Hi Julian, You can use the command "samseg" with the --recon flag. See the helper function for more details (--help)
Stefano External Email - Use Caution /Hello everyone,/ /We have been utilizing freesurfer for our brain morphometry and processing pipelines, and have recently tested the samseg segmentation algorithm on a clinical cohort./ /With respect to some regions, we currently prefer its results to the ones generated by the standard freesurfer segmentation algorithm. / /As SAMSEG only provides volume calculation (please correct me if I am wrong) and does not feature cortical thickness measurements,/ /I was wondering if the recon-all pipeline can be modified to utilize the samseg segmentation instead, and if so, which script(s) or chain of commands would be a good starting point to implement this./ /Looking forward to your feedback,/ /Julian / Julian McGinnis PhD Candidate TUM-Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany Department of Computer Science, Technical University of Munich, Munich, Germany Email:julian.mcgin...@tum.de _______________________________________________ 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.
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