FreeSurfer Run with QC - tannerjared/MRI_Guide GitHub Wiki

recon-all -s subj01 -i subj01.nii.gz -all -qcache
segmentHA_T1.sh subj01
segmentBS.sh subj01
segmentThalamicNuclei.sh subj01
mri_segment_hypothalamic_subunits --s subj01 --threads 6
pip install fsqc
run_fsqc --subjects_dir ./fs_subjects --subjects subj01 --output_dir ./fsqc_out --shape --skullstrip-html --surfaces-html --screenshots-html --fornix-html --hippocampus-html --hippocampus-label T1.v22 --hypothalamus-html

Can also run_fsqc with --outlier if running on an entire subjects_dir (in that case, remove the --subjects or modify that to include the entire list of subjects you want to run it on).

Also run the CAT12 toolbox on the raw NIfTI: subj01.nii.gz

Here is an option on a high performance cluster:

apptainer run -B $PWD:/in -B $PWD/fsqc_out:/out /blue/clp7934/share/fsqc.sif --subjects_dir /in --subjects sub-011S6303 --output_dir /out --skullstrip-html --surfaces-html --screenshots-html --fornix-html