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, /E
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maya Yablonski <ma...@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 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 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
