BASH4RfMRI
Resource Report
Resource Website
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BASH4RfMRI (RRID:SCR_005970)
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software resource
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THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI.
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algorithm or reusable library, information theory, spectral analysis, correlation, multivariate analysis, platform or development environment, magnetic resonance
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is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: FSL
is related to: Analysis of Functional NeuroImages
is related to: FreeSurfer
is related to: 1000 Functional Connectomes Project
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THIS RESOURCE IS NO LONGER IN SERVICE |
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nlx_151343 |
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SCR_005970 |
BASH Scripts, bash-rs-fcmri |
2025-05-24 08:09:22 |
0 |
NIAG Addiction Data
Resource Report
Resource Website
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NIAG Addiction Data (RRID:SCR_015523)
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data set, data or information resource
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Data set of addiction studies compiled by the NeuroImaging and Analysis Group (NIAG).
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addiction, neuroimaging, data set
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works with: SPM
works with: DTIProcess ToolKit
works with: FreeSurfer
works with: Analysis of Functional NeuroImages
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Open Source |
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http://niag.ir/ |
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SCR_015523 |
NeuroImaging and Analysis Group Addiction Data |
2025-05-26 10:54:58 |
0 |
SoftCite
Resource Report
Resource Website
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SoftCite (RRID:SCR_024411)
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portal, knowledge base, software resource, project portal, data or information resource
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Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.
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Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature,
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lists: ProteinPilot
lists: ROCit
lists: survivalROC
lists: GIFT
lists: PyWavelets
lists: pRRophetic
lists: GOplot
lists: Rgdal
lists: riskRegression
lists: RNAfold
lists: RNALocate
lists: pyPCcazip
lists: ScanProsite
lists: RapGreen
lists: ABySS
lists: AMBER
lists: ANNOVAR
lists: ASAP
lists: ASPicDB
lists: AStalavista
lists: ATSAS
lists: Alien hunter
lists: Adobe Photoshop
lists: Affymetrix
lists: Augustus
lists: Argus
lists: Adobe Illustrator
lists: ART
lists: AutoDock Vina
lists: AutoDock
lists: ANALYZE
lists: BLASTClust
lists: arrayQualityMetrics
lists: BLASTN
lists: BLASTX
lists: BLASTP
lists: Bowtie
lists: Autogrid
lists: BRB-ArrayTools
lists: BEDTools
lists: BWA
lists: BioEdit
lists: BRASS
lists: Bioconductor
lists: BioExtract
lists: BaCelLo
lists: BioMoby
lists: Brain Extraction Tool
lists: Bowtie 2
lists: BoxPlotR
lists: biomaRt
lists: BioPerl
lists: CANGS
lists: CFX Manager
lists: CEAS
lists: BlobFinder
lists: CLC Genomics Workbench
lists: BREAKDANCER
lists: CASAVA
lists: CLC Main Workbench
lists: ClustalW
lists: Clustal W2
lists: ComBat
lists: CCP4
lists: Blender
lists: Coot
lists: CGView
lists: COMSOL Multiphysics
lists: CTFFIND
lists: CalcuSyn
lists: ChIPpeakAnno
lists: Chimera
lists: CVODE
lists: DAVID
lists: Cufflinks
lists: caret
lists: ClueGO
lists: Cluster
lists: Clocklab
lists: DIANA-mirPath
lists: Cytoscape
lists: EMAN
lists: E-Prime
lists: DESeq2
lists: Definiens Developer XD
lists: Eigensoft
lists: EMBOSS
lists: Ensembl
lists: DIALIGN
lists: Design-Expert
lists: EndNote
lists: CMAP
lists: EEGLAB
lists: CMap
lists: Epi Info
lists: FASTA
lists: Ensembl Genome Browser
lists: Epik
lists: FACS
lists: FCS Express
lists: Flowlogic
lists: FSL
lists: FLASH
lists: FATCAT
lists: FastQC
lists: G*Power
lists: GOLD
lists: FGENESH
lists: FreeSurfer
lists: FlowJo
lists: GeneTools
lists: Galaxy
lists: GATK
lists: ELDA
lists: GraphPad
lists: GRADEpro
lists: Fiji
lists: Gblocks
lists: FigTree
lists: GENIE
lists: GBrowse
lists: Gemma
lists: GeneChip Operating Software
lists: GeneMapper
lists: GeneMarker
lists: GenABEL
lists: GenePattern
lists: GraphPad Prism
lists: GenePix Pro
lists: Google
lists: Genesis
lists: Hologic
lists: GeneSpring GX
lists: GeneVenn
lists: HaploReg
lists: Google Scholar
lists: HALO
lists: Gwyddion
lists: IMAGIC
lists: HKL-2000
lists: Glide
lists: Glimmer
lists: I-TASSER
lists: GenomeStudio
lists: IMOD
lists: Haploview
lists: Hmmer
lists: Hydra
lists: IUPRED
lists: HomeCageScan
lists: Geneious
lists: IGOR Pro
lists: IMPUTE
lists: Infernal
lists: Image-Pro Plus
lists: JASP
lists: LSM Image Examiner
lists: Imaris
lists: Image Pro Plus
lists: ImageQuant
lists: ImageJ
lists: Integrative Genomics Viewer
lists: jcvi
lists: InterProScan
lists: KaleidaGraph
lists: Ligprep
lists: Heidelberg Eye Explorer
lists: JMP
lists: Ingenuity Pathways Knowledge Base
lists: Leica QWin
lists: JCB DataViewer
lists: Jalview
lists: LigandScout
lists: Ingenuity Pathway Analysis
lists: LabView
lists: Kepler
lists: MAFFT
lists: Jmol
lists: ImageScope
lists: MACS
lists: Maq
lists: MUMmer
lists: MATLAB
lists: Mimics
lists: MACH
lists: MCODE
lists: Mascot
lists: Maestro
lists: MSQuant
lists: MediaWiki
lists: MINC
lists: MRIcron
lists: MOE
lists: ModFit LT
lists: LIMMA
lists: MassLynx
lists: mitopred
lists: MrBayes
lists: MolProbity
lists: MUSCLE
lists: MutationAssessor
lists: MaxQuant
lists: Minitab
lists: MODELLER
lists: MetaboAnalyst
lists: MedCalc
lists: Origin
lists: MPlus
lists: MutationTaster
lists: MuTect
lists: Multi Gauge
lists: NIA Array Analysis
lists: NIH Image
lists: Phenix
lists: MycoBank
lists: OpenClinica
lists: Nexus
lists: OMTools
lists: NIS-Elements
lists: PAST
lists: NVivo
lists: PRISM (Stanford database)
lists: Metscape
lists: PROCHECK
lists: oligo
lists: OpenEpi
lists: Pathway Commons
lists: Nanoparticle Tracking Analysis
lists: Openlab
lists: PLINK
lists: PAUP
lists: NONMEM
lists: PREFAB
lists: NetworkX
lists: PeptideProphet
lists: Primer Designer
lists: PhyML
lists: PASS
lists: PyMOL
lists: PSIPRED
lists: PROFILER
lists: PHYLIP
lists: Phobius
lists: Prime
lists: Phyutility
lists: Picard
lists: ProteinProphet
lists: Phaser
lists: ProSAS
lists: PostgreSQL
lists: Primer-BLAST
lists: ProteinLynx Global Server
lists: QUANTO
lists: Primer Express
lists: Primer3Plus
lists: ProtTest
lists: ProbCons
lists: Primer3
lists: Poretools
lists: Protein preparation Wizard
lists: QmRLFS-finder
lists: PicTar
lists: RevMan
lists: Pipeline Pilot
lists: QIIME
lists: PRISMA
lists: REDCap
lists: RAxML
lists: Proteome Discoverer
lists: Research Randomizer
lists: SPARTAN
lists: SPSS
lists: RNAstructure
lists: Refmac
lists: QuantPrime
lists: Prodigal
lists: RepeatModeler
lists: Ringo
lists: SQLite
lists: SAGE
lists: Rhinoceros
lists: SAMTOOLS
lists: SPAdes
lists: RepeatMasker
lists: SEDFIT
lists: STATISTICA
lists: RNAhybrid
lists: SlideBook
lists: STRUCTURE
lists: SABmark
lists: SPM
lists: Stata
lists: RStudio
lists: SciPy
lists: Scion Image
lists: Simulink
lists: TAGGER
lists: TopHat
lists: SAM
lists: ShortRead
lists: SIFT
lists: SCAN
lists: SignalP
lists: Scopus
lists: Strelka
lists: Trans-ABySS
lists: Statgraphics Centurion
lists: T-Coffee
lists: Statistical Analysis System
lists: TargetScan
lists: UCHIME
lists: Sequencher
lists: SigmaStat
lists: UCSC Genome Browser
lists: affy
lists: Taverna
lists: Stereo Investigator
lists: Trimmomatic
lists: Vmatch
lists: WFU PickAtlas
lists: SigmaPlot
lists: X!Tandem
lists: STAR
lists: TASSEL
lists: SyStat
lists: WEBLOGO
lists: UCSF Chimera
lists: TreeView
lists: pheatmap
lists: WinWCP
lists: microRNA.org
lists: glmnet
lists: Phenix.refine
lists: BASE
lists: beadarray
lists: RMS
lists: lumi
lists: Web of Science
lists: minfi
lists: geNORM
lists: WU-BLAST
lists: WinBUGS
lists: SPP
lists: tRNAscan-SE
lists: WebPlotDigitizer
lists: qBasePLUS
lists: Matplotlib
lists: TreeBASE
lists: pClamp
lists: TBLASTN
lists: igraph
lists: V3D
lists: survival
lists: miRanda
lists: piRNABank
lists: topGO
lists: NGmerge
lists: OMNISEC
lists: NOTUNG
lists: OpenBUGS
lists: Optimization Toolbox
lists: ProgRes Capture Pro
lists: Ocular
lists: Umediation
lists: Nano Measurer
lists: PHYLDOG
lists: VSEARCH
lists: WinNonlin
lists: WHONET
lists: ToposPro
lists: Treerecs
lists: Agilent Seahorse Wave
lists: SimPhy
lists: TomoStudio
lists: Mutation Assessor
lists: Stem
lists: SRAMP
lists: CRISPResso2
lists: geepack
lists: Evalue
lists: DAGitty
lists: FastMulRFS
lists: ggridges
lists: gamm4
lists: AutoRT
lists: CopyKAT
lists: Inference of CRISPR Edits
lists: classInt
lists: ASTRAL-Pro
lists: maftools
lists: mitml
lists: CMplot
lists: MetaPSICOV
lists: LaCyTools
lists: MADOKA
lists: Kaplan Meier Plotter
lists: IntFOLD
lists: ModFOLD
lists: lDDT
has parent organization: University of Texas at Austin; Texas; USA
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Sloan Foundation |
DOI:10.1002/asi.24454 |
Free, Available for download, Freely available |
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https://github.com/softcite/softcite_dataset_v2
https://zenodo.org/record/7995565 |
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SCR_024411 |
Software Citation |
2025-05-28 11:13:09 |
0 |
TRACULA
Resource Report
Resource Website
10+ mentions
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TRACULA (RRID:SCR_013152)
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TRACULA
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software application, software resource, data processing software
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Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.
