[WARNING: ATTACHMENT UNSCANNED]Help: Using a Different Atlas for Anatomical ROI Analysis
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Hello,
I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to "run recon-all on the AAL anatomical T1w volume template". At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines?
In summary, I am wondering if you can "walk me through" the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time.
Best,
Shawn
--- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center
3860 South Water Street Pittsburgh, PA 15203 sdf29@pitt.edumailto:sdf29@pitt.edu Email 412.246.0460 Office 630.854.0547 Mobile Neuromuscular Research Laboratoryhttp://secure-web.cisco.com/1xPYTwm1twYgyoLhqQPj3hQ3mM2mqTCUs_emm18SlHI78wPt7gnDWSa5TAwrd9ZFoLWw2gNxc-9yEQGDpE7kcjm7Rskd6FIQBp8Uw49YIY7vD1g55kfNjlqfRuTPaKqsMqEj0D670PV9w_zmcC7jiPMizI6oFLKqeJnppwyUSc9ab4MR05kEoobiL7YVF2d3H7nxMqGcWIVGRDxloyQbyB5wqY-zlLnaEgSUdeUWq07G8aVFmnSAC19P0atM7ydeJKXRcEl7hLksRx3oAb1dHBhsFGXtmXl7CMCNC9Lo7aZIeOvUoCu-sExuWIX6X5auM/http%3A%2F%2Fwww.nmrl.pitt.edu%2F
That is a label atlas; you cannot run that through FS. You will need a t1-weighted image to use as input to recon-all to start.
On 11/19/2021 1:59 PM, Flanagan, Shawn D wrote:
External Email - Use Caution
Hello,
I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to “run recon-all on the AAL anatomical T1w volume template”. At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines?
In summary, I am wondering if you can “walk me through” the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time.
Best,
Shawn
*---*
*Shawn Flanagan*, Ph.D. Assistant Professor
University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition
Neuromuscular Research Laboratory Warrior Human Performance Research Center
3860 South Water Street Pittsburgh, PA 15203 sdf29@pitt.edu mailto:sdf29@pitt.edu Email 412.246.0460 Office 630.854.0547 Mobile
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Flanagan, Shawn D