struc_pre_prep_legion_FTD.sh

#!/bin/bash

module load fsl/5.0.9
source $FSLDIR/etc/fslconf/fsl.sh
module load xorg-utils/X11R7.7
module load freesurfer/5.3.0

# this directory must the location of the .nii files
ROOT="/home/skgtika/Scratch"
ROOTOUT="/home/skgtika/Scratch/myftd" # this is the directory where the files will be copied. 

# NEED TO DEFINE AN NTAG FOR THE FTD DATA
filename='/home/skgtika/Scratch/ntag.txt'  # Load NTAGS this contains files themselves.
filelines=`cat $filename` #Get each line

cd $ROOT
counter=1


for REM in $filelines ; do # Loop through at the subject level using N-tag	 	
	fslswapdim $ROOT/NIFD/*/T1_mprage/*/*/*_mprage_*.nii LR PA IS $ROOTOUT/FTD_struc_${counter}.nii.gz # this needs to be checked
	counter=$((counter+1))
done