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https://github.com/BRAINSia/BRAINSTools

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.

Proper citation: BRAINSCortex (RRID:SCR_001082) Copy   

•   Source: SciCrunch Registry

http://www.psychopy.org

Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime.

Proper citation: PsychoPy (RRID:SCR_006571) Copy   

•   Source: SciCrunch Registry

http://labs.nri.ucsb.edu/reese/benjamin/SA3D.html

A user-friendly, graphical user interface (GUI) that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns. The analyses use files containing sets of X, Y, Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X, Y, Z coordinates for program exploration and modeling purposes.

Proper citation: Spatial Analysis 3D (RRID:SCR_002563) Copy   

•   Source: SciCrunch Registry

http://www.cise.ufl.edu/~tichen/ShapeComplexAtlas.zip

A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012

Proper citation: ShapeComplexAtlas (RRID:SCR_002553) Copy   

•   Source: SciCrunch Registry

http://www.na-mic.org/Wiki/index.php/UNC_SPHARM-PDM_Tutorial

Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures.

Proper citation: SPHARM-PDM Toolbox (RRID:SCR_002546) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/wmtrainer/

A stand-alone axecutable under all main Windows OS for training the working memory. The WM Trainer looks and behaves a little bit like a video-game and has been specifically conceived for children attending the primary school. However, it can be used purposefully by people of any age, including adult and elderly. This application features highest graphic quality, a powerful adaptive engine for the difficulty level, a database of users and statistical tools to evaluate the progress. Currently English, French and Italian are supported, but any language can be easily supported.

Proper citation: Working Memory Trainer (RRID:SCR_002617) Copy   

•   Source: SciCrunch Registry

http://scikit-learn.org/

scikit-learn: machine learning in Python

Proper citation: scikit-learn (RRID:SCR_002577) Copy   

•   Source: SciCrunch Registry

http://www.pymvpa.org

A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages.

Proper citation: PyMVPA (RRID:SCR_006099) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/software.cfm?ID=94

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. NOTE: VR Worlds 2 is no longer available as a standalone software. Software application designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate, real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs. Create complex environments with meaningful content using VR Worlds 2?s user-friendly, drag-and-drop interface. Include triggers to launch simple or intricate events, such as a conversation between characters or a customizable rating scale. VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments, including: * Residential/Urban Area * Hotel Lobby * Medical Office * Grocery Store * Neighborhood for drug and alcohol cue extinction treatment (featured on GMA, motion capture process) * Casino for gambling addiction research (featured on Canadian Discovery Channel) * Driving simulation for mild cognitive impairment research * Phobia scenarios * Spatial navigation mazes

Proper citation: VR Worlds 2 (RRID:SCR_002608) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/ProvenanceEditor

A self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.

Proper citation: LONI Provenance Editor (RRID:SCR_002483) Copy   

•   Source: SciCrunch Registry

http://tarquin.sourceforge.net/

An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses.

Proper citation: TARQUIN (RRID:SCR_002598) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cmind_2014/

A database that contains brain imaging data collected on 3T MRI scanners from over 200 normally developing healthy children from birth to 18 years. The imaging data stored in the C-MIND database are DTI, HARDI, 3DT1W, 3DT2W, concurrent ASL-BOLD scans during two language tasks (Stories and Sentence-Picture Matching), Resting State fMRI and Baseline ASL scans.

Proper citation: C-MIND Database (RRID:SCR_014094) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/brainarteries/

Stereotactic atlases with probabilistic values describing the location of the main cerebral arteries. The data collected are from the COBRA study as described in "COBRA: A prospective multimodal imaging study of dopamine, brain structure and function, and cognition" by Nevalainen et al.

Proper citation: Umea Brain Arteries (RRID:SCR_014752) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/imeka_tracto

A diffusion MRI service that handles the processing of diffusion data from raw data to structural connectivity. They provide high angular resolution (HARDI) reconstruction from DTI data with at least 20 gradient directions acquisitions.

Proper citation: Imeka Tractography Service (RRID:SCR_014124) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/jhucis_pedatlas/

Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis.

Proper citation: Atlases of amygdala and hippocampus for pediatric populations (RRID:SCR_014085) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/crl_fetal_atlas

An atlas of of the fetal brain from MRI of normal fetuses scanned prenatally generated using a mathematical framework. The atlas shows the inter-subject anatomic variability of the fetal brain over the fetal brain growth period and is currently available between 27 weeks gestational age to 35 weeks. It has been constructed following an unbiased minimum distance template estimation approach which utilizes symmetric diffeomorphic deformation and the cross-correlation (CC) similarity metric integrated with kernel regression in age.

Proper citation: CRL Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain (RRID:SCR_014176) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/whs-sd-atlas/

Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.

Proper citation: Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reliability/

Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.

Proper citation: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open (RRID:SCR_016935) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/miitra/

Atlas for studies of older adult brain. Includes T1-weighted template of older adult brain and tissue probability maps. Exhibits high image sharpness, provides higher inter-subject spatial normalization accuracy compared to other standardized templates and similar normalization accuracy to well-constructed study-specific templates.

Proper citation: MIITRA atlas (RRID:SCR_017566) Copy   

•   Source: SciCrunch Registry

https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-2

A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org

Proper citation: Integrated Manually Extracted Annotation (RRID:SCR_008876) Copy   

•   Source: SciCrunch Registry