On Thu, Mar 7, 2024, 10:07 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Have you looked at the actual surface?

On 3/7/2024 2:29 AM, Hyunchul Lee wrote:
External Email - Use Caution

Hello,

I'm using Freesurfer recon-all to create reconstructions to use with MNE-python for source estimation of SEEG data. My work relies on having correct labeling of segmentation data. For most cases, there has been no trouble but I am having trouble where the cortical parcellation shows up as dots in one hemisphere. Please see image attached. I also noticed that the lh.ribbon.mgz is also 'dotty' (also attached). There is no issue with the right hemisphere. This reconstruction was not manually edited, but only recon-all was used.

I have tried using mris_volmask --label_left_ribbon, setting the argument to various values. That didn't work that great - reducing to 0 basically whites everything out except for the white matter on the ipsilateral hemisphere and anything 1 or more produces the same 'dots'. Interestingly the pial and wm surfaces all look ok. Also, I am not sure if creating the correct ribbon.mgz is going to fix the aparc.a2009+aseg file.

I would really appreciate your advice.

Best regards,

Hyunchul Lee MBBS PhD
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .