External Email - Use Caution
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:
External Email - Use Caution
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/14WaW2f-fANC3xHzQeXbEYUREo4vtI5Pq7jeABzCxGbYV7rDoP0YxAa7tvhpbnO0c_4UZAzmvZc5dfY_kEl4kV6huDGgdZ-JP8z7zfo-HkMb5gMEWxV6x8Pn0KZ1DtpBQOdrmDQ87mqgWJeockm7dlonfT-R45XlAsp6PptAZv7rhjUMR3FYIVxPSjSgAjPIsquCsmRBnk8ISJbIpT7fHxTC_xO6P5wqOu3DCsiNkdrDZA-jo6bxyLxL-R18BVRCT/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
