it does recreate the white and pial surfaces, but not all steps, and not the segmentation step that creates the wm.mgz and hence the lh.orig and rh.orig files. Erasing dura for example shouldn't require rerunning autorecon2-wm (since the wm.mgz isn't expected to change)
cheers
Bruce
On Mon, 15 Jul 2013, ye tian wrote:
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.