You can run something like
samseg --t1w /path/to/input/volume --s subject --recon
This will run recon-all but using samseg to do the initial steps,
including the segmentation of course
We don't have a lot of experience using this as preprocessing to the
surface-based analysis, so look at your results carefully
On 6/10/2022 4:18 AM, Julian McGinnis wrote:
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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