Hi Marta
I don't see anything obviously wrong in your image, but it is hard to tell
dura from gray matter in a single slice. If you upload the subject dir we
will take a look.
Usually you only need to add gray matter voxels back to the brainmask.mgz
if there was a skull stripping problem. Is that the case?
cheers
Bruce
On Tue, 30 Sep 2014, Zamroziewicz, Marta Karolina wrote:
Hello,
We have some reconstructions with a significant amount of grey matter
excluded in the temporal cortex and are having problems using manual voxel
editing to fix this.
Our correction process for brain tissue that wasn’t included in the
pial/white matter outlines has been as follows:
1. When white matter is excluded from the white matter outline, we’ve used
control points to identify missed white matter. We then re-run using the
following command: recon-all -autorecon2-cp -autorecon3 -subjid <SUB_ID>.
2. When grey matter is excluded from the pial outline, we first make sure
that white matter is outlined appropriately. If adding control points
doesn’t fix the grey matter problem, we manually add grey matter voxels to
the brainmask volume using the voxel edit tool. We then re-run using the
following command: recon-all -autorecon-pial -subjid <SUB_ID>. In some cases
(especially in the temporal cortex), the new reconstructions don’t
incorporate the manually added grey matter voxels into the pial outline.
I’ve attached an image of a subject who didn’t have white matter problems
but did have excluded grey matter in the temporal cortex. We reran this
subject using the recon-all -autorecon-pial -subjid <SUB_ID> command and the
newly added grey matter voxels weren’t included in the new pial outline.
Is there a way to address this problem?
Thank you very much for your time!
Marta
_________________________________
Marta Zamroziewicz
MD/PhD Candidate
Decision Neuroscience Laboratory
University of Illinois Urbana-Champaign
mzam...@illinois.edu
815-980-3882
_________________________________
[IMAGE]
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