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tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging
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is related to: FreeSurfer
has parent organization: Harvard Medical School; Massachusetts; USA
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Aging |
NIH Blueprint for Neuroscience Research ;
Ellison Medical Foundation ;
NIBIB EB008129;
NIMH U01-MH093765;
NCRR P41-RR14075;
NCRR U24-RR021382;
NIBIB R01-EB006758;
NIA R01-AG022381;
National Center for Complementary and Alternative Medicine RC1-AT005728;
NINDS R01-NS052585;
NINDS R21-NS072652;
NINDS R01-NS070963 |
PMID:22016733 |
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nlx_143919 |
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SCR_013152 |
TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy |
2025-05-28 11:05:55 |
15 |
PySurfer
Resource Report
Resource Website
10+ mentions
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PySurfer (RRID:SCR_002524)
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PySurfer
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software application, data processing software, software resource, data visualization software, software toolkit, software library
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Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets.
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eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging
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is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is related to: FreeSurfer
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Free, Available for download, Freely available |
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nlx_155930 |
http://www.nitrc.org/projects/pysurfer
https://sources.debian.org/src/python3-surfer/ |
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SCR_002524 |
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2025-05-28 10:59:25 |
28 |
Wisconsin Cortical Thickness Analysis (CTA) Toolbox
Resource Report
Resource Website
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Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180)
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software application, data processing software, software resource, software toolkit, data analysis software
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A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR).
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matlab, software toolkit, cortical thickness signal, data analysis software
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uses: FreeSurfer
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
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Wisconsin Partnership Program ;
NIA R01AG040396;
NIA R01AG021155;
NSF RI 1116584;
NSF CAREER 1252725;
UW ADRC NIA P50 AG033514;
UW ICTR NCRR 1UL1RR025011;
NIA P30 AG010129;
NIA K01 AG030514 |
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http://pages.cs.wisc.edu/~wonhwa/code/CTA_toolbox.html
http://pages.cs.wisc.edu/~wonhwa/project/ctdiscrim.html |
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SCR_014180 |
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2025-05-28 11:06:25 |
0 |
RFT FDR
Resource Report
Resource Website
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RFT FDR (RRID:SCR_002533)
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RFT_FDR
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software application, software resource
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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).
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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
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is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: FreeSurfer
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Academic Free License |
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nlx_155938 |
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SCR_002533 |
RFT-FDR, RFT FDR |
2025-05-28 10:59:25 |
0 |
Biositemaps
Resource Report
Resource Website
1+ mentions
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Biositemaps (RRID:SCR_001976)
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Biositemaps
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service resource, software resource
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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites.
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broadcast, data federation, defined rdf schema, infrastructure, meta-data, rdf, retrieve, biomedical, biositemap, sitemap
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lists: Adaptively Sampled Particle Fluids
lists: DicomWorks
lists: MEDx
lists: Medical Image Processing and Visualization
lists: Surface-Based Atlases
lists: RESNET
lists: SurfRelax
lists: FEATURE
lists: Cardiovascular Model Repository
lists: Simtk.org
lists: ConTrack
lists: Allopathfinder
lists: Molecular Simulation Trajectories Archive of a Villin Variant
lists: BioPortal
lists: SumsDB
lists: NeuronDB
lists: BrainInfo
lists: Protege
lists: i2b2 Cross-Institutional Clinical Translational Research project
lists: GeneChip Operating Software
lists: Honig Lab
lists: Proteomics Identifications (PRIDE)
lists: ASAP: the Alternative Splicing Annotation Project
lists: MiMI Plugin for Cytoscape
lists: Substructure Index-based Approximate Graph Alignment
lists: Proteome Commons Tranche repository
lists: caTIES - Cancer Text Information Extraction System
lists: REDCap
lists: miniTUBA
lists: Einstein-Montefiore ICTR Research Informatics Core
lists: T-profiler
lists: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse
lists: GCG/SeqWeb
lists: Solstice
lists: California National Primate Research Center
lists: BioGPS: The Gene Portal Hub
lists: Blox
lists: Subcellular Location Image Finder
lists: PeptideAtlas
lists: Clair library
lists: Lyngby
lists: SimTKCore
lists: Velos
lists: Ingenuity Pathway Analysis
lists: Philips
lists: Talktech
lists: SUN Interface Engine
lists: Quadramed - Medicus, Quantim
lists: Wisconsin National Primate Research Center
lists: i2b2 Research Data Warehouse
lists: Merge Healthcare Incorporated
lists: Clinical Trial Management Application
lists: Cerner Millenium
lists: Open Clinical Report Repository
lists: Quovadx, Inc.
lists: VectorValuedHistogramNormalizer
lists: Morphometry BIRN
lists: Talairach Daemon
lists: LONI Visualization Tool
lists: LONI Debabeler
lists: LONI Pipeline Processing Environment
lists: Brede Wiki
lists: medInria
lists: FreeSurfer
lists: ITK-SNAP
lists: VoxBo
lists: Ensembl
lists: MRIcron
lists: Synchronized Histological Image Viewing Architecture
lists: LONI ShapeViewer
lists: LONI ShapeTools
lists: FFT Library
lists: NUTMEG
lists: bioDBcore
lists: Mutant Mouse Resource and Research Center
lists: Brainscape
lists: MindSeer
lists: University of Southern California LONI Software
lists: Statistics Online Computational Resource
lists: NIH MRI Study of Normal Brain Development
lists: Ontology Development and Information Extraction
lists: Mindtouch DekiWiki
lists: National Mesothelioma Virtual Bank
lists: MGH-USC Human Connectome Project
lists: Fusion ICA Toolbox
lists: Biomedical Resource Ontology
lists: Biomedical Informatics Research Network
lists: 3D Slicer
lists: Analysis of Functional NeuroImages
lists: Automated Image Registration
lists: TOADS-CRUISE Brain Segmentation Tools
lists: BrainImage Software
lists: Brede Toolbox
lists: Whole Brain Catalog
lists: Low Resolution Electromagnetic Tomography
lists: Cambridge Brain Activation
lists: ModelDB
lists: fMRI Data Center
lists: EEGLAB
lists: 3DViewnix
lists: MIPAV: Medical Image Processing and Visualization
lists: NeuroLens
lists: WFU PickAtlas
lists: Protein Subcellular Location Image Database
lists: STRIDE Virtual Biospecimen Bank
lists: BrainVoyager
is related to: Biomedical Resource Ontology
is related to: Software Distribution Sets
is related to: REX
is related to: Rat Genome Database (RGD)
has parent organization: National Centers for Biomedical Computing
has parent organization: National Institutes of Health
is parent organization of: Resource Discovery System
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THIS RESOURCE IS NO LONGER IN SERVICE |
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nif-0000-10583 |
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SCR_001976 |
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2025-05-28 10:59:08 |
1 |
JOSA
Resource Report
Resource Website
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JOSA (RRID:SCR_024756)
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software application, registration software, data processing software, software resource, image analysis software
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Software tool for joint surface based registration and atlas construction of brain geometry and function.Cortical registration framework that jointly models mismatch between geometry and function while simultaneously learning unbiased population specific atlas.
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joint surface based registration, atlas construction, brain, fMRI, brain structure and function, recognizing mismatch between geometry and function,
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is related to: BRAIN Initiative Cell Atlas Network
is a plug in for: FreeSurfer
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DOI:10.48550/arXiv.2311.08544 |
Restricted |
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SCR_024756 |
JOint Spherical registration and Atlas building |
2025-05-28 11:13:22 |
0 |
Harvard University; Cambridge; United States
Resource Report
Resource Website
500+ mentions
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Harvard University; Cambridge; United States (RRID:SCR_011273)
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Harvard
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university
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Institution of higher education in the United States. Private Ivy League research university in Cambridge, Massachusetts.
