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Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections?
External Email - Use Caution
The problem is solved, I just changed the freesurfer version , thnx for your help
Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum aaron.b.tanenbaum@gmail.com a écrit :
External Email - Use CautionOur lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1MkjLfq-0LdmcCfYdV5NcT8yAoB2BE40dzzC_MoD-rkVBPd... 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/1OWYAV-YeU2cSAHwKeQaKFFfccFs4KNZFzy4r3aXlDDnU6t... < https://secure-web.cisco.com/1OWYAV-YeU2cSAHwKeQaKFFfccFs4KNZFzy4r3aXlDDnU6t... . 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.
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Great. glad I was of some help. I still need my questions answered.
On Tue, Jun 14, 2022 at 4:33 PM Bouchra Guelib < bouchra.guelib@univ-constantine2.dz> wrote:
External Email - Use CautionThe problem is solved, I just changed the freesurfer version , thnx for your help
Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum aaron.b.tanenbaum@gmail.com a écrit :
External Email - Use CautionOur lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections? _______________________________________________ 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/1nQflonvh3tkXvAnWj_F4_5dClC9xAPDa5LzuhN21g8jzXa... https://secure-web.cisco.com/1MkjLfq-0LdmcCfYdV5NcT8yAoB2BE40dzzC_MoD-rkVBPdua6CFc5zuW22ZDsJQueMEBZCnW70AX1EA9jL95dEKdpGZbsJ4inOEKlO5dVFFF4PkJlpbut1xTLLHc17yBoB5G2KkBi1k3LLzxB5-bVlsKznWsIwTb7Iwelti7C1g5YI2vaZnrUhNYGrRASi4CsPMwBwFmo9P3VtXJadCivfSb3WGEvHlSCDA3UmJnguymAeZ-E8RuL-O9fiYD-f63cCgviLqzOeYlBCkowJTn74foJCctednnrv9ihTACvrglGjnB-z6jFzaRU5ZY1WjVjSmfwrDNGg9hp3pUBtqfiA/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/1zTaGdaA-lm38e2Wah9IoVmlZaCH9yEiXM6rh09mqIEb0Mz... https://secure-web.cisco.com/1OWYAV-YeU2cSAHwKeQaKFFfccFs4KNZFzy4r3aXlDDnU6tzM9Lp-CpPdVCLkQPxCFlqXbLQF4dUqp0BRNbLtoObfQLPWHM-KSsDnzytSPWc5ArJCPd7ElbIyf4Xx_3otHEjHsGh5rzmzp1POMi-hS3b7FAg81elP5SEfUeNDGPhEi_ir_M61v30UyGxuoZVhmvdlts4zq7fKkKC6nbBm2RlU_bwJUqEkYC5swx_iLvVhE0EhvJWIkU2Wl6tO7qeQUiLcNV95JelXKKbLuCsJxSz6NyYOVpoNSvdYIq2izAl7-ji7WCRA-be4QMVbGeQR4rDR-OtY_D_P9-Dksgpa0g/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/1zTaGdaA-lm38e2Wah9IoVmlZaCH9yEiXM6rh09mqIEb0Mz... https://secure-web.cisco.com/1OWYAV-YeU2cSAHwKeQaKFFfccFs4KNZFzy4r3aXlDDnU6tzM9Lp-CpPdVCLkQPxCFlqXbLQF4dUqp0BRNbLtoObfQLPWHM-KSsDnzytSPWc5ArJCPd7ElbIyf4Xx_3otHEjHsGh5rzmzp1POMi-hS3b7FAg81elP5SEfUeNDGPhEi_ir_M61v30UyGxuoZVhmvdlts4zq7fKkKC6nbBm2RlU_bwJUqEkYC5swx_iLvVhE0EhvJWIkU2Wl6tO7qeQUiLcNV95JelXKKbLuCsJxSz6NyYOVpoNSvdYIq2izAl7-ji7WCRA-be4QMVbGeQR4rDR-OtY_D_P9-Dksgpa0g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
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Actually, I didn't try this idea and also I don't know what's the difference between brain mask from previous versions.
