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:
- 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 mzamro2@illinois.edu 815-980-3882 _________________________________
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