External Email - Use Caution 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 <[email protected]> wrote: > 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. <[email protected]> > Sent: Tuesday, June 20, 2023 09:36 > To: [email protected]; 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 > [email protected]<mailto:[email protected]> > > 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 > [email protected] > https://secure-web.cisco.com/1wbKirXIlX8LkprWBLtV6p0QTP-pBy9RA9sT8Ucbk5lfvOS6C9GJNuMTbMSejAwFEyLsdf96O5Btki_MNGJiYa59pXIZy82mUhFdEFQ2uQWKxSpzx4HBaGOvZUz8ymuimGxRR-5XoPVQaEUVf2Y9JzJ3EU4be0IjUOEzXYEXu-nUhfuWvH_EiccZmrAN_DpctcLjamPLKlXJ9DwwBO3otQIIxx1khwJ69ReTGotxL9hDNFw3-2DO38BCabyJ87-zei4GocGze7oErA9iaTqPSjA6AipAZBs6k8mmiBVkr0pk5mqHlylDRMwj5IlZ6680BoDBN9Q8NNbVUXBMwLFE1ag/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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://secure-web.cisco.com/1rBep5dAMfQ0-kobtZNiF1M-E4gLwwdTqkQlgPeO7-sCr0H--T24BE9Aeyx7wDWiTZbv_3wl8bDFpaeYC3S7W8ZY7R5qDW_SsrGvpyTzSC1E4kZK04xqtw87mKXQZXngObcmrr1KMufwN1gz0Jm9nOX7Klj6TSzRHJ8RBeYT2cAkDAjyVm8P-wTv0UtV1oZTdlIB21vtFMM9XIlAJcwsA2HTPCLzUAIlGTWnUfxWaEemvWLy96Qi4Ua1Bl75ssf4wULaqQw_UnePMuEPAh-0I-Fiv0ByUGRgak7FN3LtNZCmHyrdcCVKB4nnq1KfG5YgE2HSUSwouoeDjvMZRKEzMng/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1rBep5dAMfQ0-kobtZNiF1M-E4gLwwdTqkQlgPeO7-sCr0H--T24BE9Aeyx7wDWiTZbv_3wl8bDFpaeYC3S7W8ZY7R5qDW_SsrGvpyTzSC1E4kZK04xqtw87mKXQZXngObcmrr1KMufwN1gz0Jm9nOX7Klj6TSzRHJ8RBeYT2cAkDAjyVm8P-wTv0UtV1oZTdlIB21vtFMM9XIlAJcwsA2HTPCLzUAIlGTWnUfxWaEemvWLy96Qi4Ua1Bl75ssf4wULaqQw_UnePMuEPAh-0I-Fiv0ByUGRgak7FN3LtNZCmHyrdcCVKB4nnq1KfG5YgE2HSUSwouoeDjvMZRKEzMng/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > >
_______________________________________________ Freesurfer mailing list [email protected] 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.
