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.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

 

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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!