FreeSurfer 7 Suggested Processing

If your input brains include a lot of neck, it can help the ANTs brain segmentation to remove neck. Use FSL's robustfov tool

robustfov -i __t1_mpr_sag_iso_GWcontrast_20111117065925_3.nii.gz -r sub001_T1w.nii.gz

Then recon-all (this uses 4 cores)

recon-all -s sub001 -i sub001_T1w.nii.gz -all -parallel

Then hippocampus subfields and amydgala nuclei, thalamic nuclei, brainstem structures, and hypothalamus

segmentHA_T1.sh sub001
segmentThalamicNuclei.sh sub001
segmentBS.sh sub001
mri_segment_hypothalamic_subunits --s sub001 --threads 6

Then for QC can run FSQC (https://github.com/Deep-MI/fsqc). This is run on one subject but you can remove --subjects to run on all in the subjects_dir

run_fsqc --subjects_dir ./fs_subjects --subjects sub001 --output_dir ./fsqc_out --shape --skullstrip-html --surfaces-html --screenshots-html --fornix-html --hippocampus-html --hippocampus-label T1.v22 --hypothalamus-html

Also run CAT12 toolbox for QC: https://neuro-jena.github.io/cat12-help/#intro

If you have FLAIR (or other modalities), you can also run samseg but this is primarily an alternative to the standard recon-all stream. With FLAIR, however, it will provide white matter hyperintensity volumes: https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg Can use CUDA if installed. The run_samseg command will use 8 cores so change that number if you want/have more or fewer.

mri_coreg --mov flair.nii --ref t1.nii --reg flairToT1.lta
mri_vol2vol --mov  flair.nii  --reg flairToT1.lta  --o flair_reg.nii --targ t1.nii
run_samseg --input t1.nii flair_reg.nii --pallidum-separate --output output/ --lesion --lesion-mask-pattern 0 1 --threads 8