upport list
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 '.
1. Create file mri_synthseg.opt, and have this line in it
mri_synthseg -robust
1. Pass
people can answer it too? Also can you keep
previous exchanges?
Best,
Yujing
From: Maya Yablonski
Sent: Wednesday, November 1, 2023 3:05 PM
To: Huang, Yujing
Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
External Email - Use Caution
Thanks! This see
It looks like seg2recon is also looking for FREESURFER. Set it to your
Freesurfer install directory, same as FREESURFER_HOME.
From: Maya Yablonski
Sent: Tuesday, October 31, 2023 7:08 PM
To: Huang, Yujing
Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
rd.edu
On Behalf Of Iglesias Gonzalez, Juan E.
Sent: Tuesday, October 31, 2023 5:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
I'll defer to the software engineers for the first issue!
For the second: does it work if you c
:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
External Email - Use Caution
Thanks! When I tried
"recon-all -synthseg -subjid sub-xx -i .nii.gz"
I get an error that only says: ERROR: cannot use ML routine
External Email - Use Caution
Thanks! When I tried
"recon-all -synthseg -subjid sub-xx -i .nii.gz"
I get an error that only says: ERROR: cannot use ML routines
The same happened on an HPC cluster (linux) and on my local mac. I tried both
Freesurfer 7.3.2 and 7.4.1.
I have no issues
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Maya Yablonski
Date: Monday, October 30, 2023 at 1:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
External Email - Use Caution
Hello,
I am working with a pediatric
External Email - Use Caution
Hello,
I am working with a pediatric sample for which we are seeing many segmentation
errors using the standard recon-all pipeline (version 7.3.2). Running synthseg
on the same input files improves the segmentations dramatically, and I would
like to
