Surface registration: recon-surfreg.sh

recon-surfreg.sh adds the spherical registration (?h.sphere and ?h.sphere.reg) to a subject that was processed with --no_surfreg. The registration to FreeSurfer’s fsaverage is needed for any cross-subject analysis of thickness maps, so this lets you add it later without running the surface reconstruction again. It needs a FreeSurfer license, like the surface reconstruction.

Usage:

<fastsurfer_home>/recon_surf/recon-surfreg.sh --sd <subjects_dir> \
    --sid <subject_id> --fs_license <freesurfer_license_path>

Full commandline interface of recon-surfreg.sh

./recon_surf/recon-surfreg.sh --help

Usage: recon-surfreg.sh --sid <subject_id> --sd <subjects_dir> [OPTIONS]

recon-surfreg.sh creates the ?h.sphere and ?h.sphere.reg from an existing
subject directory, if this step was skipped in recon-surf.sh with --no_surfreg

FLAGS:
  --sid <subject_id>      Subject ID to create directory inside $SUBJECTS_DIR
  --sd  <subjects_dir>    Output directory $SUBJECTS_DIR (or pass via env var)
  --threads <int>         Total thread budget, "auto" or "max". With 2 or more
                            the two hemispheres run at the same time and split
                            it, so 2 gives one thread each and 8 gives four
                            each. Use 1 to keep every binary single threaded.
                            Without the flag, OMP_NUM_THREADS sets the budget
                            if exported, else auto: the allocation of a cgroup
                            quota or a scheduler job, or else the physical
                            cores less one (on Apple silicon all performance
                            cores), at least 2 and at most 8. "max" uses all
                            available CPUs.
  --parallel              Run the hemispheres at the same time with one thread
                            each, even at --threads 1. That keeps every binary
                            single threaded, and so reproducible, while still
                            using two cores. No effect at --threads 2 or more,
                            where the hemispheres already run at the same time.
  --py <python_cmd>       Command for python, default python3 -s
  --fs_license <freesurfer_license_path>
                          Path to FreeSurfer license key file. Register at
                            https://surfer.nmr.mgh.harvard.edu/registration.html
                            for free to obtain it if you do not have FreeSurfer
                            installed already
  -h --help               Print Help

Dev Flags:
  --ignore_fs_version     Switch on to avoid check for FreeSurfer version.
                            Program will otherwise terminate if 8.2.0 is
                            not sourced. Can be used for testing dev versions.

REFERENCES:

If you use this for research publications, please cite:

Henschel L, Conjeti S, Estrada S, Diers K, Fischl B, Reuter M, FastSurfer - A
 fast and accurate deep learning based neuroimaging pipeline, NeuroImage 219
 (2020), 117012. https://doi.org/10.1016/j.neuroimage.2020.117012

Henschel L*, Kuegler D*, Reuter M. (*co-first). FastSurferVINN: Building
 Resolution-Independence into Deep Learning Segmentation Methods - A Solution
 for HighRes Brain MRI. NeuroImage 251 (2022), 118933.
 https://doi.org/10.1016/j.neuroimage.2022.118933