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Dear Community, I am currently working on visualizing ROI boundaries on the brain surface using the Harvard-Oxford brain atlas. My goal is to generate a surface plot that overlays ROI boundaries from the atlas in a clear and accurate manner. I also tried visualizing in Freeview, connectome_workbench, and I could plot the surface but I was unable to plot the boundaries correctly. Specific challenges I’m facing: I don’t know how to combine the ROI boundaries with a functional surface overlay while keeping the boundaries visible. [image]https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg image800×330 95 KBhttps://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg I would really appreciate any tips, example commands, or references to similar workflows. Thank you in advance for your help!
I'm not sure what you are trying to do. The HO atlas is volume-based, isn't it?
On 1/3/2025 4:41 PM, Zeng, Xinglin wrote:
External Email - Use Caution
Dear Community, I am currently working on visualizing ROI boundaries on the brain surface using the Harvard-Oxford brain atlas. My goal is to generate a surface plot that overlays ROI boundaries from the atlas in a clear and accurate manner. I also tried visualizing in Freeview, connectome_workbench, and I could plot the surface but I was unable to plot the boundaries correctly. Specific challenges I’m facing: I don’t know how to combine the ROI boundaries with a functional surface overlay while keeping the boundaries visible. image https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg
*image800×330 95 KB https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg* I would really appreciate any tips, example commands, or references to similar workflows. Thank you in advance for your help!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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HO atlas is volume-based,but it can be projected to surface for plot. ________________________________ 发件人: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu 代表 Douglas N. Greve dgreve@mgh.harvard.edu 发送时间: 2025年1月6日 9:13 收件人: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] How to Plot Surface with ROI Boundaries Using Harvard-Oxford Brain Atlas?
I'm not sure what you are trying to do. The HO atlas is volume-based, isn't it?
On 1/3/2025 4:41 PM, Zeng, Xinglin wrote:
External Email - Use Caution
Dear Community, I am currently working on visualizing ROI boundaries on the brain surface using the Harvard-Oxford brain atlas. My goal is to generate a surface plot that overlays ROI boundaries from the atlas in a clear and accurate manner. I also tried visualizing in Freeview, connectome_workbench, and I could plot the surface but I was unable to plot the boundaries correctly. Specific challenges I’m facing: I don’t know how to combine the ROI boundaries with a functional surface overlay while keeping the boundaries visible. [image]https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg image800×330 95 KBhttps://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg I would really appreciate any tips, example commands, or references to similar workflows. Thank you in advance for your help!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14jbHYLoZU0552PCkI54YOHNE8xnbqjNjrsP6eheYmdl1eI...
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Zeng, Xinglin