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I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this?
External Email - Use Caution
You can do this with wb_command. Dunno if FreeSurfer offers this.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Aaron Tanenbaum aaron.b.tanenbaum@gmail.com Reply-To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Date: Friday, March 3, 2023 at 7:26 PM To: Freesurfer Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Apply a nonlinear transform to a surface.
External Email - Use Caution I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this?
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
I think that only works for gifti files. I need it in freesurfer coordinates. Thank you for responding.
On Fri, Mar 3, 2023, 7:30 PM Glasser, Matt glasserm@wustl.edu wrote:
External Email - Use CautionYou can do this with wb_command. Dunno if FreeSurfer offers this.
Matt.
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Aaron Tanenbaum aaron.b.tanenbaum@gmail.com *Reply-To: *Freesurfer support list Freesurfer@nmr.mgh.harvard.edu *Date: *Friday, March 3, 2023 at 7:26 PM *To: *Freesurfer Freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Apply a nonlinear transform to a surface.
External Email - Use Caution *I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this?
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1CAAhrYdZR5VTtd8N09tYPEaCu6OrE2DcPI3y72kXEO-6-o... 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/1CpU9y3_HNapCthnbfX5DZpSEoA3SQlkSHfoQxlR3HBQ-Qo... < https://secure-web.cisco.com/1CpU9y3_HNapCthnbfX5DZpSEoA3SQlkSHfoQxlR3HBQ-Qo... .
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You can use mris_convert between the formats.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Aaron Tanenbaum aaron.b.tanenbaum@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, March 3, 2023 at 8:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Apply a nonlinear transform to a surface.
External Email - Use Caution I think that only works for gifti files. I need it in freesurfer coordinates. Thank you for responding.
On Fri, Mar 3, 2023, 7:30 PM Glasser, Matt <glasserm@wustl.edumailto:glasserm@wustl.edu> wrote:
External Email - Use Caution You can do this with wb_command. Dunno if FreeSurfer offers this.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> Date: Friday, March 3, 2023 at 7:26 PM To: Freesurfer <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Apply a nonlinear transform to a surface.
External Email - Use Caution I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this?
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________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
You can try mris_transform, although you might need to convert the nonlinear warp to our format. I’m pretty sure others have done this, so maybe someone else can comment?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Aaron Tanenbaum Sent: Friday, March 3, 2023 9:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Apply a nonlinear transform to a surface.
External Email - Use Caution I think that only works for gifti files. I need it in freesurfer coordinates. Thank you for responding.
On Fri, Mar 3, 2023, 7:30 PM Glasser, Matt <glasserm@wustl.edumailto:glasserm@wustl.edu> wrote:
External Email - Use Caution You can do this with wb_command. Dunno if FreeSurfer offers this.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> Date: Friday, March 3, 2023 at 7:26 PM To: Freesurfer <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Apply a nonlinear transform to a surface.
External Email - Use Caution I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this?
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1CAAhrYdZR5VTtd8N09tYPEaCu6OrE2DcPI3y72kXEO-6-ou-3oxYZ27zHGa4etHaWS3UYuKFUB325aJB3LwS1aIRv4nlK9NshN6PHbwUcupYQ8OFjvc7uocBe-JNNTo5YThFO_NIz5D3Da6MdISW7byjm-ivaaQkohzYEvRT0JIX87xZgN0a04MNaTdQx-chukRMUnHI8da0t0-HWLyNcYHXxHE3cCFgpEZVg-amJq8xDgnZOlKNkj3zmn1X8xMSzQkltEM0k7KqmlAs6xpALI2Ewogqy0NmWtDpcAWoU-AlU6kKGyfbfIM4IogMA4OF5_EDjpwgluYhKLEfLq-Zjw/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/compliancelinehttps://secure-web.cisco.com/1CpU9y3_HNapCthnbfX5DZpSEoA3SQlkSHfoQxlR3HBQ-QoEXeYzj7WTYvIQ7abfibjlGGV1u0mV5HQBkOhjkH1EscGyzjXtyZhN_rlLeHmsBU0YMwnG1P5xAKmT5Q0btwZK1a56OYjb557aoU3pLeeet6B8lzzv-APImRdbF8Lo25HI7uHlNim52_MeikChFM01eNEihKR6kz_vDucwXAgPAWweR5K9qg0P4uDyWrrgCHXXlwtE-eqjkSVakra0ZFN6krNJ4Fnfj1KMdq8g9KsHE9wcswjEo13kpV7izSXOyZRogtUCmUULz2H6KJYCXmEyimjYr31E_ZeoZikxbEA/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/compliancelinehttps://secure-web.cisco.com/1CpU9y3_HNapCthnbfX5DZpSEoA3SQlkSHfoQxlR3HBQ-QoEXeYzj7WTYvIQ7abfibjlGGV1u0mV5HQBkOhjkH1EscGyzjXtyZhN_rlLeHmsBU0YMwnG1P5xAKmT5Q0btwZK1a56OYjb557aoU3pLeeet6B8lzzv-APImRdbF8Lo25HI7uHlNim52_MeikChFM01eNEihKR6kz_vDucwXAgPAWweR5K9qg0P4uDyWrrgCHXXlwtE-eqjkSVakra0ZFN6krNJ4Fnfj1KMdq8g9KsHE9wcswjEo13kpV7izSXOyZRogtUCmUULz2H6KJYCXmEyimjYr31E_ZeoZikxbEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
or use mris_apply_reg with the --m3z option
On 3/4/2023 10:56 AM, Fischl, Bruce R.,PHD wrote:
You can try mris_transform, although you might need to convert the nonlinear warp to our format. I’m pretty sure others have done this, so maybe someone else can comment?
