In order to add data downloaded from SCNAT, create a file that copies data from the Data_raw directory to this directory, create a file like this: Data_raw/EDDY/20180222/copy-to-bids.sh

Actually, that file is probably out of date by the time you read this. You should find the latest version of copy-to-bids.sh. I usually use: find -maxdepth 3 -name "copy-to-bids.sh" -exec ls -lt {} + (from the Data_raw/EDDY directory) although the timestamps can get messed up with synchronization tools.

This pipeline uses NiPype to create the data that tries to adhere to BIDS.

There is documentation in the python scripts and at: https://github.com/VisionandCognition/Process-NHP-MRI/blob/master/docs/BIDS_processing.md