Atlas Catalog¶

fsatlas ships with 31 built-in atlases across 8 families. All atlases are downloaded automatically on first use (including LUT generation) and cached to ~/.cache/fsatlas/atlases/.

Use fsatlas list-atlases to view the catalog in your terminal.

Cortical Atlases (Surface)¶

Surface atlases are stored as FreeSurfer annotation files (.annot) in fsaverage space. fsatlas transfers them to each subject's native surface via mri_surf2surf. A LUT TSV (index, label, hemisphere) is auto-generated from the .annot colour table at download time.

Schaefer 2018¶

A popular functional parcellation of the cerebral cortex derived from resting-state fMRI functional connectivity. Available in multiple resolutions and two network assignment schemes (7 or 17 Yeo networks).

Citation: Schaefer A, Kong R, Gordon EM, et al. (2018). Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI. Cerebral Cortex, 28(9):3095–3114.

7-network parcellations:

Atlas ID	Parcels	Networks	Hemispheres
`schaefer100-7`	100	7	bilateral
`schaefer200-7`	200	7	bilateral
`schaefer300-7`	300	7	bilateral
`schaefer400-7`	400	7	bilateral
`schaefer500-7`	500	7	bilateral
`schaefer600-7`	600	7	bilateral
`schaefer700-7`	700	7	bilateral
`schaefer800-7`	800	7	bilateral
`schaefer900-7`	900	7	bilateral
`schaefer1000-7`	1000	7	bilateral

17-network parcellations:

Atlas ID	Parcels	Networks	Hemispheres
`schaefer100-17`	100	17	bilateral
`schaefer200-17`	200	17	bilateral
`schaefer300-17`	300	17	bilateral
`schaefer400-17`	400	17	bilateral

Network labels (7-network): Vis, SomMot, DorsAttn, SalVentAttn, Limbic, Cont, Default

Network labels (17-network): VisCent, VisPeri, SomMotA, SomMotB, DorsAttnA, DorsAttnB, SalVentAttnA, SalVentAttnB, LimbicB, LimbicA, ContA, ContB, ContC, DefaultA, DefaultB, DefaultC, TempPar

Region naming example: 7Networks_LH_Vis_1

HCP-MMP 1.0¶

The Human Connectome Project Multi-Modal Parcellation — 360 cortical areas defined by combining architecture, function, connectivity, and topography from HCP data.

Citation: Glasser MF, Coalson TS, Robinson EC, et al. (2016). A multi-modal parcellation of human cerebral cortex. Nature, 536:171–178.

Atlas ID	Parcels	Notes
`hcp-mmp`	360	180 per hemisphere

Region naming example: L_V1_ROI

FreeSurfer Built-ins¶

These atlases are already present in every recon-all output and require no download. fsatlas uses them directly from the subject's label/ directory.

Atlas ID	Name	Format	Parcels	Notes
`desikan`	Desikan-Killiany	annot	68	Default FreeSurfer atlas
`destrieux`	Destrieux 2010	annot	148	High-resolution sulco-gyral
`dkt`	DKT	annot	62	Mindboggle compatible
`aseg`	FreeSurfer aseg	nifti	49	Automatic subcortical segmentation

Citation (Desikan): Desikan RS et al. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31(3):968–980.

Citation (Destrieux): Destrieux C et al. (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage, 53(1):1–15.

Brainnetome Atlas¶

A connectivity-based parcellation of the human cerebral cortex.

Citation: Fan L et al. (2016). The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture. Cerebral Cortex, 26(8):3508–3526.

Atlas ID	Format	Parcels	Notes
`BN_Atlas`	annot	246	123 per hemisphere, cortical
`BN_Atlas_subcotex`	nifti	36	Subcortical component

Local files required

The Brainnetome atlas is not available for public download via URL. Set local_source_dir in your environment or use the atlas after manual placement.

Gordon 2016¶

A resting-state parcellation of the cerebral cortex.

Citation: Gordon EM et al. (2016). Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cerebral Cortex, 26(1):288–303.

Atlas ID	Format	Parcels	Notes
`gordon333`	annot	333	Cortical
`gordon333_subcortical`	nifti	52	CIT168 + Cerebellum extension

Subcortical Atlases (Volumetric)¶

Volumetric atlases are NIfTI files in MNI152 space. fsatlas registers them to each subject's native space using mri_vol2vol and the talairach.xfm transform. A LUT TSV is required (either bundled in the package or downloaded alongside the atlas).

Tian 2020 — Melbourne Subcortex Atlas¶

A multi-scale subcortical atlas derived from resting-state fMRI, with parcellations ranging from coarse (Scale I) to fine-grained (Scale IV).

Citation: Tian Y, Margulies DS, Breakspear M, Zalesky A. (2020). Topographic organization of the human subcortex unveiled with functional connectivity gradients. Nature Neuroscience, 23:1421–1432.

Atlas ID	Scale	Regions	Coverage
`tian-s1`	I	16	8 bilateral structures
`tian-s2`	II	32	16 bilateral structures
`tian-s3`	III	50	25 bilateral structures
`tian-s4`	IV	54	27 bilateral structures

Structures covered: Caudate, Putamen, Pallidum, Hippocampus, Amygdala, Accumbens, Thalamus (and more at finer scales).

Region naming example: CAU-lh, PUT-rh, HIP-lh

HCPex Subcortical¶

Subcortical extension of the HCP-MMP atlas covering thalamus, amygdala, hippocampus, and related structures.

Citation: Huang CC et al. (2022). Subcortical brain atlas using the Human Connectome Project parcellation. Cerebral Cortex.

Atlas ID	Format	Parcels	Space
`hcpex_subcortical`	nifti	66	MNI152NLin2009cAsym

AICHA 2015¶

Atlas of Intrinsic Connectivity of Homotopic Areas — 384 bilateral cortical regions derived from resting-state fMRI.

Citation: Joliot M et al. (2015). AICHA: An atlas of intrinsic connectivity of homotopic areas. Journal of Neuroscience Methods, 254:46–59.

Atlas ID	Format	Parcels	Notes
`aicha384`	nifti	384	Full cortical atlas
`aicha384_subcortical`	nifti	50	Subcortical subset

AAL 2002¶

The classic Automated Anatomical Labeling atlas.

Citation: Tzourio-Mazoyer N et al. (2002). Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain. NeuroImage, 15(1):273–289.

Atlas ID	Format	Parcels	Space
`aal116`	nifti	116	MNI152NLin2009cAsym

Region naming example: Precentral_L, Hippocampus_R

4S-156 Subcortical¶

A subcortical atlas with 56 regions derived from the 4S parcellation framework.

Atlas ID	Format	Parcels	Space
`4s156_subcortical`	nifti	56	MNI152NLin2009cAsym

Choosing the Right Atlas¶

Use case	Recommended atlas
Functional connectivity alignment	`schaefer100-7`, `schaefer400-17`
Fine-grained cortical parcellation	`hcp-mmp`
Compatibility with HCP pipelines	`hcp-mmp`
Subcortical segmentation	`tian-s2` or `tian-s3`
Legacy / broad compatibility	`desikan`
High-resolution sulcal	`destrieux`
Mindboggle / label fusion	`dkt`

Pre-downloading Atlases¶

Before running a batch job, pre-download all needed atlases:

fsatlas download schaefer400-17
fsatlas download tian-s2
fsatlas download hcp-mmp

The cache directory is:

~/.cache/fsatlas/atlases/{atlas_id}/

To force re-download of a cached atlas:

fsatlas download --force schaefer400-7