SPM/Atlases

=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