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research, private, undergraduate, graduate, master's, doctoral, phD, institution, university
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uses: ShareLaTeX
uses: Overleaf
uses: ReadCube
uses: DIRECT2experts
uses: Benchling
uses: Writefull
uses: Paperpile
uses: GenomeCompiler
is affiliated with: Broad Institute
is related to: Beta Cell Biology Consortium
is related to: ShareLaTeX
is related to: CalR
is related to: dcmqi
is related to: PROMIS 2 MY Health
is parent organization of: EGO - Eukaryotic Gene Orthologs
is parent organization of: Drosophila RNAi Screening Center
is parent organization of: FAS Center For Systems Biology
is parent organization of: DF/HCC Health Communication Core
is parent organization of: DF/HCC Specialized Histopathology Services Core
is parent organization of: Harvard HSCI iPS Cell Core Facility
is parent organization of: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility
is parent organization of: Wyss Institute Imaging Core
is parent organization of: Harvard FAS Bauer Core Laboratory
is parent organization of: Harvard - Oxford Cortical Structural Atlas
is parent organization of: Harvard Medical School, Department of Systems Biology: The Megason Lab - MegaCapture Software
is parent organization of: Dataverse Network Project
is parent organization of: edX
is parent organization of: Authorea
is parent organization of: BioNumbers
is parent organization of: SNPHunter
is parent organization of: NeuroImaging Tools and Resources Collaboratory (NITRC)
is parent organization of: Digital Access to Scholarship at Harvard
is parent organization of: Data Scientist Training for Librarians
is parent organization of: Arnold Arboretum of Harvard University: Weld Hill Microscopy Lab
is parent organization of: Arnold Arboretum of Harvard University: Weld Hill Molecular Lab
is parent organization of: 3D Slicer
is parent organization of: GeneMerge
is parent organization of: High Resolution Mouse Brain Atlas
is parent organization of: Journal of Comparative Neurology Antibody database
is parent organization of: FlyBase
is parent organization of: CardioGenomics
is parent organization of: Harvard Medical School Division of Medical Sciences
is parent organization of: DPInteract
is parent organization of: Gene Ontology Partition Database
is parent organization of: MHCPEP
is parent organization of: SDR: Specificity-Determining Residues in Protein Families
is parent organization of: Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software
is parent organization of: MedGene
is parent organization of: New England Primate Research School
is parent organization of: Boston Area Diabetes Endocrinology Research Center Metabolic Physiology and Energy Balance Core Facility
is parent organization of: Harvard FAS Magnetic Resonance Laboratory
is parent organization of: Cheng Li Lab of Computational Genomics
is parent organization of: Motif Extractor
is parent organization of: HIV Brain Sequence Database
is parent organization of: Arnold Arboretum of Harvard University: Weld Hill Growth Facilities
is parent organization of: HSDM Micro CT Core
is parent organization of: DF/HCC Biostatistics Core Facility
is parent organization of: DF/HCC Cancer Pharmacology Core
is parent organization of: Dana Farber and Harvard Cancer Center Cancer Proteomics Center
is parent organization of: DF/HCC Cell Manipulation Core Facility
is parent organization of: DF/HCC Community Practice Research Core
is parent organization of: DF/HCC High-Throughput Polymorphism Detection Core
is parent organization of: DF/HCC Monoclonal Antibody Core
is parent organization of: DF/HCC Pathology Specimen Locator
is parent organization of: DF/HCC Rodent Histopathology Core Facility
is parent organization of: DF/HCC Tissue Microarray and Imaging Core Facility
is parent organization of: DF/HCC Tumor Imaging Metrics Core Facility
is parent organization of: HMS Microfluidics Core Facility
is parent organization of: HSCI Humanized Neonatal Mouse Center
is parent organization of: Harvard Bioinformatics Core at Joslin Diabetes Center
is parent organization of: Harvard CNS Imaging and Analysis Facility
is parent organization of: Harvard CNS NNIN/C Computational Facility
is parent organization of: Harvard CNS Nanofabrication Facility
is parent organization of: Harvard CNS Nanomaterial Facility
is parent organization of: Harvard Center for Biological Imaging
is parent organization of: Harvard Digestive Diseases Center Biomedical CORE B: Microscopy and Histopathology
is parent organization of: Harvard FAS Bauer Core: Mass Spectrometry and Proteomics Core Laboratory
is parent organization of: Harvard FAS Center for Brain Science - Electron Microscopy Core Facility
is parent organization of: Harvard PCMM Flow and Imaging Cytometry Resource
is parent organization of: Harvard FAS Center for Brain Science - Imaging Core Facility
is parent organization of: Harvard FAS Center for Brain Science - Neuroengineering Core Facility
is parent organization of: Harvard FAS Center for Brain Science - Neuroimaging Core Facility
is parent organization of: Harvard FAS Center for Crystallographic Studies
is parent organization of: Harvard FAS Research Computing Core
is parent organization of: Harvard FAS Small Molecule Mass Spectrometry Facility
is parent organization of: Harvard PCPGM Genotyping Facility
is parent organization of: Harvard Genome Modification Facility Harvard University
is parent organization of: Harvard PCMM Optical Microscopy Core
is parent organization of: Harvard PCPGM Biorepository for Medical Discovery
is parent organization of: Harvard PCPGM Biosample Services Facility
is parent organization of: Harvard PCPGM DNA Sequencing Facility
is parent organization of: Harvard PCPGM Microarray Facility
is parent organization of: Harvard Partners Research Computing Core
is parent organization of: MGH HSCI-CRM Flow Cytometry Core Facility
is parent organization of: Ragon Institute Biostatistics Core
is parent organization of: Ragon Institute Imaging Core Flow Cytometry
is parent organization of: Ragon Institute Imaging Core Microscopy
is parent organization of: SERI Flow Cytometry Core Facility
is parent organization of: Wyss Institute Machine Shop / 3D Prototyping Core
is parent organization of: Wyss Institute Materials Characterization Core
is parent organization of: Computational Biology and Functional Genomics Laboratory at Harvard
is parent organization of: Harvard Medical School; Massachusetts; USA
is parent organization of: Harvard T.H. Chan School of Public Health
is parent organization of: Harvard Tumor Imaging Metrics Core Facility
is parent organization of: Harvard SERI Graphic Services Core
is parent organization of: Harvard Digestive Diseases Center Biomedical CORE D: Gnotobiotic Mice, Microbiology and Metagenomics
is parent organization of: Harvard University Labs and Facilities
is parent organization of: HNDC Drug Discovery in Neurodegeneration
is parent organization of: Eagle I
is parent organization of: PolyPhen: Polymorphism Phenotyping
is parent organization of: PLINK/SEQ
is parent organization of: FreeSurfer
is parent organization of: Magnaporthe comparative Database
is parent organization of: CTSAconnect
is parent organization of: International Stroke Database
is parent organization of: International Stroke Database/Software
is parent organization of: ChemBank
is parent organization of: EM-DECODER
is parent organization of: Ruby NIfTI
is parent organization of: CummeRbund
is parent organization of: BINOCh
is parent organization of: Harvard Digestive Disease Center
is parent organization of: GraPhlAn
is parent organization of: biobakery
is parent organization of: DeepNeuro
is parent organization of: Joslin Diabetes Center
is parent organization of: PAGODA
is parent organization of: Harvard School of Public Health Microbiome Analysis Core Facility
is parent organization of: Diffusion Toolkit
is parent organization of: Cistrome
is parent organization of: ADMIXTOOLS
is parent organization of: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation
is parent organization of: Harvard Medical School PCMM Microscopy Core Facility
is parent organization of: PolicyModels
is parent organization of: Cistrome
is parent organization of: Biofactoid
is parent organization of: Camera Control project
is parent organization of: Harvard University Bauer Core Facility
is parent organization of: Harvard Tissue Atlas
is parent organization of: Harvard Medical School Center for Cancer Systems Pharmacology
is parent organization of: SPRING
is parent organization of: Minerva
is parent organization of: scimap
is parent organization of: moseq2-app
is parent organization of: Keypoint MoSeq
is parent organization of: Harvard University Chan School of Public Health Bioinformatics Core Facility
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SCR_016676, Wikidata:Q13371, ISNI:000000041936754X, Crossref funder ID:100007229, nlx_90063, grid.38142.3c |
https://ror.org/03vek6s52 |
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SCR_011273 |
Harvard University |
2025-05-24 08:12:00 |
725 |
NeuroImaging Tools and Resources Collaboratory (NITRC)
Resource Report
Resource Website
100+ mentions
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NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430)
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NITRC
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service resource, storage service resource, portal, data repository, software repository, community building portal, software resource, data or information resource
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Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.
