C. Atlas Preparation and FC Computation

This project uses the 200 ROI version of the Schaefer Atlas sorted according to the 7 Yeo Networks. This atlas is publicly available here.

To prepare this atlas for the project, please perform the following operations:

1. Create a local folder for brain parcellations: (e.g., /data/SFIMJGC_Introspec/2023_fc_intrsopection/atlases)

2. Assign the full path of that folder to variable ATLASES_DIR in basics.py.

3. Assign the name of the atlas (Schaefer2018_200Parcels_7Networks) to the ATLAS_NAME variable in basics.py.

   NOTE: Unless you are using a different version of the Schaefer Atlas, you can skip this step.

4. Create a sub-folder for the 200 Schaefer Atlas:

cd ${ATLASES_DIR}
mkdir ${ATLAS_NAME}

5. Copy the following files from their original location in CBIG repo (link above) to your local Schaefer Atlas folder:

• Schaefer2018_200Parcels_7Networks_order_FSLMNI152_2mm.nii.gz: 200 ROI Atlas / 7 Yeo Networks in MNI space on a 2mm grid.

• Schaefer2018_200Parcels_7Networks_order.txt: list of all ROI, their network membership and color code (RGB).

• Schaefer2018_200Parcels_7Networks_order.lut: same as above, but coded for FSL eyes.

• Schaefer2018_200Parcels_7Networks_order_FSLMNI152_2mm.Centroid_RAS.csv: information about each ROI centroid coordinates.

6. Once those files are available, we will still need to perform the following operations on the publicly available atlas files. In particular, we need to: 1) bring the atlas to the common grid of all pre-processed scans, 2) generate a label table so AFNI can correctly recognize this file as an atlas, 3) remove limbic areas with incomplete coverage, 4) re-compute ROI IDs following the removal of limbic regions. All these operations are performed in section 1 of notebook S07_ExtractROIts