bash script to create a dummy BIDS data set to test the MP2RAGE JSON file naming

DummyBIDS.sh

#!/bin/bash

# small bash script to create a dummy BIDS data set to test the MP2RAGE JSON file naming

# defines where the BIDS data set will be created 
StartDir=`pwd` # relative to starting directory
echo $StartDir/../../../BIDS/7t_mp2rage/
StartDir=$StartDir/../../../BIDS/7t_mp2rage/
mkdir $StartDir

SubList='01 02 03 04 05 06 07 08 09 10 11 12' # subject list
SesList='01 02' # session list

for Subject in $SubList # loop through subjects
do 

		mkdir $StartDir/sub-$Subject # create folder for subject
		
		for Ses in $SesList # loop through sessions
		do 
		
			# create folder for each session and functional and fmap
			mkdir $StartDir/sub-$Subject/ses-$Ses
			mkdir $StartDir/sub-$Subject/ses-$Ses/fmap
			mkdir $StartDir/sub-$Subject/ses-$Ses/func
			
			# only creates folder for anat and empty mp2rage files for session 1
			if [ $Ses = 01 ]
			then
				mkdir $StartDir/sub-$Subject/ses-$Ses/anat
				touch $StartDir/sub-$Subject/ses-$Ses/anat/sub-$Subject\_ses-$Ses\_inv-1_part-mag_MPRAGE.nii.gz
				touch $StartDir/sub-$Subject/ses-$Ses/anat/sub-$Subject\_ses-$Ses\_inv-1_part-phase_MPRAGE.nii.gz
				touch $StartDir/sub-$Subject/ses-$Ses/anat/sub-$Subject\_ses-$Ses\_inv-2_part-mag_MPRAGE.nii.gz
				touch $StartDir/sub-$Subject/ses-$Ses/anat/sub-$Subject\_ses-$Ses\_inv-2_part-phase_MPRAGE.nii.gz
				touch $StartDir/sub-$Subject/ses-$Ses/anat/sub-$Subject\_ses-$Ses\_T1w.nii.gz
				touch $StartDir/sub-$Subject/ses-$Ses/anat/sub-$Subject\_ses-$Ses\_Tmap.nii.gz
			fi
		done
		
done;