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collaboration, information, resource, structural, functional, neuroimaging, MRI, fMRI, EEG, MEG, PET
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is used by: NIF Data Federation
is used by: Consortium for Reliability and Reproducibility
is used by: DataLad
is recommended by: National Library of Medicine
lists: Dipy
lists: 3DMeshMetric
lists: MPScope
lists: VectorValuedHistogramNormalizer
lists: Faceted Search Based Ontology Visualizer
lists: Morphometry BIRN
lists: Colin 3T/7T High-resolution Atlas
lists: CMFreg
lists: BrainFX
lists: dinifti
lists: Center for Computational Biology at UCLA
lists: Convert MNI coordinates to or from XYZ
lists: Licensing issues in software and data
lists: Local Binary Pattern Analysis Tools for MR Brain Images
lists: MIView
lists: uManager
lists: Penn Hippocampus Atlas
lists: RapidArt
lists: Scribe
lists: ShapeWorks
lists: Vervet Probabilistic Atlas
lists: Talairach Daemon
lists: ADHD-200 Preprocessed Data
lists: LORIS - Longitudinal Online Research and Imaging System
lists: NVM
lists: Maps4Mipav (Exploratory JIST)
lists: Autism Tissue Program
lists: MEG Tools
lists: PyNIfTI
lists: LONI Visualization Tool
lists: Mind Research Network - COINS
lists: OpenElectrophy
lists: CIFTI Connectivity File Format
lists: 3DSlicerLupusLesionModule
lists: BrainNetworkConstructionAnalysisPlatform
lists: COMPARE
lists: Data Format Tools
lists: GesTr
lists: I/OWA
lists: MINC Example files
lists: cbiNifti: Matlab/Octave Nifti library
lists: BRAINSCut
lists: C-PAC
lists: Connectir
lists: DicomBrowser
lists: Hitachi Optical Topography System
lists: Net Station API
lists: imcalc: SPM batch image calculator
lists: BRAINSCortex
lists: Insight Segmentation and Registration Toolkit
lists: LONI Debabeler
lists: LONI Pipeline Processing Environment
lists: NiLearn
lists: MRI Studio
lists: BraVa
lists: Brede Wiki
lists: Center for Functional Neuroimaging Technologies
lists: Philips Users Community
lists: medInria
lists: Beijing: Eyes Open Eyes Closed Study
lists: vIST/e
lists: Camino
lists: Diffusion Tensor Imaging ToolKit
lists: TORTOISE
lists: NIDAG: Neuroimaging Data Access Group
lists: MRI CVPR
lists: vuTools
lists: Medical Image Processing and Visualization in Virtual Environments
lists: Brainstorm
lists: Atlas3D
lists: FMRISTAT - A general statistical analysis for fMRI data
lists: FreeSurfer
lists: Rosetta Bit
lists: Laboratory of Neuro Imaging
lists: Group ICA of fMRI Toolbox
lists: Hierarchical Attribute Matching Mechanism for Elastic Registration
lists: Internet Brain Segmentation Repository
lists: Neural ElectroMagnetic Ontologies (NEMO) Project
lists: Wavelet-based Image Fusion
lists: ITK-SNAP
lists: Internet Brain Volume Database
lists: Statistical non-Parametric Mapping
lists: VoxBo
lists: NITRC Computational Environment
lists: Spatially Constrained Parcellation
lists: Cluster reporter
lists: Cluster Extent Correction
lists: 4D Atlases Construction
lists: CIGAL
lists: CleanLine
lists: Computational Morphometry Toolkit
lists: Cognitive Paradigm Ontology
lists: aBEAT
lists: MR Connectome Automated Pipeline
lists: International Neuroinformatics Coordinating Facility
lists: Functional Regression Analysis of DTI Tract Statistics
lists: MCIC
lists: MGDM: Multi Geometric Deformable Model
lists: MIAS Registration Toolkit
lists: Medical Image Visualization and Analysis
lists: Microstructural correlation toolbox
lists: MisterI
lists: MriWatcher
lists: Multiple Correlation Function Tool
lists: NITRC Community Conferences Workshops and Meetings
lists: BRAINSFit
lists: INCF Software Center
lists: BrainVision Analyzer
lists: COGNISION
lists: DPARSF
lists: GLIRT
lists: MINC
lists: Group Level Imputation of Statistic Maps
lists: MRIcron
lists: Inter-Group Registration Toolbox
lists: MCML and CONV
lists: MEGSIM
lists: MIRIAD
lists: MRI Defacer
lists: MS lesion segmentation challenge 2008
lists: Measure Projection Toolbox
lists: Mindboggle
lists: Mindboggle-101 atlases
lists: ModelGUI
lists: Multi-Modal MRI Reproducibility Resource
lists: MultiTracer
lists: Multicomponent T2 estimation with stimulated echo correction
lists: NCANDA: Data Integration Component
lists: NFT
lists: Net Station EEG Software
lists: Network Based Statistic Toolbox
lists: NeuroScope
lists: Numerical Fibre Generator
lists: PST MRI Simulator
lists: cortex
lists: iBEAT
lists: M3
lists: Group ICA Of EEG Toolbox
lists: 4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration
lists: Automatic Segmentation Tool Adapter
lists: DTI-TEMPLATE-RHESUS-MACAQUES
lists: LONI Provenance Editor
lists: MNI N3
lists: MRI Digital Projection System
lists: NIDB - Neuroinformatics Database
lists: NIPY
lists: NIRAL Utilities
lists: NIRx NIRS Neuroimaging
lists: NIRx2nirs: A NIRx to .nirs data converter
lists: NITRC Enhanced Services
lists: NITRC GForge Extensions
lists: NPTK
lists: NeuroImaging Analysis Kit (NIAK)
lists: NiBabel
lists: NiftyRec
lists: Nipype
lists: Nirfast
lists: Nitime
lists: Non-Rigid Image Registration Evaluation Project
lists: Normative Independent Component Analysis
lists: OEI fMRI compatible olfactometer
lists: ORS Visual SI
lists: OpenMEEG
lists: PANDA
lists: PESTICA fMRI Physio Detection/Correction
lists: PHYCAA+: adaptive physiological noise correction for BOLD fMRI
lists: ParaView
lists: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR)
lists: Presentation
lists: PySurfer
lists: Pythagorean Displacement and Motion Regressors
lists: Quantitative Diffusion Tools
lists: R-package for adaptive DWI analysis
lists: R-package for adaptive fMRI analysis
lists: REX
lists: RFT FDR
lists: ROBEX
lists: RT Image
lists: Resource Ontology Discussion Group
lists: Rodent Brain Extraction Tool
lists: Rodent Cortical Thickness Analysis
lists: S-rep Fitting Statistics and Segmentation
lists: SCIRun
lists: SCRalyze
lists: SOCK
lists: SPHARM-MAT
lists: SPHARM-PDM Toolbox
lists: SRI24 Atlas: Normal Adult Brain Anatomy
lists: Seg3D
lists: ShapeComplexAtlas
lists: Signed Differential Mapping
lists: Sleuth
lists: Slice:Drop
lists: Slicer3 Example Modules
lists: Source Information Flow Toolbox
lists: Spanish Resting State Network
lists: Spatial Analysis 3D
lists: Stereoscopic Atlas of Intrinsic Brain Networks
lists: UNC Infant 0-1-2 Atlases
lists: UNC Primate Brain Atlas
lists: XCEDE Schema
lists: peak nii
lists: pydicom
lists: pyxnat
lists: scikit-learn
lists: shapeAnalysisMANCOVA - SPHARM tools
lists: VMTK in 3D Slicer
lists: 3D Interactive Chemical Shift Imaging
lists: BRAINSSurfaceStats
lists: Brain lesion segmentation tool using SVM
lists: Diffusion Tractography with Kalman Filter
lists: Fast Nonlocal Means for MRI denoising
lists: Monte Carlo Simulation Software: tMCimg
lists: Web Interfaces for Multiscale Images
lists: STAPLE
lists: Segmentation Validation Engine
lists: Spatial Statistical Parametric Mapping
lists: SpineSegmentation module for 3DSlicer
lists: Stochastic Tractography System
lists: Subject Library
lists: TAPIR
lists: TARQUIN
lists: Template Image Processing Library
lists: TetraMetrix
lists: TractoR: Tractography with R
lists: Triangle BioSystems
lists: TumorSim
lists: TurtleSeg
lists: UNC Human Brain Atlas
lists: VR Worlds 2
lists: Vaa3D
lists: ValMap: simple statistical mapping tool
lists: WFU Biological Parametric Mapping Toolbox
lists: WFU Pipeline
lists: Working Memory Trainer
lists: vis: SPM Visualized Statistics toolbox
lists: Synchronized Histological Image Viewing Architecture
lists: LONI ShapeViewer
lists: LONI ShapeTools
lists: FFT Library
lists: Automated recognition of brain region mentions in neuroscience literature.
lists: NUTMEG
lists: Cognitive Atlas
lists: Mouse BIRN Atlasing Toolkit
lists: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat
lists: FSL
lists: LEAD-DBS
lists: Brainscape
lists: EONS
lists: BioImage Suite
lists: ADNI - Alzheimer's Disease Neuroimaging Initiative
lists: MindSeer
lists: XNAT - The Extensible Neuroimaging Archive Toolkit
lists: brainmap.org
lists: ImageJ
lists: Neuroimaging Informatics Technology Initiative
lists: IMOD
lists: Statistics Online Computational Resource
lists: signalml.org
lists: Mouse Biomedical Informatics Research Network
lists: NIH MRI Study of Normal Brain Development
lists: MGH-USC Human Connectome Project
lists: Fusion ICA Toolbox
lists: Corpus Callosum Thickness Profile Analysis Pipeline
lists: ABIDE
lists: Mouse Connectome Project
lists: NITRC-IR
lists: Open Connectome Project
lists: neurodebian
lists: NIMH Data Archive
lists: ANTS - Advanced Normalization ToolS
lists: XNAT Extras
lists: TrackVis
lists: Brain Connectivity Toolbox
lists: FieldTrip
lists: LONI Inspector
lists: BrainLiner
lists: OpenNeuro
lists: Biomedical Informatics Research Network
lists: McConnell Brain Imaging Center MNI Macaque Atlas
lists: SINOMO
lists: DONE: Detection of Outlier NEurons
lists: Neuro Bureau
lists: ADHD-200 Sample
lists: 1000 Functional Connectomes Project
lists: PubBrain
lists: CBRAIN
lists: ENIGMA: Enhancing Neuro Imaging Genetics Through Meta-Analysis
lists: Bisque
lists: 3D Slicer
lists: Internet Analysis Tools Registry
lists: Neuromorphometrics
lists: Analysis of Functional NeuroImages
lists: Automated Image Registration
lists: BASH4RfMRI
lists: MNE software
lists: Object-Oriented Development Interface for NMR
lists: NYU CSC TestRetest
lists: Optseq - fMRI Event Scheduler
lists: TOADS-CRUISE Brain Segmentation Tools
lists: MouseTracker
lists: Hammer And WML Modules for 3D Slicer
lists: ABC (Atlas Based Classification)
lists: Allen Brain Atlas API
lists: Viking Viewer for Connectomics
lists: ARCTIC
lists: ArtRepair for robust fMRI
lists: Automatic Registration Toolbox
lists: Artifact Detection Tools
lists: Segmentation of Hippocampus Subfields
lists: ASL data processing tool box
lists: Bioelectromagnetism Matlab Toolbox
lists: PyMVPA
lists: Human Imaging Database
lists: BrainImage Software
lists: Brede Toolbox
lists: Computerized Anatomical Reconstruction and Editing Toolkit
lists: BrainColor: Collaborative Open Labeling Online Resource
lists: Registry Builder Data Harmonization and Aggregation Tool
lists: PsychoPy
lists: NiftySim
lists: NiftyReg
lists: Neurobiological Image Management System
lists: BRAINSTools
lists: MeshValmet: Validation Metric for Meshes
lists: BrainSuite
lists: DW-MRI Random Walk Simulator