Cheers Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Aaron Tanenbaum *Sent:* Friday, March 3, 2023 9:59 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Apply a nonlinear transform to a surface.
* External Email - Use Caution *
I think that only works for gifti files. I need it in freesurfer coordinates. Thank you for responding.
On Fri, Mar 3, 2023, 7:30 PM Glasser, Matt glasserm@wustl.edu wrote:
* External Email - Use Caution * You can do this with wb_command. Dunno if FreeSurfer offers this. Matt. *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Aaron Tanenbaum <aaron.b.tanenbaum@gmail.com> *Reply-To: *Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, March 3, 2023 at 7:26 PM *To: *Freesurfer <Freesurfer@nmr.mgh.harvard.edu> *Subject: *[Freesurfer] Apply a nonlinear transform to a surface. ** * External Email - Use Caution * I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this? ------------------------------------------------------------------------ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ 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/1CAAhrYdZR5VTtd8N09tYPEaCu6OrE2DcPI3y72kXEO-6-ou-3oxYZ27zHGa4etHaWS3UYuKFUB325aJB3LwS1aIRv4nlK9NshN6PHbwUcupYQ8OFjvc7uocBe-JNNTo5YThFO_NIz5D3Da6MdISW7byjm-ivaaQkohzYEvRT0JIX87xZgN0a04MNaTdQx-chukRMUnHI8da0t0-HWLyNcYHXxHE3cCFgpEZVg-amJq8xDgnZOlKNkj3zmn1X8xMSzQkltEM0k7KqmlAs6xpALI2Ewogqy0NmWtDpcAWoU-AlU6kKGyfbfIM4IogMA4OF5_EDjpwgluYhKLEfLq-Zjw/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/1CpU9y3_HNapCthnbfX5DZpSEoA3SQlkSHfoQxlR3HBQ-QoEXeYzj7WTYvIQ7abfibjlGGV1u0mV5HQBkOhjkH1EscGyzjXtyZhN_rlLeHmsBU0YMwnG1P5xAKmT5Q0btwZK1a56OYjb557aoU3pLeeet6B8lzzv-APImRdbF8Lo25HI7uHlNim52_MeikChFM01eNEihKR6kz_vDucwXAgPAWweR5K9qg0P4uDyWrrgCHXXlwtE-eqjkSVakra0ZFN6krNJ4Fnfj1KMdq8g9KsHE9wcswjEo13kpV7izSXOyZRogtUCmUULz2H6KJYCXmEyimjYr31E_ZeoZikxbEA/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/1CpU9y3_HNapCthnbfX5DZpSEoA3SQlkSHfoQxlR3HBQ-QoEXeYzj7WTYvIQ7abfibjlGGV1u0mV5HQBkOhjkH1EscGyzjXtyZhN_rlLeHmsBU0YMwnG1P5xAKmT5Q0btwZK1a56OYjb557aoU3pLeeet6B8lzzv-APImRdbF8Lo25HI7uHlNim52_MeikChFM01eNEihKR6kz_vDucwXAgPAWweR5K9qg0P4uDyWrrgCHXXlwtE-eqjkSVakra0ZFN6krNJ4Fnfj1KMdq8g9KsHE9wcswjEo13kpV7izSXOyZRogtUCmUULz2H6KJYCXmEyimjYr31E_ZeoZikxbEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
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Aaron Tanenbaum -
Douglas N. Greve -
Fischl, Bruce R.,PHD -
Glasser, Matt