You might have introduced a new defect, or just made an existing one
worse. If there are topo defects, you can't just ignore them. You don't
necessarily have to remove all the dura. Typically there is a
"peninsula" where the main WM attaches to the the "island" of dura. All
you have to do is cut that peninsula.
On 10/15/2021 9:21 AM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
Hi all,
I ran recon-all successsfully on a subject. I then did some manual edits on
both the brainmask (removal of dura) and wm and then ran recon again for the
edits. This usually works fine, however for one subject the recon (after edits)
fails because of time limit on my process. It gets stuck on the fix toplogical
errors stage, as there is a defect with 36000+ vertices included. I looked at
the lh.inflated.nofix and lh.orig.nofix and indeed you can see there is a lot
of dura/skull being included in the surface on the lh. However, recon did work
just fine the first time where these did happen, and the final surfaces look
fine (the manual edits I did were few!) Gcut also does not work because it
removed too much of the temporal areas and the cerebellum.
Are there any suggestions on how to fix this without having to go in and
manually remove all the dura (it is a lot!). I attach the recon.all log so you
can see how the first recon ran (without errors) and then after edits where it
fails. Could I perhaps use the -nofix flag?
Thanks,
Marianna
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1PQXVpHHHzmaj81WDM7Hq3HYRz6L5gMf9eXQ3fjM9XnO1F3RegqHUeD14PustCaM5IfuZYKZXTKQHcm0Qi0rHaYcOF9NvX1xqUS7uc4OUgyR5alV1Ut_Th5iSLvzlXdEUYdeWacfREUfJUFIlXPtp5XVQEDoFeRHi8Z5dkre_3cfk1eD9755OCC7UViFC3ycEMLmiHXOp3qY6Rc0dzWDXhysds9lrUuYOi5rxH1thn5YaGO-1eWYXoJ_RMxpWpLoz/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
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.