lists: Web Game for Collaborative Labeling
lists: BrainVoyager Brain Tutor
lists: POLGUI - Matlab Polhemus Interface
lists: BrainVoyager Brain Viewer
lists: NeuroPub Visualizer
lists: NODDI Matlab Toolbox
lists: MITK Diffusion
lists: Federal Interagency Traumatic Brain Injury Research Informatics System
lists: BrainMaps.org
lists: PRoNTo
lists: Scalable Brain Atlas
lists: NIH Human Connectome Project
lists: Mesh-based Monte Carlo (MMC)
lists: Matlab Neuroshare Library
lists: MRtrix
lists: MABMIS: Multi-Atlas Based Multi-Image Segmentation
lists: Monte Carlo eXtreme
lists: Whole Brain Catalog
lists: BCILAB
lists: ABSORB: Atlas Building by Self-Organized Registration and Bundling
lists: VAMCA
lists: SPM
lists: Low Resolution Electromagnetic Tomography
lists: SurfStat
lists: Cambridge Brain Activation
lists: CLEAVE
lists: CoCoMac
lists: fMRI Data Center
lists: Function BIRN
lists: EEGLAB
lists: BrainVISA / Anatomist
lists: MIPAV: Medical Image Processing and Visualization
lists: NeuroLens
lists: WFU PickAtlas
lists: Open Access Series of Imaging Studies
lists: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis
lists: xjView: A Viewing Program For SPM
lists: Human Connectome Coordination Facility
lists: ASL spm8
lists: Integrated Manually Extracted Annotation
lists: JIST: Java Image Science Toolkit
lists: Functional Analysis of Diffusion Tensor
lists: AHEAD
lists: ANTsR
lists: 3DBar
lists: Cancer Imaging Archive (TCIA)
lists: Pediatric Imaging Neurocognition and Genetics
lists: Atlasing of the basal ganglia
lists: cmrep
lists: 3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood
lists: AutoSeg
lists: BXH/XCEDE Tools
lists: Baby Brain Toolkit
lists: Best Practices for Software Development
lists: Brain Catalogue
lists: Draw3D and Meshinator
lists: Brain Segmentation Testing Protocol
lists: BrainNet Viewer
lists: BrainSolution
lists: Brainvox
lists: C8: Corpus Callosum Computations
lists: CAMINO-TRACKVIS
lists: CANDI Share: Schizophrenia Bulletin 2008
lists: CBS High-Res Brain Processing Tools
lists: CCSeg - Corpus Callosum Segmentation
lists: Cerebral Blood Flow Database and Analysis Pipeline
lists: Create DWI Atlas
lists: DFBIdb
lists: DIAMOND
lists: DICOM UploadGUI
lists: DOTS WM tract segmentation
lists: DTI Fiber Tract Statistics
lists: DW-MRI registration in FSL
lists: DbGaP Cleaner
lists: DentalTools
lists: Diffusion MRI - In-vivo and Phantom Data
lists: Diffusion MRI at DKFZ Heidelberg
lists: Diffusion Warp
lists: Disease State Prediction
lists: EEG human categorization data
lists: Epsilon Radial Networks
lists: FBIRN Image Processing Scripts
lists: FSL extensions
lists: False Discovery Rate Weighted
lists: Fiber Tracking Tool
lists: Fiber-tracking based on Finsler distance
lists: FiberViewerLight
lists: Finsler tractography module for Slicer
lists: Fluid Registration and Atlas Toolkit
lists: Framework for Open Programmatic Access
lists: Functional Connectivity Community
lists: Functional ROI Atlas
lists: Functional and Structural Neuroimaging Journals Listing
lists: GAMBIT
lists: GAMMA
lists: BRAINSMush
lists: GPU based affine registration
lists: GRETNA
lists: Generalized Covariance Analysis
lists: Generalized PPI Toolbox
lists: Group Information Guided ICA
lists: Groupwise Image Registration Toolbox
lists: HD Neuro-Informatics
lists: Hitachi2nirs
lists: IDeA Lab brain image processing suite
lists: INCF Neuroimaging Data Sharing
lists: INIA19 Primate Brain Atlas
lists: JHU Proj. in Applied Medical Imaging
lists: JIST Resources for Algorithm Development
lists: BRAINSROIAuto
lists: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI
lists: Landman NeuroImaging Tools
lists: Local Label Learning Segmentation
lists: MASI Label Fusion
lists: MASIMatlab
lists: MATLAB Tutorial on Diffusion Tensor MRI
lists: Multi-Echo Independent Component Regression Group-Level Connectivity Dataset
lists: Multi-fiber Reconstruction from DW-MRI
lists: NITRC Books
lists: Network Modification Tool Lite
lists: Non-rigid groupwise registration method
lists: Rockland Download Link Script
lists: Subject Order-Independent Group ICA
lists: Task Independent Fluctuations Discussion
lists: UNC Human DTI Brain Atlas
lists: BRAINSTestData
lists: cPPI Toolbox for fMRI
lists: fMRI Classification in R
lists: fMRI-CPCA
lists: fNIRS Data Analysis Environment
lists: factory t1 dti
lists: BRAINSDemonWarp
lists: AMILab
lists: ADJUST
lists: ALVIN
lists: Age Related Atrophy Dataset
lists: B0 and eddy current correction for DTI
lists: BESA
lists: BSMac
lists: BVQXtools
lists: BioMesh3D
lists: BrainBrowser
lists: BrainGraph Editor
lists: BrainMagix SPM Viewer
lists: BrainMask Volume Processing Tool
lists: Brainsight
lists: Brainwaver
lists: CANDI Neuroimaging Access Point
lists: CBFBIRN
lists: CDF-HC PointSetReg
lists: GIMIAS
lists: CURRY
lists: CalaTK
lists: CoCoMac-Paxinos3D viewer
lists: INVIZIAN
lists: CONN
lists: Connectome File Format
lists: Connectome Viewer
lists: Cytoseg
lists: DICCCOL predictor
lists: DRAMMS
lists: DSI Studio
lists: Level-set Segmentation for Slicer3
lists: DTI BrainImageScope
lists: DTI-Reg
lists: DTIProcess ToolKit
lists: DWI/DTI Quality Control Tool: DTIPrep
lists: Diffusional Kurtosis Estimator
lists: Distributome
lists: ImageVis3D
lists: E-Prime
lists: E-Prime Extensions for fMRI
lists: EEGVIS
lists: EEProbe
lists: EMSE Suite
lists: LONI Brain Parser
lists: EPILAB
lists: ERPLAB
lists: FIV
lists: FMRIpower
lists: Fiber Optic Button Response System
lists: Free-D
lists: GIFTI
lists: GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data
lists: HAMMER Suite
lists: HERMES
lists: HI-SPEED Software Packets
lists: Homer2
lists: IIT Human Brain Atlas
lists: JIP Analysis Toolkit
lists: Jim
lists: LDDMM
lists: LIBEEP
lists: LIMO EEG
lists: LONI De-identification Debablet
lists: Waxholm Space
lists: Lipsia
lists: Lumina LP- 400 Response System
lists: MRI Dataset for Hippocampus Segmentation
lists: MaCH-Admix
lists: Mach2dat
lists: Mag Design and Engineering
lists: MagPro Magnetic Stimulator
lists: SR Research EyeLink Eye Trackers
lists: Mango
lists: Manually Labeled MRI Brain Scan Database
lists: MarsBaR region of interest toolbox for SPM
lists: MazeSuite
lists: MoTrak Head Motion Tracking System
lists: NCIGT Fast Imaging Library
lists: NeuroWeb - NeuroImaging Database
lists: Neuroimaging Made Easy Blog
lists: Neurophysiological Biomarker Toolbox
lists: SVV
lists: Slicer3 Module Rician noise filter
lists: UNC/Utah NAMIC DTI Fiber Analysis Framework
lists: caGWAS
lists: eConnectome
lists: elastix
lists: fMRI Artefact rejection and Sleep Scoring Toolbox
lists: MACH
lists: fMRI Grocer
lists: fNIR Devices
lists: fanDTasia Java Applet: DT-MRI Processing
lists: g.BSanalyze
lists: iTools
lists: iView X MRI-LR - Eye Tracking for fMRI
lists: map3d
lists: NICE-SIGN
lists: NIRS-SPM
lists: NITRC Community
lists: NordicNeuroLab
lists: PICSL Multi-Atlas Segmentation Tool
lists: Paradigm
lists: Pipeline Neuroimaging VirtualEnvironment
lists: Pipeline System for Octave and Matlab
lists: ProbabilisticBiasCorrection
lists: Program for optimal design of blocked fMRI experiments
lists: QCQP
lists: REST: a toolkit for resting-state fMRI
lists: Robust Biological Parametric Mapping
lists: SPM SS - fMRI functional localizers
lists: Solar Eclipse Imaging Genetics tools
lists: VIEWPixx /3D
lists: resting-state pediatric imaging template
lists: DATAPixx
lists: GTRACT
lists: Wisconsin White Matter Hyperintensities Segmentation Toolbox
lists: COBRE
lists: AngioCalc Cerebral Aneurysm Calculator
lists: USC Multimodal Connectivity Database
lists: BRAINSConstellationDetector
lists: ASA - Advanced Source Analysis
lists: BRAINSTracer
lists: EYE-EEG (combined eye-tracking & EEG)
lists: BrainVoyager
lists: Mean Machine
lists: ERP PCA Toolkit
lists: LiverSegm
lists: GSA-SNP
lists: FastICA
lists: DTI Atlas Builder
lists: Neuroimaging in Python
lists: Brain Decoder Toolbox
lists: iso2mesh
lists: CUDA-SPHERE-FWD-MEEG
lists: BrainCSI
lists: BrainVisa Morphology extensions
lists: VIEWPixx
lists: PROPixx
lists: GenGen
lists: MACH 1.0
lists: PennCNV
lists: SumsDB
lists: Integrated Software
lists: NeuroLex
lists: Parkinson's Progression Markers Initiative
lists: NeuroSynth
lists: Textpresso
lists: ANNOVAR
lists: Graphtools
lists: Grantees Meeting for NITRC
lists: FP-CIT SPECT brain template in MNI space
lists: Brain Computer Interface 2000 Software Package
lists: BEAST
lists: Brian Simulator
lists: Connectome Workbench
lists: ConnectomeDB
lists: DIAN - Dominantly Inherited Alzheimer Network
lists: NKI-RS Enhanced Sample
lists: EPILEPSIE database
lists: GEneral NEural SImulation System: The Neurospaces Project
lists: Hippocampome.org
lists: Kitware
lists: Kymata Atlas
lists: L-Measure
lists: MDR
lists: neuroConstruct
lists: Neurolucida
lists: NeuroMorpho.Org
lists: NEURON
lists: NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification
lists: NeuroVault
lists: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS)
lists: NINDS Repository
lists: NKI/Rockland Sample
lists: ODIN
lists: OBART
lists: Open Science Framework
lists: PLINK
lists: Stereo Investigator
lists: studyforrest.org
lists: Virtual brain
lists: TREES toolbox
lists: APERTURE
lists: 3dsvm
lists: 7T Structural MRI scans ATAG
lists: Atlases of amygdala and hippocampus for pediatric populations
lists: BetA-Series COrrelation
lists: bic-mni-models
lists: BiofilmQuant
lists: Biomag Discussion Group on Yahoo
lists: Brain Entropy in space and time (BEst)
lists: Brainnetome Atlas Viewer
lists: Brainnetome fMRI toolkit
lists: BROCCOLI
lists: C-MIND Database
lists: CARLsim: a GPU-accelerated SNN Simulator
lists: Clinical Toolbox for SPM
lists: CMIND PY
lists: COST
lists: dcm2nii
lists: DICOMConvert
lists: Displacement Field Viewer
lists: DTI denoising
lists: Efficient Longitudinal Upload of Depression in the Elderly (ELUDE)
lists: Efficient Permutation Testing
lists: DTI-TK
lists: ERPwavelab
lists: ExPosition Packages
lists: Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation
lists: Forward: Accurate finite element electromagnetic head models
lists: freesurfR
lists: Functional Connectivity Analysis Tool for near-infrared spectroscopy data
lists: GazeReader
lists: gCCA
lists: Generation R Pediatric MRI Resources
lists: GIMME
lists: GLMdenoise: a fast, automated technique for denoising task-based fMRI data
