Running FreeSurfer in batch mode

by manuel on August 17th, 2015

Here is a quick way to run FS for each MRI image as a Nifti file in a folder.

Start by creating a new text file in the terminal (eg vi run.sh).

Put in the following code:

for file in *
do
recon-all -i $file -subjid $(cut -d '.' -f 1 <<< $file)
recon-all -all -subjid $(cut -d '.' -f 1 <<< $file)
done

for file in *

recon-all -i $file -subjid $(cut -d '.' -f 1 <<< $file)

recon-all -all -subjid $(cut -d '.' -f 1 <<< $file)

done

Save it an run it from inside the folder containing the images.

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