Hi Maya,

It looks like you need to have 'synthseg -robust' in the file instead of "mri_synthseg -robust".

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Wednesday, November 1, 2023 6:06 PM To: Maya Yablonski mayay@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 <mayay@stanford.edumailto:mayay@stanford.edu> Sent: Wednesday, November 1, 2023 3:05 PM To: Huang, Yujing <YHUANG43@mgh.harvard.edumailto: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!