Hi Matt,
Could you upload that subject to our filedrop and I will take a look.
https://gate.nmr.mgh.harvard.edu/filedrop2/
-Allison
On 06/12/2015 01:04 AM, Matthew Peverill wrote:
(I'm working with Kate on this one)
The problem is with the white matter surface. The pial surface is
usually fine, but the white matter boundary doesn't budge. I've
attached the image. Thanks for your help!
-Matt
On Thu, Jun 11, 2015 at 12:42 PM, Allison Moreau
<almor...@nmr.mgh.harvard.edu <mailto:almor...@nmr.mgh.harvard.edu>>
wrote:
Hi Kate,
I am having trouble viewing the image. Could you send it as an
attachment?
When you say main surface, are you referring to the pial or white
surface?
-Allison
On 06/11/2015 03:07 PM, McLaughlin, Katie wrote:
Hello Freesurfer Experts,
I'm trying to troubleshoot a problem where the main surface in
our brains is not adjusting following white matter edits using
Freesurfer 5.3. To be clear, the procedure here is:
1) Make edits to wm.mgz
2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3
Following this process, what we see is that the main surface in
the brain still encompasses areas that were deleted from wm.mgz.
Here is an example (at bottom of the inferior temporal lobe):
Inline image 1
This seems to be true for all the edits we've made on this set of
brains.
There are no errors in recon-all.log, and the right brain is
being recon'd. Files in the surf directory seem to be updated as
expected. Any idea what we're missing here? We haven't had
trouble with this process in the past. Any help would be much
appreciated!
Thanks,
Kate
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