Bash_script_for_bids_format

#!/bin/bash

echo "starting to convert files from old to bids format..."

i=0

for sub_path in ./old/*; do

        let "i+=1"
        printf -v index "%02d" $i
        sub=${sub_path:6}
        echo "$sub $index"

        # creating bids directories and moving files
        mkdir "./bids/sub-$index"
        mkdir "./bids/sub-$index/anat"
        mkdir "./bids/sub-$index/func"
        mv "./old/${sub}/rest/rest.nii" "./bids/sub-${index}/func/sub-${index}_task-rest_bold.nii"
        mv "./old/${sub}/t1/t1.nii" "./bids/sub-${index}/anat/sub-${index}_T1w.nii"


#a line needs to be added to modify the json file name also. e.g., mv "./old/${sub}/rest/____.json" "./bids/sub-${index}/anat/sub-${index}_task-rest_bold.json"

done