCR_002951 | Alternative Splicing Analysis Tool | 2026-08-15 11:29:38 | 86 | |||||
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Colorado Assessment Tests - Symptom Validity Resource Report Resource Website |
Colorado Assessment Tests - Symptom Validity (RRID:SCR_003520) | CAT Symptom Validity | assessment test provider, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Memory impairment is one of the most common complaints after head injury, and accordingly, individuals may attempt to feign memory impairment or exaggerate symptoms of memory impairment. This free neuropsychological evaluation software contains some of the most common tests used to detect malingering of memory impairment. This software package contains a number of tests of declarative memory that assess recall of information that has a personal and temporal context. The typical example of declarative tests used for detecting malingering are the auditory verbal learning test and forced choice test. These tests are included in Symptom Validity along with other tests of declarative memory (e.g., prose recall, questionnaire tests). Unfortunately, classification of individuals is not completely accurate even with the use of multiple declarative memory tests. Thus, other tests that can complement previously used declarative memory measures by enhancing classification accuracy may be of great value to the neuropsychologist assessing the possibility of malingering. Your software contains two tests of nondeclarative memory that have been previously shown to be useful in the detection of malingered memory deficits (Davis et al., 1997a, 1997b). These tests take advantage of the general laypersons misunderstanding of the test performance of a truly memory impaired individual. That is, amnesic patients have been shown to perform normally on these nondeclarative memory tests and this is counterintuitive to the memory performance expectations of the general layperson. The nondeclarative tests included in Symptom Validity are two repetition priming tests of word stem completion and two tests of pattern categorization learning. Note: At this time this program will run only on Windows 98. We are currently working on a version that will run under the newer operating systems. | auditory verbal learning test, craniocerebral trauma, declarative memory, disfunctional, human, memory, memory impairment, memory recall, neuropsychological assessment, nondeclarative memory, prose recall | has parent organization: University of Colorado; Colorado Springs; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00213 | SCR_003520 | Symptom Validity | 2026-08-15 11:29:29 | 0 | |||||||
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SPHARM-MAT Resource Report Resource Website 1+ mentions |
SPHARM-MAT (RRID:SCR_002545) | SPHARM-MAT | software toolkit, software application, software resource | 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 | Free, Available for download, Freely available | nlx_155952 | http://www.nitrc.org/projects/spharm-mat | SCR_002545 | 2026-08-15 11:29:40 | 2 |
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