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Neuroparc

This repository contains a number of useful parcellations, templates, masks, and transforms to (and from) MNI152NLin6 space. The files are named according to the BIDs specification

Atlas Info Summary

Atlas Name # Regions Symmetrical? Hierarchical? Labelled? Generation Method Average Vol/Region Native coordinate space Description Reference Publication Year of Origin File Source/Download URL
AAL 116 No No Yes Delineated with respect to anatomical landmarks (following sulci course in brain) 12758.353 MNI Automated anatomical labelling based on sulci. https://www.ncbi.nlm.nih.gov/pubmed/11771995 2002 https://www.gin.cnrs.fr/en/tools/aal/ http://www.gin.cnrs.fr/wp-content/uploads/aal2_for_SPM12.tar.gz
AICHA 384 No No Yes Built by estimation of resting-state networks, k-means clustering, homotopic regional grouping based on maximal inter-hemispheric functional correlation, and ROI labeling. 3004.333 N/A Adaptation of AAL focused on the idea that each region in one hemisphere has a homologue in the other hemisphere https://www.ncbi.nlm.nih.gov/pubmed/26213217 2015 Included in mricron: https://people.cas.sc.edu/rorden/mricron/index.html
Brodmann 40 Yes Yes No Corticall parcellation separating regions based on cellular morphology and organization 32978.512 N/A Brodman areas separated by gyri http://digital.zbmed.de/zbmed/id/554966 1909 https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps
CAPRSC 333 Yes No Yes Automatic using resting-state functional connectivity (RSFC) boundary maps 1389.09 N/A Created using RSFC-boundary maps to define parcels that represent putative cortical areas. Focuses on the cortical surface and was created using functional MRI scans. https://www.ncbi.nlm.nih.gov/pubmed/25316338 2016 Obtained from Freesurfer: https://sites.wustl.edu/petersenschlaggarlab/parcels-19cwpgu/
CPAC200 200 No No No Created by parcellating whole brain resting-state fMRI data into spatially coherent regions of homogeneous functional connectivity. 5860.755 N/A ROIs with anatomic homology https://pubmed.ncbi.nlm.nih.gov/21769991/ 2018 https://fcp-indi.s3.amazonaws.com/data/Projects/ABIDE_Initiative/Resources/cc200_roi_atlas.nii.gz
Desikan 70 Yes No No Anatomical Landmarks based on gyri. Averaged based on majority voting 24786.857 N/A Surface parcellation https://www.sciencedirect.com/science/article/pii/S1053811906000437?via%3Dihub 2006 Obtained from FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
DesikanKlein 97 No No No Automated labeling system that subdivided the human cerebral cortex into gyral based regions of interest. 74443.62 N/A Gyral based parcellations https://www.sciencedirect.com/science/article/pii/S1053811906000437?via%3Dihub 2006 Obtained from FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
Destrieux 75 Yes No Yes Automatically assigned a neuroanatomical label to each location on a cortical surface model based on probabilistic information estimated from a manually labeled training set. 96280.43 MNI152 Cortical surface probabilitstic atlas https://academic.oup.com/cercor/article/14/1/11/433466 2004 Obtained from FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
DKT 84 Yes No No Automatic 85964.66 N/A Created by using a modified Desikan protocol in order to improve segmentation and make it more suited for FreeSurfer’s classifier algorithm. https://www.frontiersin.org/articles/10.3389/fnins.2012.00171/full 2012 Obtained from FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
Glasser 360 Yes Yes Yes Semi-automated. Separated based on function, connectivity, cortical architecture, topography, and expert analysis 521.994 MNI Cortical parcellation from multi-modal images of 210 adults in HCP https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/ 2016 https://balsa.wustl.edu/file/show/3VLx
Hammersmith 83 No No Yes Algorithm using prior information from 30 normal adult brain MR images, which had been manually segmented to create 30 atlases, each labeling 83 anatomical structures. 19947.72 MNI152 Automatic segmentation of young children's brains into 83 regions of interest. https://www.sciencedirect.com/science/article/pii/S1053811907010634?via%3Dihub 2003 http://brain-development.org/brain-atlases/adult-brain-atlases/adult-brain-maximum-probability-map-hammers-mith-atlas-n30r83-in-mni-space/
HarvardOxford 48 No Yes Yes Created by subdividing neocortex by topographic criteria into 48 parcellation units corresponding to the principal cerebral gyri. 21966.104 N/A Neuroanatomic subdivisions delineated by this general segmentation generaly corresponding to natural gray matter boundaries. https://www.sciencedirect.com/science/article/pii/S0920996405004998?via%3Dihub 2005 Included in FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases
