External Email - Use Caution 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
_______________________________________________ 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.
