# Atlas tools

* Jülich probabilistic cytoarchitectonic maps (SPM Anatomy Toolbox)
* FreeSurfer cortical parcellations
* AFNI framework: 1 and 2
* WFU PickAtlas
* IBASPM
* Template-O-Matic Toolbox
* FSL atlasquery
* SPM12 spm_atlas.m
* multi-species Scalable Brain Atlas
* Online Brain Atlas Reconciliation Tool (OBART)

# Sets of atlases

* Jülich probabilistic cytoarchitectonic maps (SPM Anatomy Toolbox)
* Atlases available from FSL, see also MGH CMA Harvard-Oxford Atlases
* Yeo's connectivity-based parcellation (cortical and MNI volumetric)
* LONI Atlases
* ICBM Atlases (original)
* ICBM Atlases (2009)
* Brain Development Atlases
* Mindboggle
* Allen Brain Atlas, (see also and )
* IIT Human Brain Atlas

# Atlases with whole-brain coverage

* Talairach Daemon
* AAL Anatomical Automatic Labeling
* AAL2 New parcellation of the orbitofrontal cortex in AAL
* LONI Probabilistic Brain Atlas (LPBA40) (56 structures)
* SRI24 Atlas (group-wise average atlas with two parcellations based on AAL and LPBA40)
* "Hammers-mith atlas"; n30r83, see 1 & 2
* Brainvisa Sulci atlas
* ICBM 152 Nonlinear atlases version 2009 (some variants with lobar parcellations)
* Group-level functional parcels
* Stanford atlas of functional ROIs
* Atlas of frequency of vascularization
* Innovation-driven co-activation patterns (iCAPs) from resting-state fMRI
* AICHA: atlas of intrinsic connectivity of homotopic areas

## Whole-brain atlases for specific populations

* Pediatric Brain Templates
* Infant Template, see
* Baboon MRI Atlas

## Whole-brain white-matter tract / diffusion-imaging atlases

* JHMI Human White Matter Probabilistic Atlases
* SRI24 Atlas (basic diffusion metrics)

## Whole-brain tissue-class atlases

* BrainWeb (One subject with 9 non-background tissue classes; 20 subjects with 11)
* ICBM 152 Nonlinear atlases version 2009 (Group-wise average atlas variants with GM, WM and CSF classes)
* LPBA40 (Group-wise average atlas with GM, WM and CSF classes)
* SRI24 Atlas (Group-wise average atlas with GM, WM and CSF classes)

# Atlases for specific regions

* Probabilistic atlas of the human cerebellum
* Connectivity-based cerebellar parcellation (see also this)
* Subthalamic nucleus atlas (see also )
* Hippocampal subfield atlases
* Connectivity-based parcellation atlases
* ChroMa cerebellum atlas
* Probabilistic maps of visual topography in human visual cortex
* Human Motor Area Template (HMAT), Basal Ganglia Human Area Template (BGHAT), Sensorimotor Area Tract Template (S-MATT), Transcallosal Tractography Template (TCATT)

# Labelled individual images

* MICCAI 2013 Challenge Workshop on Segmentation: Algorithms, Theory and Applications ("SATA") (47 mid-brain, 45 canine leg, and 155 cardiac datasets)
* MICCAI 2012 Multi-Atlas Labeling Workshop and Challenge (30 subjects, 134 consistent labels, provided by Neuromorphometrics -- see below)
* Neuromorphometrics (Currently 63 subjects with 157 regions, but available only with paid subscription, see also NITRC project page)
* Mindboggle (101 subjects, 31 cortical regions per hemisphere, no subcortical structures)
* LPBA40 (40 subjects, 56 regions)
* NIREP NA0 (16 subjects, 32 gray matter regions)
* Internet Brain Segmentation Repository (IBSR) (version 2 has 18 subjects with 34 regions)
* Arno Klein's registration evaluation data (Klein et al., 2009) (includes CUMC12 and MGH10)
* Hammers' Individual Adult Brain Atlases (20 subjects, 67 regions)
* Child and Adolescent NeuroDevelopment Initiative (CANDI) (103 subjects with CMA segmentations)

# Other atlas listings

* Atlas & Template (Chuang's Lab)
* Human brain atlas
* Cortical Atlas Parcellations (MNI-Space) from Lead-DBS