JHU 48 Yes No Yes One subject manually labelled and warped to 29 other adult atlases (Large Deformation Diffeomorphic Metric Mapping) 3541.792 N/A A small version of a larger (289 ROI) atlas composed based on parcellation of deep white matter. Split into 4 groups: Tracts in the brainstem, projection fibers, association fibers, and commisural fibers https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724595/ 2004 https://neurovault.org/collections/264/
Juelich 103 No No Yes Probabilistic atlas created by averaging multi-subject post-mortem cyto- and myelo-architectonic segmentations. 69433 N/A N/A https://linkinghub.elsevier.com/retrieve/pii/S1053-8119(04)00792-X 2005 https://interactive-viewer.apps.hbp.eu/?templateSelected=MNI+Colin+27&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas
MICCAI 136 No No No N/A 52708.26 N/A N/A MICCAI 2012 Workshop: https://my.vanderbilt.edu/masi/workshops/ 2012 http://www.neuromorphometrics.com/2012_MICCAI_Challenge_Data.html
Princeton 49 Yes Yes Yes Identified 25 topographic maps in a large population of individual subjects and transformed them into either surface- or volume-based standardized space. 1217.388 N/A Atlas exclusively containing parcellations of the visual cortex. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4585523/ 2015 https://scholar.princeton.edu/napl/resources
Schaefer1000 1000 No No No Automatic using gwMRF 1055.685 N/A Gradient-weighted Markov Random Fields (gwMRF) to group similar fMRI regions (dependent on # of regions specified) http://people.csail.mit.edu/ythomas/publications/2018LocalGlobal-CerebCor.pdf 2017 https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal https://minhaskamal.github.io/DownGit/#/home?url=https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations
Schaefer200 200 No No No Automatic using gwMRF 5278.425 N/A Gradient-weighted Markov Random Fields (gwMRF) to group similar fMRI regions (dependent on # of regions specified) http://people.csail.mit.edu/ythomas/publications/2018LocalGlobal-CerebCor.pdf 2017 https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal https://minhaskamal.github.io/DownGit/#/home?url=https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations
Schaefer300 300 No No No Automatic using gwMRF 3518.95 N/A Gradient-weighted Markov Random Fields (gwMRF) to group similar fMRI regions (dependent on # of regions specified) http://people.csail.mit.edu/ythomas/publications/2018LocalGlobal-CerebCor.pdf 2017 https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal https://minhaskamal.github.io/DownGit/#/home?url=https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations
Schaefer400 400 No No No Automatic using gwMRF 2639.213 N/A Gradient-weighted Markov Random Fields (gwMRF) to group similar fMRI regions (dependent on # of regions specified) http://people.csail.mit.edu/ythomas/publications/2018LocalGlobal-CerebCor.pdf 2017 https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal https://minhaskamal.github.io/DownGit/#/home?url=https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations
Slab1068 1068 No No No Calculated spatially averaged time series for each of 1068 regions of interest placed in a regular 12-mm grid throughout the brain 493.719 N/A Grid of ROI points spanning entire MNI brain volume. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507181/ 2017 https://umich.app.box.com/s/w46icx4bng1mw1nc3sg72t13ug5ecyib https://www.nitrc.org/projects/kessler_jama16/
Slab907 907 No No No Placed 907 ROIs at regular intervals throughout the cortex 7952.68 N/A Grid of ROI points spanning entire MNI brain volume https://pubmed.ncbi.nlm.nih.gov/25225387/ 2014 https://umich.app.box.com/s/jowv4pogzhbfevt301n8
Talairach 1105 No Yes Yes Semi-automated? 1698.114 Talairach coordinates A hierarchical atlas split into 5 leves: Hemisphere, Lobe, Gyrus, Tissue Type, and Cell Type https://www.ncbi.nlm.nih.gov/pubmed/7008525 1980 http://www.talairach.org/
Tissue 3 No No N/A 609031.667 N/A (Tissue-based segmentation: WM, GM, CSF) 2018
Yeo 17 17 Yes No Yes Clustered to identify networks of functionally coupled regions 31040.294 FreeSurfer surface space Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/ 2011 https://ftp.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011
Yeo 17 Liberal 17 Yes No Yes Clustered to identify networks of functionally coupled regions 62043.118 FreeSurfer surface space Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/ 2011 https://ftp.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011
Yeo 7 7 Yes No Yes Clustered to identify networks of functionally coupled regions 75383.571 FreeSurfer surface space Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/ 2011 https://ftp.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011
Yeo 7 Liberal 7 Yes No Yes Clustered to identify networks of functionally coupled regions 150676.143 FreeSurfer surface space Local networks confined to sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/ 2011 https://ftp.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011
DS Family 71 - 72784 No No No Grid segmentation of entire MNI brain Variable N/A Grid segmentation of entire MNI brain https://ieeexplore.ieee.org/document/6736874 2013 N/A