Hi Mehul,
if you set them to white matter hypointensities in the aseg.mgz I think they will get filled properly.
cheers Bruce
On Tue, 4 May 2010, Mehul Sampat wrote:
Hi Folks,
We have some subjects with very large white matter (WM) lesion loads. We noticed that the pial and main are pial surfaces are not affected by WM lesions. However, they seem to be affection by the juxta-cortical WM lesions (which have dark intensity)
In the past, my colleagues have manually outlined the lesions and created a binary lesion masks.
I was wondering if :
- I can pass this white matter lesion mask as input to recon-all as an
input variable ? essentially the idea is to find a way to make recon-all to consider these as white matter (i am only interested in the cortical thickness measurements and not the WM volume so i think it is okay to do so )
- if this is not possible, can i use this white matter lesion mask to edit
wm.mgz ? in this option, i could find the locations of the non-zero pixels of the lesion mask and then set the corresponding locations in wm.mgz to 110. Does this sound like a bad idea ? or would you suggest a different way to do this ?
thanks Mehul