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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