Using GNU Parallel with Freesurfer

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To parallelise (for instance):

recon-all -i subjects/subject_001/mri.nii -sd subjects/subject_001 -s subject_001 -all
recon-all -i subjects/subject_002/mri.nii -sd subjects/subject_002 -s subject_002 -all
recon-all -i subjects/subject_003/mri.nii -sd subjects/subject_003 -s subject_003 -all
recon-all -i subjects/subject_004/mri.nii -sd subjects/subject_004 -s subject_004 -all

Use:

./parallel recon-all -i subjects/{1}/mri.nii -sd subjects/{1} -s {1} -all ::: subject_001 subject_002 subject_003 subject_004

NB: Output of Freesurfer will only be displayed once a file has been processed, thus in the beginning it will look like it isn't doing anything. (Unless it tells you something along the lines of using parallel in the terminal is for expert users and press Ctrl+D to exit -- this means that your recon-all command has failed, so exit parallel and fix the command)

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