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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)
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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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 https://secure-web.cisco.com/1lhsNy4BOjHHWMklbBmpOHEyEiVnqOmxu5YZuPeMGaSF5Bq...
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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:
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14WaW2f-fANC3xHzQeXbEYUREo4vtI5Pq7jeABzCxGbYV7r...
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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 MHOFFMANN@mgh.harvard.edu wrote:
External Email - Use CautionHi 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:
External Email - Use CautionHi 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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https://secure-web.cisco.com/14WaW2f-fANC3xHzQeXbEYUREo4vtI5Pq7jeABzCxGbYV7r...
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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 MHOFFMANN@mgh.harvard.edu 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. <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: 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dOAq_B4TDCmBXW34e1GhNZkCmCHm3MulAsVtiIPJFAizt_dUKdXlCEbWXIn6OfGmUkzDdcsrOEfAvPmYNaiPJbpFhGzBDE4BBHGKOxtdMk1rIrY54NRVH2qClyPrnAUdSuGlN4AJQJlgBK4BIsu2cn0epLFCyvHHkzM4jtRCoDU6XOBdH0QM7BiGKvaftwXNn9X01PRrvUDdhu90V9ysh2GUEOHxnuZyS4WiRNy9VFTVgrD_bC5toWphbIWg6GLC/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1_XgCc-5GTCnLjCiMoMzqprdSScuDwuCO2IXnqmw47om34kP3hwDVfSi45aumUPRx6eN95r3umStgbK1Mr8BRpOuLZ2JF016Us_pbDS97jxwFC2tX21FtTAuYWcnsa40Q4BL5zCtmEZIG23fAxB15G7uIKP4XcrsSggGJyA6Lx8iYn-FtyUW6jbEWnirQR_qEJ0gUT0uQiIfyqWKLx4xqNrER4Mz4OU0hOI2sPWbr6OGNkVnc4us2O_R8Uu1iL-sG/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> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1_XgCc-5GTCnLjCiMoMzqprdSScuDwuCO2IXnqmw47om34kP3hwDVfSi45aumUPRx6eN95r3umStgbK1Mr8BRpOuLZ2JF016Us_pbDS97jxwFC2tX21FtTAuYWcnsa40Q4BL5zCtmEZIG23fAxB15G7uIKP4XcrsSggGJyA6Lx8iYn-FtyUW6jbEWnirQR_qEJ0gUT0uQiIfyqWKLx4xqNrER4Mz4OU0hOI2sPWbr6OGNkVnc4us2O_R8Uu1iL-sG/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>> .
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Douglas N. Greve -
Hoffmann, Malte,PhD -
Ruifeng Dong