recon all using PBS

First ensure your PBS system is set up and your subjects directory is pointing to the right location.

recon-all-pbs -s mysub1 -f /path/to/structural_dicom_or_nifti_file -q recon

For multiple subjects you can extend the command as:

recon-all-pbs -s mysub1 mysub2 -f /path/to/structural_dicom_or_nifti_file_sub1 /path/to/structural_dicom_or_nifti_file_sub2 -q recon

You can always see help by typing:

recon-all-pbs -h

While the above commands allow submitting fresh recon-all jobs to the queue, other jobs can be submitted quite easily with the ezsub command.

ezsub -h