lists: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity
lists: HAMMER: Deformable Registration
lists: HBM Hackathon
lists: HDBIG
lists: High-quality diffusion-weighted imaging of Parkinsons disease
lists: MGA - Multimodal Glioma Analysis
lists: Image Synthesis Tools
lists: Imeka Tractography Service
lists: International Imaging Genetics Conference
lists: Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0
lists: Iterative dual-regression with sparse prior
lists: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI
lists: KWScene: MRML-based Atlas and Scene Builder/Reader/Writer
lists: L-Neuron
lists: Laplace Beltrami Filter on QuadEdge Meshes
lists: libSBML
lists: Lightweight Data Pipeline
lists: Longitudinal MS Lesion Imaging Archive
lists: MARS (Multi-Atlas Robust Segmentation)
lists: minc-toolkit
lists: minc-toolkit-testsuite
lists: MISST - Microstructure Imaging Sequence Simulation ToolBox
lists: MRI Neuroanatomy Labeling Services
lists: MRIcroS
lists: Multivariate General Linear Models (MGLM) on Riemannian Manifolds
lists: Neoseg
lists: NeoSegPipeline
lists: NeuriteTracer
lists: NeuroElf
lists: Neuron-C
lists: NIH Pediatric MRI Data Repository
lists: NIH-CIDI Lung Segmentation Tool
lists: NiiStat
lists: Northwestern University Schizophrenia Data and Software Tool (NUSDAST)
lists: Notion ResearchPACS
lists: NTU-DSI-122: a DSI template in ICBM-152 space
lists: OpenViBE
lists: OpenWalnut
lists: Orientation Distribution Function in Constant Solid Angle (CSA-ODF)
lists: Parkinsons Disease Discovery Database
lists: Prediction and Diagnosis for Depression and Schizophrenia
lists: Preprocessed Connectomes Project
lists: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data
lists: Ruby NIfTI
lists: SCORE
lists: SFMProject
lists: ShapePopulationViewer
lists: Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations
lists: SPIKECOR: fMRI tool for automated correction of head motion spikes
lists: Spinal Cord Toolbox
lists: Stark Cross-Sectional Aging
lists: Brain Coactivation Map
lists: Multiscale Object Orientation Simulation Environment
lists: Striatal Subregional VOImap
lists: Topographica
lists: Turbo-BrainVoyager
lists: CRL Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain
lists: UNC-Wisconsin Neurodevelopment Rhesus MRI Database
lists: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX)
lists: VMTK in 3D Slicer
lists: Wisconsin Cortical Thickness Analysis (CTA) Toolbox
lists: XFSL: An FSL toolbox
lists: XNBC
lists: YMDTI: Diffusion Tensor Images of Healthy Young Males
lists: BraTumIA (Brain Tumor Image Analysis)
lists: CAWorks
lists: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND)
lists: Graph Theory GLM (GTG) MATLAB Toolbox
lists: Functional Mixed Processes Models
lists: Papaya
lists: Parallel Stochastic Ion Channel Simulator
lists: Advanced Connectivity Analysis (ACA)
lists: International Imaging Genetics Conference
lists: Analyze Software System
lists: Optseq
lists: ENIGMA-DTI Pipeline
lists: Umea Brain Arteries
lists: MetaSearch
lists: BrainBox
lists: BluePyOpt
lists: MultiXplore
lists: Automatic Tractography-based Parcellation Pipeline
lists: Epilepsy T1 and Hippocampal Segmentation Datasets
lists: Mixed Effect Model of Genetic-Set and Environment Interaction
lists: masked ICA (mICA) Toolbox
lists: Altered States Database
lists: User Friendly Functional Connectivity - UF²C
lists: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open
lists: Region to Region
lists: Waxholm Space Atlas of the Sprague Dawley Rat Brain
lists: Nutil - Neuroimaging utilities
lists: MeshView
lists: vini: A viewer for fMRI data
lists: brainGraph
lists: Diffusion Toolkit
lists: Neurodocker
lists: HeuDiConv: a heuristic-centric DICOM converter
lists: Knowing what you know (kwyk) - Bayesian Brain Parcellation
lists: Rhesus Macaque Brain Atlases
lists: MIITRA atlas
lists: MonkeyCBP
lists: ReproNim/containers
lists: ReproMan
lists: ABCD-ReproNim Course
lists: Ventricular Morphometry Analysis System
lists: ONPRC18 Multimodal MRI Atlas
lists: volBrain
lists: Waxholm Space
is affiliated with: Manual Align RTS2000
is related to: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR
has parent organization: Harvard University; Cambridge; United States
has parent organization: NIH Blueprint for Neuroscience Research
is parent organization of: Licensing issues in software and data
is parent organization of: NITRC Enhanced Services
is parent organization of: Resource Ontology Discussion Group
is parent organization of: NITRC-IR
is parent organization of: 1000 Functional Connectomes Project
is parent organization of: NYU CSC TestRetest
is parent organization of: NITRC Books
is parent organization of: NITRC Community
is parent organization of: ABIDE
is parent organization of: COBRE
is parent organization of: Group Sparse Canonical Correlation Analysis
is parent organization of: Challenge Competitions Collection
is parent organization of: 1000 Functional Connectomes Project
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|
NIH Blueprint for Neuroscience Research ;
NIMH ;
NIDA ;
NIBIB U24 EB023398;
NINDS R44 NS074540 |
PMID:26044860
PMID:18999128 |
Free, Freely available, Registration suggested |
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nif-0000-00202 |
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SCR_003430 |
Neuroimaging Informatics Tools and Resources Clearinghouse, , NeuroImaging Tools and Resources Collaboratory, Neuroimaging Informatics Tools Resources Clearinghouse, NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse, NITRC - Neuroimaging Informatics Tools Resources Clearinghouse |
2025-05-28 10:59:55 |
299 |
Automatic Analysis
Resource Report
Resource Website
1+ mentions
|
Automatic Analysis (RRID:SCR_003560)
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aa
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software application, time-series analysis software, data processing software, software resource, software toolkit, image processing software, image analysis software, data analysis software, workflow software
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Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets,
like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps.
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Neuroimaging workflows, processing multimodal datasets, brain integrated views, fmri, eeg, meg, dwi, morphometry, parallel-processing, scripting, record-keeping,
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uses: FreeSurfer
uses: MATLAB
uses: SPM
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NSERC Discovery and the Canada Excellence Research Chair (CERC) in Cognitive Neuroimaging ;
NSERC/CIHR CHRP ;
NIA R01 AG038490;
NIDCD R01 DC013063 |
PMID:25642185 |
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nlx_157695 |
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SCR_003560 |
automaticanalysis, AutomaticAnalysis |
2025-05-28 11:00:01 |
8 |
FMRLAB
Resource Report
Resource Website
1+ mentions
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FMRLAB (RRID:SCR_005164)
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FMRLAB
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software application, software resource, data processing software
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A Matlab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive Matlab graphic user interface (GUI). All the necessary processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with Matlab scripts using the FMRLAB functions and data structure. Since fMRI data analysis is a complex enterprise, including digital image processing, statistical analysis and data visualization, an integrated framework combining processing elements is desired eagerly by users in the neuroimaging community. Recently, large number of software tools for data analysis and visualization have been developed for this purpose. However, most of these tools use model-based statistical methods which assume that the users know the hemodynamic response (HR) for their paradigm in advance and can specify a reasonable HR model. Often, however, accurate or reasonable response HR models are unavailable. An alternative data-driven method, infomax ICA (McKeown et al., 1998), does not require that an a priori HR model, instead deriving HRs of spatially independent components of the entire data set from the higher-order statistics of the data themselves. FMRLAB is a toolbox running under Matlab containing necessary components for data-driven fMRI data analysis using the highly reliable infomax ICA algorithm (Bell & Sejnowski, 1995), normalized (Amari, 1999), extended (Lee, Girolami and Sejnowski, 1999) and automated by Makeig et al. FMRLAB has been developed under Matlab 6.1 running on Red Hat Linux. FMRLAB Features * Graphic user interface * Flexible data importing * Interactive data plotting * Computationally efficient * Defined FMRI data structure * Independent component browser * Smooth, transparent component exporting and spatial normalization process * Interface with other software for further analysis or visualization. * SPM-style component plots (MIP, 2-D slice overlay and 3-D)
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fmri, fmr lab, anatomy, brain mapping, data analysis, independent component analysis, neuroimaging, image processing, statistical analysis, data visualization, matlab
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is related to: FreeSurfer
has parent organization: Swartz Center for Computational Neuroscience
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NIMH 5RO1MHO61619-03 |
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nif-0000-00077 |
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SCR_005164 |
|
2025-05-28 11:01:08 |
3 |
NHP Freesurfer
Resource Report
Resource Website
1+ mentions
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NHP Freesurfer (RRID:SCR_021814)
|
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software application, software resource, data processing software
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Software tool as guide to process NHP anatomical MRI data with adapted version of Freesurfer to generate surfaces and flatmaps.
