Freesurfer 8.0.0 plus custom post-processing

The base container is rocky 8. Freesurfer is installed via RPM, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/8.0.0/freesurfer-Rocky8-8.0.0-1.x86_64.rpm

Additional system packages are added to support freeview and imagemagick (see the Dockerfile).

Some custom postprocessing code -

• Reformats and combines stats outputs to a simpler CSV format

• Adds additional relabelings of the hippocampal subfield segmentation, following McHugo M, Talati P, Woodward ND, Armstrong K, Blackford JU, Heckers S. Regionally specific volume deficits along the hippocampal long axis in early and chronic psychosis. Neuroimage Clin. 2018;20:1106-1114. doi: 10.1016/j.nicl.2018.10.021. PMID: 30380517; PMCID: PMC6202690.

• Produces two PDF-format QC reports

Entrypoints

The default entrypoint is run-everything.sh, which performs recon-all plus subfield segmentations of hippocampus/amygdala, brainstem, thalamus; then performs the postprocessing. Command line options are

--t1_niigz        The T1 image to process
--subjects_dir    Freesurfers SUBJECTS_DIR
--label_info      A label to affix to the QC PDFs
--out_dir         Outputs directory

A postproc-entrypoint.sh is also available if the main freesurfer pipeline has already been run. Its command line options are

--subjects_dir    Freesurfers SUBJECTS_DIR
--label_info      A label to affix to the QC PDFs
--out_dir         Outputs directory

SUBJECT is used as the Freesurfer subject ID throughout.