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!