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Hi there,
Apologies if this is a basic question: I have two surfaces and I would like to make a ribbon/mask of the area between the surfaces. How could I go about this? Is mris_fill the right tool to use?
Thanks for your help! Isaac
Hi Isaac
Yes, you can use mris_fill on the two surfaces, then intersect the resulting volumes. We use the binary mri_ribbon that does this for you, you can try that out instead if you want.
Cheers Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of I. Kelleher-Unger Sent: Thursday, September 30, 2021 9:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fill between two surfaces
External Email - Use Caution
External Email - Use Caution
Hi there,
Apologies if this is a basic question: I have two surfaces and I would like to make a ribbon/mask of the area between the surfaces. How could I go about this? Is mris_fill the right tool to use?
Thanks for your help! Isaac
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gTXqklbsr-4pqG6TrIAm-Au1STvfRQucNL5eohltU4mKu3...
External Email - Use Caution
Hi Bruce,
Thanks for your quick reply!
mri_ribbon is exactly what I was looking for! Thanks for your help on that.
Ultimately I want to find the overlap between the output of mri_ribbon and an atlas ROI.
Is there a tool in freesurfer for this (preferred option to keep within the same ecosystem) or would I be best off using something like fslmaths with the -mas flag?
Thanks again for your help! Isaac
On 30 Sep 2021, at 3:19 pm, Fischl, Bruce BFISCHL@MGH.HARVARD.EDU wrote:
Hi Isaac
Yes, you can use mris_fill on the two surfaces, then intersect the resulting volumes. We use the binary mri_ribbon that does this for you, you can try that out instead if you want.
Cheers Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of I. Kelleher-Unger Sent: Thursday, September 30, 2021 9:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fill between two surfaces
External Email - Use Caution External Email - Use CautionHi there,
Apologies if this is a basic question: I have two surfaces and I would like to make a ribbon/mask of the area between the surfaces. How could I go about this? Is mris_fill the right tool to use?
Thanks for your help! Isaac
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gTXqklbsr-4pqG6TrIAm-Au1STvfRQucNL5eohltU4mKu3...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HAnZpOXhW_8d7HriRCHTH4-O_DdCj8zLUTzGLjuqxpd28r... 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 http://secure-web.cisco.com/1MaDLtofhenbzzxDg3V1wbmWbeinvyKbQ-f1KiMntfocwZ37... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.
Hi Isaac
You can use tools like mri_and mri_or to generate results, or use the FSL tools, either way is fine Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of I. Kelleher-Unger Sent: Thursday, September 30, 2021 10:38 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fill between two surfaces
External Email - Use Caution
External Email - Use Caution
Hi Bruce,
Thanks for your quick reply!
mri_ribbon is exactly what I was looking for! Thanks for your help on that.
Ultimately I want to find the overlap between the output of mri_ribbon and an atlas ROI.
Is there a tool in freesurfer for this (preferred option to keep within the same ecosystem) or would I be best off using something like fslmaths with the -mas flag?
Thanks again for your help! Isaac
On 30 Sep 2021, at 3:19 pm, Fischl, Bruce BFISCHL@MGH.HARVARD.EDU wrote:
Hi Isaac
Yes, you can use mris_fill on the two surfaces, then intersect the resulting volumes. We use the binary mri_ribbon that does this for you, you can try that out instead if you want.
Cheers Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of I. Kelleher-Unger Sent: Thursday, September 30, 2021 9:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fill between two surfaces
External Email - Use Caution External Email - Use CautionHi there,
Apologies if this is a basic question: I have two surfaces and I would like to make a ribbon/mask of the area between the surfaces. How could I go about this? Is mris_fill the right tool to use?
Thanks for your help! Isaac
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gTXqklbsr-4pqG6TrIAm-Au1STvfRQucNL5eohlt U4mKu3MedWgxCmO6OU2Av58IIqfJO31EkmCNvxBCjK5t_0TYOLngxyhC7wzuC9at3f5xuB xdUXSjl7xO7Cs1I8DaYa44E3qG-oJm3N7wkt5Z38ZRCr0cQnLX5eclE0JOYegRvDOLOBsI T4hB4TurPSPballfKIXxEMLmTnLPPvPC14g86VS_1cJ2MR6jMM7btVOEVeDSB2FZb8bTMG 5fP_RNkUmf5nxSzsde131hUGmqdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F mailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HAnZpOXhW_8d7HriRCHTH4-O_DdCj8zLUTzGLjuq xpd28rMbQ4ELeop5UqDhB68TmK9u2vVM9DL20RNhyh28UhFwzggoUfar2gbEKUz3UmwoDW 8jjnQdUpOZTBZbmfCkkZodWtHZq-vofHWcrflh1qwN03_4eAx5m_vXz2Wgkpb7_lhL76UT oFXfgxd-bLYRUO8cOEIsZSXrWipE7wnVzglyfyf7jv2dxKHTsft1_GJv5plKOAO2QwFCRr EnskOViZWieQfJHMWgkz5sPT0v5Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F mailman%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 http://secure-web.cisco.com/1MaDLtofhenbzzxDg3V1wbmWbeinvyKbQ-f1KiMntfocwZ37... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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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