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 <MHOFFMANN@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. <DGREVE@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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