Hi Valentin,

Glad to hear that.

Did you use the command "samseg" with the --recon flag? If yes, there are a couple of flags that you can add so that the output of SAMSEG ("seg.mgz") is used in more steps in the recon-all stream:

" --fill : use samseg to create filled.mgz instead of recon-all" " --normalization2 : use samseg to create brain.mgz instead of recon-all (with --recon) "

Would you be able to run the command with these flags (--fill and --normalization2) and let us know if you obtain better surfaces and hence cortical parcellations?

Thanks, Stefano

Date: Thu, 16 Feb 2023 23:32:49 +0000 From: "Stepanov, Valentin" Valentin.Stepanov@nyulangone.org Subject: [Freesurfer] Samseg cortex parcellation To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 7D31C671-938E-456E-A533-8A132B6E66A3@nyulangone.org Content-Type: text/plain; charset="utf-8"

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Hello, I hope this email finds you well.

I am using Samseg for the MS patients' data and am very impressed with its performance in terms of lesions segmentation along with posteriors and probability maps saving. Also, compared to freesurfer, it has a remarkably better quality of cortical gray matter segmentation, particularly in subjects with juxta/intracortical lesions. However, to my knowledge, it does not allow doing a cortex parcellation. I used it with the ?recon option, but in that case, the output (aparc+aseg.mgz) is identical or very close to those freesurfer provides and commonly has some segmentation errors, whereas seg.mgz saved in samseg directory demonstrates significantly better segmentation. I wonder if there is any way to run cortex parcellation using exact samseg seg.mgz output? I have attached a couple of images demonstrating the difference of segmentation output for freesurfer and samseg.

Thank you,

Best regards Valentin

Valentin Stepanov Postdoctoral Fellow Center for Biomedical imaging Department of Radiology NYU Grossman School of Medicine 660 1st Avenue, office 212 New York, NY 10016