Hi Dan,
I'm afraid these options aren't currently easy to find as they are being parsed by scripts/rca-config. You can find a set of recon-all options along with a description in distribution/etc/recon-config.yaml [1].
To pass additional options to SynthStrip, you'll need to specify an expert options file by calling recon-all with the `-expert` flag [2]. That file could then include the line `synthstrip --no-csf`, for example.
Malte
[1] https://github.com/freesurfer/freesurfer/blob/dev/distribution/etc/recon-con... [2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Dan Levitas djlevitas208@gmail.com Sent: Thursday, June 6, 2024 10:55 To: Freesurfer support list Subject: [Freesurfer] Incoporating synthstrip and synthseg into recon-all
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Hello,
I am using freesurfer version 7.4.1, and would like to incorporate the recently introduced synthstrip and synthseg functions into my recon-all command, if that's possible. From this archive message (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75148.html) it seems that adding the -synthstrip option enables synthstrip; however, I don't see this as an option in the recon-all documentation (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) nor as a command line option for recon-all.
Assuming that both synthstrip and synthseg can be used in recon-all, would the command need to look something like this: recon-all -subjid sub-${sub}_ses-${ses} -i $anat_file -3T -synthstrip --no-csf -synthseg -qcache -all
I'm adding the --no-csf synthstrip option based on this comment (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75172.html).
I should also note that I'm performing a longitudinal analysis, so this specific recon-all pertains to the cross-sectional portion of the workflow.
Thanks,
Dan