roixtractor Atlases

roixtractor also supports several atlases:

HO-CB includes the Harvard-Oxford cortical and subcortical atlas regions in addition to the cerebellar regions. This was the original set of atlas regions used in the 2015 paper.

PROS: This is useful because, by combining three standard atlases, it covers a lot of the brain (except that white matter is not well covered)
CONS: Regions generally include both white and grey matter.

HCP-MMP1 Glasser 2016: Multimodal cortical parcellation from the Human Connectome Project. This atlas focuses on just cortical grey matter. It divides the cortex into 180 regions in each hemisphere!

PROS: This is probably the best and most detailed cortical atlas in existence because it is multimodal and based on hundreds of high-quality scans. Its regions are based on connectivity information from dMRI and fMRI, in addition to cortical thickness and myelination derived from T1w and T2w images.
CONS: Its divisions have very unfamiliar names. It only identifies regions in the thin cortical grey matter ribbon. It is meant to be used with surface-based data rather than volumetric data (so, this volumetric version is a bit of a stretch). Thus it may be most useful for getting a rough idea of how the divisions are named and distributed.

Caution: Left-Right Issues!

The HCP-MMP1 atlas I provide uses the ID label conventions that MRtrix3 uses for HCP-MMP1 and that most volumetric atlases use, i.e., the labels start on the left. For the HCP-MMP1 atlas, that means regions on the left are labeled 1-180, and regions on the right are labeled 201-281. Unfortunately, the original HCP-MMP1 surface atlas uses the opposite convention: regions on the right are labeled 1-180, and regions on the left are labeled 201-280!

ARTERIAL Liu 2021 Arterial territory atlases: These atlases identify arterial territories. They are likely to be of particular use for characterizing differences in perfusion measures.

PROS: If there are similar atlases, I have not found them
CONS: GM, WM and CSF are not distinguished in the arterial territories. This is a potential problem for ASL, because tissue type has a HUGE influence on resulting perfusion. A third custom atlas provides tissue type for each arterial territory.

Watch this 4.75-minute video clip.

Atlases & ROIs 1 (5)