Re: [Freesurfer] Samseg cortex parcellation

[Douglas N. Greve]

when you say that it is better cortex segmentation, do you mean better 
than the aseg.mgz=aparc+aseg.mgz or better than the aseg.presurf.mgz? Do 
you mean in general or just near the WMH? The aseg/aparc+aseg use the 
surfaces to refine the gray/white boundary, and usually the surfaces do 
a much better job there.


On 2/16/2023 6:32 PM, Stepanov, Valentin wrote:


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 1^st Avenue, office 212

New York, NY 10016


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Re: [Freesurfer] Samseg cortex parcellation

[Cerri, Stefano,PHD]

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 +
From: "Stepanov, Valentin" 
Subject: [Freesurfer] Samseg cortex parcellation
To: "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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 .
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