Hi folks, a cog neuro neophyte here! I am using the Schaefer 200 atlas in ROI analysis, and I am hoping to map anatomy onto the parcellations. Currently, most of the Schaefer labels are numerical and do not offer any biological meaning (ie: what regions map to the sgACC or amygdala?). I’m hoping to conduct an a priori analysis based on a literature review, but I’m unsure of how to map anatomy onto the parcellations except manually. Any advice, help, and clarifying questions would be greatly appreciated. Thank you so much!
The Schaefer-Yeo atlases are distributed with parcellations ranging from 100-1000 and with 7 or 17 network definitions. The regions are labeled by their overlap with some structural regions and with the predefined networks. The most recent and improved version is distributed here:
afni_sydist_atlas_v1.0.tgz
See more about that atlas here:
Schaefer-Yeo_AFNI_Atlas_OHBM2021_Poster.pdf
You can see the names of the ROIs either interactively in AFNI GUI with the whereami feature or query the command line with this command:
3dinfo -atlas_points ~/schaefer_yeo/afni_sy_atlas/Schaefer_17N_200.nii.gz | grep "STRUCT="
STRUCT="LH_VisCent_ExStr_1"
STRUCT="LH_VisCent_ExStr_2"
STRUCT="LH_VisCent_Striate_1"
STRUCT="LH_VisCent_ExStr_3"
STRUCT="LH_VisCent_ExStr_4"
STRUCT="LH_VisCent_ExStr_5"
STRUCT="LH_VisPeri_ExStrInf_1"
STRUCT="LH_VisPeri_ExStrInf_2"
STRUCT="LH_VisPeri_ExStrInf_3"
STRUCT="LH_VisPeri_StriCal_1"
STRUCT="LH_VisPeri_ExStrSup_1"
STRUCT="LH_VisPeri_ExStrSup_2"
You can query any coordinate in MNI space with the whereami command on the command line, and it will return the regions associated with it from all available atlases distributed with AFNI. You can also query with a mask of any particular region to get the overlap of that mask with regions in other atlases (whereami -omask)