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MRI, NHP, process NHP anatomical MRI data, generate surfaces and flatmaps
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uses: FreeSurfer
has parent organization: Royal Netherlands Academy of Arts and Sciences; Amsterdam; Netherlands
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Free, Available for download, Freely available |
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SCR_021814 |
NHP-Freesurfer |
2025-05-28 11:10:56 |
1 |
Debian
Resource Report
Resource Website
10+ mentions
|
Debian (RRID:SCR_006638)
|
Debian
|
software repository, source code, database, software resource, data or information resource
|
Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
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operating system, software package, FASEB list
|
lists: GUARDD
lists: FACS
lists: SNAVI
lists: Fusion Analyser
lists: GEOquery
lists: MIMOSA
lists: RNAcontext
lists: AffyRNADegradation
lists: Patchwork
lists: GraBCas
lists: GENIE3
lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks
lists: Megraft
lists: PeptideProphet
lists: VARiD
lists: Flicker
lists: ARACHNE
lists: Quant
lists: riboPicker
lists: cn.FARMS
lists: ProteinProphet
lists: dbSTS
lists: flowPeaks
lists: SODOCK
lists: PEPPER
lists: POPBAM
lists: Micro-Analyzer
lists: MuTect
lists: Mfuzz
lists: PGS
lists: TAPyR
lists: ContEst
lists: FPSAC
lists: FlipFlop
lists: SRMA
lists: Pindel
lists: PhenoFam
lists: DSRC
lists: SOAP
lists: TriageTools
lists: StringTie
lists: SplitSeek
lists: BLASR
lists: Bowtie
lists: Barrnap
lists: MUSCLE
lists: GimmeMotifs
lists: massiR
lists: CUDA-EC
lists: Illuminator
lists: SplicePlot
lists: SLOPE
lists: PARalyzer
lists: VAAL
lists: BreakSeq
lists: ProGlycProt
lists: OmicsOffice for NGS SeqSolve
lists: TileQC
lists: NGSUtils
lists: QUAST
lists: GenomicTools
lists: piCALL
lists: SNPchip
lists: TALLYMER
lists: SABER
lists: wateRmelon
lists: QualiMap
lists: BFCounter
lists: ADMIXTURE
lists: OLIN
lists: DEXUS
lists: limmaGUI
lists: KAnalyze
lists: oneChannelGUI
lists: BeadDataPackR
lists: affylmGUI
lists: SAMBLASTER
lists: PyLOH
lists: fRMA
lists: CYCLE
lists: FARMS
lists: MACAT
lists: GlyProt
lists: YinOYang
lists: Sequedex
lists: DictyOGlyc
lists: ToppCluster
lists: Biocatalogue - The Life Science Web Services Registry
lists: ProbRNA
lists: HAPLOPAINTER
lists: Chilibot: Gene and Protein relationships from MEDLINE
lists: GERMLINE
lists: FACTA+.
lists: CisGenome
lists: asSeq
lists: unifiedWMWqPCR
lists: HOMOZYGOSITYMAPPER
lists: Prediction of Amyloid Structure Aggregation
lists: InterMine
lists: TANGO
lists: CQN
lists: MEME Suite - Motif-based sequence analysis tools
lists: pRESTO
lists: S-MART
lists: PhosphoSitePlus: Protein Modification Site
lists: myExperiment
lists: DINDEL
lists: Skylign
lists: PEDIGRAPH
lists: ADaCGH2
lists: CCAT
lists: AnimalTFDB
lists: TEMP
lists: CanSNPer
lists: Candida Genome Database
lists: SamSPECTRAL
lists: InteroPorc
lists: MetaBase
lists: Pecan
lists: cisRED: cis-regulatory element
lists: AffyPipe
lists: SHORTY
lists: BISC
lists: Pathway Commons
lists: Cake
lists: SNVer
lists: WebGeSTer DB
lists: FlyFactorSurvey
lists: ASPGD
lists: TcoF
lists: cpnDB: A Chaperonin Database
lists: ZOOM
lists: CAMERA - Collection of annotation related methods for mass spectrometry data
lists: BEETL-fastq
lists: NGSrich
lists: ShotGun
lists: Iterative Signature Algorithm
lists: SBARS
lists: SNPAAMapper
lists: Autophagy Database
lists: RUbioSeq
lists: COSMIC - Catalogue Of Somatic Mutations In Cancer
lists: EchoBASE
lists: QualitySNPng
lists: Pathview
lists: pymzML
lists: RopeBWT2
lists: ExomeDepth
lists: NetPathMiner
lists: leeHom
lists: PurBayes
lists: libCSAM
lists: SuperPred: Drug classification and target prediction
lists: HGNC
lists: Coding Potential Calculator
lists: T3DB
lists: CPTRA
lists: BioNumbers
lists: GATE
lists: ProRata
lists: GreenPhylDB
lists: BREAKDANCER
lists: GeneFisher
lists: tweeDEseq
lists: HYDEN
lists: Eukaryotic Linear Motif
lists: Primer3Plus
lists: MethylAid
lists: Triplex
lists: Distant Regulatory Elements
lists: hot scan
lists: MFEprimer
lists: Proteome Analyst Specialized Subcellular Localization Server
lists: mrsFAST
lists: BioJS
lists: FastSNP
lists: Gene Set Enrichment Analysis
lists: Pipeliner
lists: ms lims
lists: GenePattern
lists: rBiopaxParser
lists: QDNAseq
lists: MutDB
lists: Piano
lists: NovelSeq
lists: MAGE-TAB
lists: Database of Interacting Proteins (DIP)
lists: Weighted Gene Co-expression Network Analysis
lists: Blood Group Antigen Gene Mutation Database
lists: drFAST
lists: pairheatmap
lists: MiST - Microbial Signal Transduction database
lists: AltAnalyze - Alternative Splicing Analysis Tool
lists: SplicingCompass
lists: deFuse
lists: Assembly Based ReAligner
lists: ggbio
lists: miR-PREFeR
lists: ALDEx2
lists: HTqPCR
lists: NanoStringNorm
lists: T-profiler
lists: Snakemake
lists: jmzTab
lists: MIPgen
lists: Bpipe
lists: PoPoolation
lists: L-Measure
lists: MultiPhen
lists: PheWAS R Package
lists: InsertionMapper
lists: Quantitative Enrichment of Sequence Tags
lists: INMEX
lists: Segway - a way to segment the genome
lists: SeWeR - SEquence analysis using WEb Resources
lists: TagDust
lists: BSRD
lists: DER Finder
lists: Stem Cell Discovery Engine
lists: Kdetrees
lists: Tree and reticulogram REConstruction
lists: BioPig
lists: NCBI BioSystems Database
lists: Distributed String Mining Framework
lists: NEWT
lists: PILGRM
lists: Selectome: a Database of Positive Selection
lists: SVMerge
lists: Parseq
lists: SVseq
lists: Small Molecule Pathway Database
lists: miRNAKey
lists: DELLY
lists: Apo and Holo structures DataBase
lists: BioSample Database at EBI
lists: MetaPhyler
lists: MG-RAST
lists: SLIQ
lists: SOPRA
lists: Information Hyperlinked Over Proteins
lists: AmphoraNet
lists: SINA
lists: SSPACE
lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets
lists: STING Report
lists: G-BLASTN
lists: RNA-eXpress
lists: MethPipe
lists: SoyBase
lists: Strelka
lists: RUM
lists: SPOT - Biological prioritization after a SNP association study
lists: VFS
lists: PHAge Search Tool
lists: MLTreeMap
lists: SEECER
lists: GeneTalk
lists: ERANGE
lists: rQuant
lists: NCBO Annotator
lists: ShoRAH
lists: Yabi
lists: ORMAN
lists: FusionMap
lists: CoPub
lists: Scripture
lists: SolexaQA
lists: Kismeth
lists: EMAGE Gene Expression Database
lists: SAMStat
lists: Knime4Bio
lists: Bis-SNP
lists: GobyWeb
lists: Jellyfish
lists: PRINSEQ
lists: PASS
lists: GSNAP
lists: SOAPaligner/soap2
lists: MethylViewer
lists: READSCAN
lists: DistMap
lists: MicrobesOnline
lists: mrFAST
lists: FLASH
lists: TIGRFAMS
lists: TMA Navigator
lists: Bambino
lists: TreQ
lists: SeqMap
lists: SeqTrace
lists: TRANSFAC
lists: GoFish
lists: MethylomeDB
lists: CLIPZ
lists: SerbGO
lists: ToppGene Suite
lists: ngsTools
lists: PePr
lists: DMRforPairs
lists: CharProtDB: Characterized Protein Database
lists: Expression Profiler
lists: SNPsandGO
lists: GoSurfer
lists: WEGO - Web Gene Ontology Annotation Plot
lists: SOURCE
lists: Stampy
lists: DiseaseMeth
lists: BLESS
lists: GraphProt
lists: GoPubMed
lists: ccPDB - Compilation and Creation of datasets from PDB
lists: Europe PubMed Central
lists: Dr.VIS - Human Disease-Related Viral Integration Sites
lists: DOMMINO - Database Of MacroMolecular INteractiOns
lists: DBETH - Database for Bacterial ExoToxins for Humans
lists: VirHostNet: Virus-Host Network
lists: GWASdb
lists: HFV Database
lists: HotRegion - A Database of Cooperative Hotspots
lists: eQuilibrator
lists: FunTree
lists: Cascade
lists: 959 Nematode Genomes
lists: ICEberg
lists: IndelFR - Indel Flanking Region Database
lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature
lists: ProRepeat
lists: NRG-CING
lists: InterEvol database
lists: MMMDB - Mouse Multiple tissue Metabolome DataBase
lists: Newtomics
lists: MIPModDB
lists: DistiLD - Diseases and Traits in LD
lists: Polbase
lists: UMD-BRCA1/ BRCA2 databases
lists: ScerTF
lists: VIRsiRNAdb
lists: ProPortal
lists: OGEE - Online GEne Essentiality database
lists: RecountDB
lists: PRED-GPCR
lists: RNA CoSSMos
lists: PRED-SIGNAL
lists: SNPedia
lists: SpliceDisease
lists: HMM-TM
lists: deepSNV
lists: OMPdb
lists: PRED-LIPO
lists: VICUNA
lists: Predictive Networks
lists: COEUS
lists: GeneTrail
lists: epigenomix
lists: ADGO
lists: SRAdb
lists: QCGWAS
lists: Flycircuit
lists: MouseBook
