Dear Maya,

You can use then -synthseg flag with recon-all to use SynthSeg instead of the standard algorithm 😉

For fmriprep: which is the offending volume? There are very minor differences with the standard recon-all output.

Cheers,

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Maya Yablonski <mayay@stanford.edu>
Date: Monday, October 30, 2023 at 1:09 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs

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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 be able to fix the surface files (?h.white, ?h.pial) according to the synthseg segmentation. I could not find how to do this in the documentation? Can I place the synthseg.nii.gz file somewhere and rerun recon-all? or autorecon? Would appreciate any pointers to the right way to go about this!

Alternatively, I ran recon-all-clinical and that also seems to work well on our data, however the output folder is not identical to the standard recon-all folder, so I can not use that with other preprocessing pipelines that rely on freesurfer output (e.g. fmriprep).

I would appreciate any advice on how to leverage the synthseg outputs instead of manually editing the segmentations!

Thank you,

Maya