Dear Bruce,

Thank you very much!

In my experience, autorecon-pial does seem to alter white matter assignment, which seems to contradict the statement that autorecon-pial "regenerates all final surfaces".

Sincerely,
Ye



On Mon, Jul 15, 2013 at 12:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
if the edits are aimed at only correcting the pial surface you don't need to run autorecon2-wm. Sometimes the pial is incorrect because the white is also wrong, then you need to run them both

cheers
Bruce


On Mon, 15 Jul 2013, ye tian wrote:

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


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 Partners Compliance HelpLine at
http://www.partners.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.