Hi Maya, It looks like you need to have 'synthseg -robust' in the file instead of "mri_synthseg -robust".
Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Wednesday, November 1, 2023 6:06 PM To: Maya Yablonski <ma...@stanford.edu> Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs 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 <ma...@stanford.edu<mailto:ma...@stanford.edu>> Sent: Wednesday, November 1, 2023 3:05 PM To: Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@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!
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