#!/bin/sh
for line in $(cat rats.txt)
do
rm -rf ${line}_nifti/dwi/noddi
mkdir ${line}_nifti/dwi/noddi
cp ${line}_nifti/dwi/B0_mask.nii.gz ${line}_nifti/dwi/noddi/data_mask.nii.gz ;
cp ${line}_nifti/dwi/data_ecc.nii.gz ${line}_nifti/dwi/noddi/data.nii.gz ;
cp ${line}_nifti/dwi/rotated_bvecs.bvec ${line}_nifti/dwi/noddi/data.bvec ;
cp ${line}_nifti/dwi/data.bval ${line}_nifti/dwi/noddi/data.bval ;
fslchfiletype ANALYZE ${line}_nifti/dwi/noddi/data_mask.nii.gz ;
fslchfiletype ANALYZE ${line}_nifti/dwi/noddi/data.nii.gz ;
done