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:

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/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.mcginnis@tum.de

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