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
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