Hi Taylor,
here is the command I am using (which worked for the T1 images):
for folder in /Users/lab/Desktop/MRI/*/
do
echo $folder
id=$(basename "$folder")
echo $id
t1="$folder"*"FLAIR"*".ni"*
echo $t1
mkdir /Users/lab/Desktop/MRI/$id/
/Users/lab/abin/@afni_refacer_run -input "$FLAIR" -mode_reface -anonymize_output -prefix /Users/lab/Desktop/MRI//$id/"$id"_FLAIR_reface.nii.gz
done
echo 'done with script'
Thank you very much!
Johannes
Edited 1 time(s). Last edit at 08/24/2022 09:19AM by ptaylor.