Dear Lilla,

Here is a snapshot of the aseg volume, which rescues some gray matter not included in the pia. I am not sure if the aseg is ok, as the portion extending in the lesion is labeled gray matter (intensity 42). I guess this is not a problem. If I generate a surface from aseg as you suggested: a. I would need to generate a surface for each of the two hemispheres; b. If a is doable, is there a way to make it 'pial' in the sense that it gets registered with sphere and gets to be applied the DK atlas? A corrolary would be whether I can trick FS by labeling the new surface as smth.pial during the recon pipeline and further complete the rest of the processing steps to generate a true pia.

Thank you for your assist,

 

 

Octavian