lists: Immune Epitope Database and Analysis Resource (IEDB)
lists: SitEx
lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit
lists: MSIsensor
lists: TSSer
lists: ATRHUNTER
lists: Phytozome
lists: Decombinator
lists: ViralZone
lists: COLT-Cancer
lists: Gene Expression Database
lists: BEDTools
lists: waviCGH
lists: Pseudomonas Genome Database
lists: BIGpre
lists: MyHits
lists: CAPS Database
lists: SpliceTrap
lists: EagleView
lists: IMGT/LIGM-DB
lists: RIKEN integrated database of mammals
lists: COHCAP
lists: DARC - Database for Aligned Ribosomal Complexes
lists: canSAR
lists: GWAMA
lists: AutismKB
lists: zfishbook
lists: PomBase
lists: Myrna
lists: PLEXdb - Plant Expression Database
lists: RamiGO
lists: PhenoM - Phenomics of yeast Mutants
lists: IMGT/GENE-DB
lists: HIstome: The Histone Infobase
lists: SCOP: Structural Classification of Proteins
lists: CuticleDB
lists: agriGO
lists: Expression Database in 4D
lists: ESEfinder 3.0
lists: TriTrypDB
lists: VIDA
lists: Database of Arabidopsis Transcription Factors
lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology
lists: AgBase
lists: Hyper Cell Line Database
lists: Midbody, Centrosome and Kinetochore
lists: Chromosome 7 Annotation Project
lists: MfunGD - MIPS Mouse Functional Genome Database
lists: Taipan
lists: VISTA Browser
lists: T1DBase
lists: lobSTR
lists: VISTA Enhancer Browser
lists: MEROPS
lists: Gene Array Analyzer
lists: Network Analysis, Visualization and Graphing TORonto
lists: Candidate Genes to Inherited Diseases
lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD)
lists: eTBlast
lists: hiPathDB - human integrated Pathway DB with facile visualization
lists: MuSiC
lists: miRNEST
lists: QuasiRecomb
lists: neXtProt
lists: DNAtraffic
lists: BeeBase
lists: NetOGlyc
lists: GenoTan
lists: GMAP
lists: LegumeIP
lists: SeqBuster
lists: elastix
lists: iMir
lists: WEBLOGO
lists: MaCH-Admix
lists: Pathema
lists: SNPinfo Web Server
lists: MOSCPHASER
lists: NEBcutter
lists: Atlas2
lists: FGDP
lists: Velvet
lists: HomSI
lists: MicroSNiPer
lists: MIRA
lists: ALLPATHS-LG
lists: CUPSAT
lists: SVDetect
lists: omiRas
lists: CopySeq
lists: MutSig
lists: HapFABIA
lists: DIANA-LncBase
lists: MutationTaster
lists: HMCan
lists: Geneious
lists: kmer-SVM
lists: SICER
lists: ZINBA
lists: Pedimap
lists: MAnorm
lists: PlantTFcat
lists: MethMarker
lists: NPS
lists: PeakRanger
lists: SEAL
lists: OligoArray
lists: PSAR-Align
lists: CEQer
lists: CloudBurst
lists: nucleR
lists: RACE
lists: Asterias
lists: PatMaN
lists: RobiNA
lists: LitInspector
lists: Btrim
lists: ArrayAnalysis.org
lists: CANGS
lists: GeneStitch
lists: ProDesign
lists: JiffyNet
lists: AlienTrimmer
lists: GenoREAD
lists: HSLPred
lists: CancerResource
lists: FABIA
lists: PlnTFDB
lists: easyRNASeq
lists: OBI-Warp
lists: PREDDIMER
lists: ECHO
lists: ICPL ESIQuant
lists: PRIDE Converter 2
lists: SlideSort-BPR
lists: COBRApy
lists: MFPaQ
lists: TopHat-Fusion
lists: miRPlant
lists: SNP ratio test
lists: compomics-utilities
lists: PLEK
lists: multiplierz
lists: Allim
lists: ISDTool
lists: NetCoffee
lists: MToolBox
lists: Scalpel
lists: DNaseR
lists: LocalAli
lists: NAIL
lists: iceLogo
lists: GPU-Meta-Storms
lists: AMS
lists: rqubic
lists: ANNOVAR
lists: A5-miseq
lists: PhosphoSiteAnalyzer
lists: Cell motility
lists: MethylCoder
lists: CAZy- Carbohydrate Active Enzyme
lists: CPFP
lists: GENE-counter
lists: PoolHap
lists: LOCAS
lists: CloudAligner
lists: HeurAA
lists: Mouse Genome Database
lists: MitoBreak
lists: PolyPhen: Polymorphism Phenotyping
lists: GSA-SNP
lists: featureCounts
lists: Crossbow
lists: CSAR
lists: seqMINER
lists: BEADS
lists: IUPHAR/BPS Guide to Pharmacology
lists: QuantiSNP
lists: Cube-DB
lists: Death Domain database
lists: psRNATarget
lists: DSAP
lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase
lists: GeneSigDB
lists: MACS
lists: NGSmethDB
lists: GENSCAN
lists: INCLUSive
lists: MINAS - Metal Ions in Nucleic AcidS
lists: Composition Profiler
lists: NNcon
lists: EGSEA
lists: SCRATCH
lists: Telescoper
lists: Buccaneer
lists: ProtTest
lists: Morpheus
lists: KAVIAR
lists: DISEASES
lists: SPEX2
lists: RAST Server
lists: GeneWise
lists: Crystallography and NMR System (CNS)
lists: FATCAT
lists: Membrane Protein Explorer
lists: LTR_Finder
lists: PALEOMIX
lists: TISSUES
lists: MetaMapR
lists: primers4clades
lists: MS-GF+
lists: PLAN2L
lists: Off-Spotter
lists: ProteomicsDB
lists: CHiCAGO
lists: SC3
lists: Bio-tradis
lists: ApiDB CryptoDB
lists: HISAT2
lists: PhyD3
lists: LoRDEC
lists: Bamtools
lists: ALTER
lists: MultiQC
lists: TFBS
lists: EnrichmentMap
lists: Poretools
lists: Exonerate
lists: 3D-footprint
lists: Genesis
lists: oligo
lists: DISULFIND
lists: Fastml
lists: mentha
lists: Oufti
lists: eXpression2Kinases
lists: IDEPI - IDentify EPItopes
lists: SMAGEXP
lists: ProCon - PROteomics CONversion
lists: TRANSIT
lists: DINIES
lists: Splicing Express
lists: FluxModeCalculator
lists: Lifebit Deploit
lists: ngsRelate
lists: SARTools
lists: OmicsNet
lists: SPICE
lists: Microscopy Image Browser
lists: Thunder STORM
lists: clusterProfiler
lists: NetworkAnalyst
lists: ANOCVA
lists: Rsubread
lists: Subread
lists: ConsensusClusterPlus
lists: CIBERSORT
lists: FRETBursts
lists: CCTOP
lists: scran
lists: ScaffMatch
lists: Heatmapper
lists: Goseq
lists: PRSice
lists: UMI-tools
lists: Proovread
lists: BinPacker
lists: JAMM
lists: CentroidFold
lists: ComplexHeatmap
lists: PatchDock
lists: FastProject
lists: ExPASy ABCD database
lists: Gigwa
lists: shinyGEO
lists: GeSeq
lists: EMBOSSMatcher
lists: Geneshot
lists: Mousebytes
lists: trimAl
lists: AmoebaDB
lists: STRUCTURE
lists: PASTEClassifier
lists: NetPhos
lists: HiC-Pro
lists: SWISS-MODEL
lists: Blood Exposome Database
lists: HingeProt
lists: ChiCMaxima
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lists: Dictyostelium discoideum genome database
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lists: IMG
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lists: miROrtho: the catalogue of animal microRNA genes
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lists: Noncoding RNA database
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lists: Orientations of Proteins in Membranes database
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lists: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers
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lists: SWISS-2DPAGE
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lists: Transporter Classification Database
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lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs
lists: FLUX CAPACITOR
lists: TB PORTALS
lists: TAndem Splice Site DataBase
lists: VirusHunter
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lists: Trowel
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lists: TropGENE DB
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lists: Gene Index Project
lists: Tool recommender system in Galaxy
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lists: Computational Morphometry Toolkit
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is related to: FreeContact
is parent organization of: neurodebian
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Free, Freely available |
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nlx_151598 |
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SCR_006638 |
Debian - The universal operating system, Debian GNU/Linux |
2025-05-28 11:02:06 |
47 |
freesurfR
Resource Report
Resource Website
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freesurfR (RRID:SCR_014110)
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software application, data processing software, software resource, software toolkit, data analysis software
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A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2.
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data analysis software, software package, group analysis, freesurfer, surface data, r linear model
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uses: FreeSurfer
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
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Available for download |
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SCR_014110 |
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2025-05-28 11:06:21 |
0 |
