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.stepa...@nyulangone.org>
Subject: [Freesurfer] Samseg cortex parcellation
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <7d31c671-938e-456e-a533-8a132b6e6...@nyulangone.org>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
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
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