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

The hippocampus subfields and amydgala nuclei

segmentHA_T1.sh sub001

Thalamic nuclei and brainstem structures

segmentThalamicNuclei.sh sub001 segmentBS.sh sub001

Then samseg (to be updated when clearer instructions are available) samseg --s sub001 --t1w sub001/mri/T1.mgz --t2w sub001_T2w.nii.gz --refmode t1w --threads 6