Month: August 2015

  • Running FreeSurfer in batch mode

    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…