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
sd...@pitt.edu <mailto:sd...@pitt.edu> Email
412.246.0460 Office
630.854.0547 Mobile
Neuromuscular Research Laboratory
<http://secure-web.cisco.com/1xPYTwm1twYgyoLhqQPj3hQ3mM2mqTCUs_emm18SlHI78wPt7gnDWSa5TAwrd9ZFoLWw2gNxc-9yEQGDpE7kcjm7Rskd6FIQBp8Uw49YIY7vD1g55kfNjlqfRuTPaKqsMqEj0D670PV9w_zmcC7jiPMizI6oFLKqeJnppwyUSc9ab4MR05kEoobiL7YVF2d3H7nxMqGcWIVGRDxloyQbyB5wqY-zlLnaEgSUdeUWq07G8aVFmnSAC19P0atM7ydeJKXRcEl7hLksRx3oAb1dHBhsFGXtmXl7CMCNC9Lo7aZIeOvUoCu-sExuWIX6X5auM/http%3A%2F%2Fwww.nmrl.pitt.edu%2F>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline . 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.