Le mar. 14 juin 2022 à 22:39, Aaron Tanenbaum aaron.b.tanenbaum@gmail.com a écrit :
External Email - Use CautionGreat. glad I was of some help. I still need my questions answered.
On Tue, Jun 14, 2022 at 4:33 PM Bouchra Guelib < bouchra.guelib@univ-constantine2.dz> wrote:
External Email - Use CautionThe problem is solved, I just changed the freesurfer version , thnx for your help
Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum < aaron.b.tanenbaum@gmail.com> a écrit :
External Email - Use CautionOur lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections? _______________________________________________ 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/13frz6J0eC9SploapeNuv0sQBnKOuZK1FYWnbNLZZfOvYD0... https://secure-web.cisco.com/1MkjLfq-0LdmcCfYdV5NcT8yAoB2BE40dzzC_MoD-rkVBPdua6CFc5zuW22ZDsJQueMEBZCnW70AX1EA9jL95dEKdpGZbsJ4inOEKlO5dVFFF4PkJlpbut1xTLLHc17yBoB5G2KkBi1k3LLzxB5-bVlsKznWsIwTb7Iwelti7C1g5YI2vaZnrUhNYGrRASi4CsPMwBwFmo9P3VtXJadCivfSb3WGEvHlSCDA3UmJnguymAeZ-E8RuL-O9fiYD-f63cCgviLqzOeYlBCkowJTn74foJCctednnrv9ihTACvrglGjnB-z6jFzaRU5ZY1WjVjSmfwrDNGg9hp3pUBtqfiA/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/1dIDGTgK9j3NMfEh9qFJMRdvl0r52kj2OTYwuN75QTuunpq... https://secure-web.cisco.com/1OWYAV-YeU2cSAHwKeQaKFFfccFs4KNZFzy4r3aXlDDnU6tzM9Lp-CpPdVCLkQPxCFlqXbLQF4dUqp0BRNbLtoObfQLPWHM-KSsDnzytSPWc5ArJCPd7ElbIyf4Xx_3otHEjHsGh5rzmzp1POMi-hS3b7FAg81elP5SEfUeNDGPhEi_ir_M61v30UyGxuoZVhmvdlts4zq7fKkKC6nbBm2RlU_bwJUqEkYC5swx_iLvVhE0EhvJWIkU2Wl6tO7qeQUiLcNV95JelXKKbLuCsJxSz6NyYOVpoNSvdYIq2izAl7-ji7WCRA-be4QMVbGeQR4rDR-OtY_D_P9-Dksgpa0g/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/1dIDGTgK9j3NMfEh9qFJMRdvl0r52kj2OTYwuN75QTuunpq... https://secure-web.cisco.com/1OWYAV-YeU2cSAHwKeQaKFFfccFs4KNZFzy4r3aXlDDnU6tzM9Lp-CpPdVCLkQPxCFlqXbLQF4dUqp0BRNbLtoObfQLPWHM-KSsDnzytSPWc5ArJCPd7ElbIyf4Xx_3otHEjHsGh5rzmzp1POMi-hS3b7FAg81elP5SEfUeNDGPhEi_ir_M61v30UyGxuoZVhmvdlts4zq7fKkKC6nbBm2RlU_bwJUqEkYC5swx_iLvVhE0EhvJWIkU2Wl6tO7qeQUiLcNV95JelXKKbLuCsJxSz6NyYOVpoNSvdYIq2izAl7-ji7WCRA-be4QMVbGeQR4rDR-OtY_D_P9-Dksgpa0g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
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You should be able to run 7.2 on top of the 5.3 and at will take all your edits (make a copy of your 5.3 data first:)
On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Are there special flags. There are differences between autorecon1 for both pipeline. Does 7.2 update some of the files like for instance the T1.mgz do to differences in the normalizations.
On Sun, Jun 19, 2022, 3:55 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
You should be able to run 7.2 on top of the 5.3 and at will take all your edits (make a copy of your 5.3 data first:)
On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:
External Email - Use CautionOur lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections?
