recon_surf: long_compat_segmentHA.py

long_compat_segmentHA.py is a compatibility script. It creates files that are not created by the FastSurfer longitudinal pipeline, but needed by other longitudinal tools such as FreeSurfer’s longitudinal Hippocampus and Amygdala processing.

Full commandline interface of recon_surf/long_compat_segmentHA.py

long_compat_segmentHA.py takes a longitudinally processed subject and creates files missing for other longitudinal processing like the hippocampal subfields stream of FreeSurfer.

usage: recon_surf/long_compat_segmentHA.py [-h] --sid subject id --sd
                                           SUBJECTS_DIR [--threads THREADS]
                                           [--fs_license FS_LICENSE]
                                           [--version] [--ignore_fs_version]

Named Arguments

--sid, --tid

Template to create directory inside $SUBJECTS_DIR.

--sd

Output directory, default: SUBJECTS_DIR env var ().

Default: /

--threads

Set openMP and ITK threads to <int>.

Default: 1

--fs_license

Path to FreeSurfer license key file.

Default: .

--version

show program’s version number and exit

--ignore_fs_version

Switch on to avoid check for FreeSurfer version. Program will otherwise terminate if FreeSurfer 7.4.1 is not sourced.

Default: False

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 (co-first), Reuter M.. FastSurferVINN: Building Resolution-Independence into

Deep Learning Segmentation Methods - A Solution for HighRes Brain MRI. NeuroImage 251 (2022), 118933. http://dx.doi.org/10.1016/j.neuroimage.2022.118933