Hi Maya,
I think you can pass extra parameters to mri_synthseg with recon-all option '-expert <opt-file>'.
1. Create file mri_synthseg.opt, and have this line in it mri_synthseg -robust
1. Pass '-expert mri_synthseg.opt' to your recon-all
Can you reply to the list so other people can answer it too? Also can you keep previous exchanges?
Best,
Yujing
From: Maya Yablonski mayay@stanford.edu Sent: Wednesday, November 1, 2023 3:05 PM To: Huang, Yujing YHUANG43@mgh.harvard.edu Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
External Email - Use Caution Thanks! This seems to be working now. Can I set recon-all to use synthseg with the robust algorithm? I tried the flag -robust as it appears for the command mri_synthseg, but that doesn't seem to be a recognized flag by recon-all. Thanks!