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You can add -synthstrip in 7.3+ to use synthstrip instead of watershed
On 6/21/2023 5:53 PM, Ruifeng Dong wrote:
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Thank you, Douglas and Malte!
In terms of mask volume, synthstrip and watershed method in FS7.3.2
gave us very similar results. But synthstrip takes better care of dura
in our case.
Best,
Ruideng
On Wed, Jun 21, 2023, 1:00 PM Hoffmann, Malte,PhD
<mhoffm...@mgh.harvard.edu> wrote:
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Hi Ruifeng,
While we intend to replace the skull-stripping in recon-all with
SynthStrip in the long run, I think this is not fully implemented
yet, I'm afraid. In general, the --no-csf flag would be
recommended as this produces a skull strip similar to what the
current watershed algorithm does. Whether the -T2 option would
still help remains to be seen...
Cheers,
Malte
________________________________________
From: Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
Sent: Tuesday, June 20, 2023 09:36
To: freesurfer@nmr.mgh.harvard.edu; Hoffmann, Malte,PhD
Subject: Re: [Freesurfer] Use synthetic in recon-all pipeline
On 5/28/2023 1:32 PM, Ruifeng Dong wrote:
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Hi all,
I am running freesurfer 7.3.2 for segmentation of T1 data. It
seems like still using the old skull stripping tools by default.
How should we change it to using synthstrip? (Question 1)
Add -synthstrip
Also, is it a good idea to also turn on the --no-csf flag for
cortex and subcortical segmentation? (Question 2)
If using synthstrip, do we still need the -T2 option for better
treatment of dura regions? (Question 3)
Thank you.
Best,
Ruifeng
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