#!/bin/bash

# settings ; PLEASE ADAPT
LOCAL_FOLDER=/Users/XXX/Desktop/CPU
SUBJ_PATTERN=CPU*
SUBFOLDERS="functional onsets structural"
RAWFOLDER=raw

# Note: the SUBFOLDERS variable can be easily adapted to create
# several levels of folders:
# SUBFOLDERS="functional functional/raw functional/prepro ..."

# for every folder found (matching the pattern)
find $LOCAL_FOLDER -type d -mindepth 1 -maxdepth 1 -name "$SUBJ_PATTERN" | while read subject_folder ; do

    # make sure all subfolders we need exist
    for sub in $SUBFOLDERS ; do
        mkdir $subject_folder/$sub 2>/dev/null
      done
    
    # rename original folder, if existent, to raw
    find $subject_folder -type d -mindepth 1 -maxdepth 1 -name "$SUBJ_PATTERN" -exec mv {} $RAWFOLDER \;
  done