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16UJfiN-oybLEPTjfQtzd784e8KzTazVOL_oFmv5VAYJO0Z... 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/1CUE98fgtNp0aXzXYeHf4sOHFOCAi_kbMMvqPpy-TX6wgSr... < https://secure-web.cisco.com/1CUE98fgtNp0aXzXYeHf4sOHFOCAi_kbMMvqPpy-TX6wgSr... . 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.
no special flags. 7.2 will update all of the files, it should preserve all your edits though
On 6/21/2022 7:21 AM, Aaron Tanenbaum wrote:
External Email - Use Caution
Are there special flags. There are differences between autorecon1 for both pipeline. Does 7.2 update some of the files like for instance the T1.mgz do to differences in the normalizations.
On Sun, Jun 19, 2022, 3:55 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
You should be able to run 7.2 on top of the 5.3 and at will take all your edits (make a copy of your 5.3 data first:) On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:External Email - Use Caution Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/16UJfiN-oybLEPTjfQtzd784e8KzTazVOL_oFmv5VAYJO0ZGHj5B86GZi8IHjJyaeuQzbTXMWXWz27I2k3p3x7J78AINvo036QSiIerDbSqRvZGEsTi8ccjxvIqwE4qePmvzg4Vm6r9yfNZcPd7g0GIqEPLyXzMyMk-Zuw0T_oljT89J3zqPGtCqE74Dy2yzH43Jc3FACxe4h67zoWZdTtmuZx_SPssrzAm86pElQhJmrety0k8K1ii0svdagcBAj-zlE3N0LVFAfCOWlr-c3Ye16SvP2lnBBoArQl9-mth2fq9qg_d9gtB-lWvndwdLeGTTRE9XtUYdyEPS60gteBQ/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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/16UJfiN-oybLEPTjfQtzd784e8KzTazVOL_oFmv5VAYJO0ZGHj5B86GZi8IHjJyaeuQzbTXMWXWz27I2k3p3x7J78AINvo036QSiIerDbSqRvZGEsTi8ccjxvIqwE4qePmvzg4Vm6r9yfNZcPd7g0GIqEPLyXzMyMk-Zuw0T_oljT89J3zqPGtCqE74Dy2yzH43Jc3FACxe4h67zoWZdTtmuZx_SPssrzAm86pElQhJmrety0k8K1ii0svdagcBAj-zlE3N0LVFAfCOWlr-c3Ye16SvP2lnBBoArQl9-mth2fq9qg_d9gtB-lWvndwdLeGTTRE9XtUYdyEPS60gteBQ/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://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1CUE98fgtNp0aXzXYeHf4sOHFOCAi_kbMMvqPpy-TX6wgSrOTvm3ew1P7IPrF5gHJmcGmXavgwCL4pNUrXna75M005RAibYlaPX9Gc0Ngd1h7YmhTeZqRBEHjG76O3j3qOOuNPwPIL3MWV5RMCYB_hJN-H4VX9I8rzWa867kwluBvSOjeemxD185d7R4DYV3Gz6FTGNGDCBWdC_D6-qCNB11FH98M3TLG-heWUJFu205KjqJwGjfXx_wG7_FdtfhU9QUMYoY8nvknytxHYuF22q6hpB_BY6esjkor4jC3n64JUfdPSNvtkK7rHBGd54fJC4R_4yFFAgP12EWlsL7WDg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1CUE98fgtNp0aXzXYeHf4sOHFOCAi_kbMMvqPpy-TX6wgSrOTvm3ew1P7IPrF5gHJmcGmXavgwCL4pNUrXna75M005RAibYlaPX9Gc0Ngd1h7YmhTeZqRBEHjG76O3j3qOOuNPwPIL3MWV5RMCYB_hJN-H4VX9I8rzWa867kwluBvSOjeemxD185d7R4DYV3Gz6FTGNGDCBWdC_D6-qCNB11FH98M3TLG-heWUJFu205KjqJwGjfXx_wG7_FdtfhU9QUMYoY8nvknytxHYuF22q6hpB_BY6esjkor4jC3n64JUfdPSNvtkK7rHBGd54fJC4R_4yFFAgP12EWlsL7WDg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> . 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.
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Aaron Tanenbaum -
Bouchra Guelib -
Douglas N. Greve