Dear Bruce and freesurfers,
I still don't fully understand how deleting a few voxels in brainmask.mgz affects the assignment of the white matter.
The troubleshooting tutorial has a similar example to the attached image below, where we were instructed to delete the extra voxels in wm.mgz. In the attached example, I just deleted the dura in brainmask.mgz and re-ran using autorecon-pial and it seemed to work, too. Would it make a difference if I edited wm.mgz and re-run using -autorecon2-wm -autorecon3?
I guess I fundamentally don't understand what each of autorecon-pial and autorecon2-wm does.
Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 3:37 PM, ye tian tianye730@gmail.com wrote:
Dear Bruce,
Thank you very much!
Sincerely, Ye
On Sat, Jul 13, 2013 at 10:07 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Nope, it won't matter Cheers Bruce
On Jul 12, 2013, at 7:50 PM, ye tian tianye730@gmail.com wrote:
Dear Freesurfers,
I deleted some extra dura that was included in the pial surface. I
recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well?
The wm.mgz before and after manual editing are shown on the left and
right panels of the attachment.
Thank you very much!
Sincerely, Ye <before_after.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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