Hi,
I'm using Freesurfer to segment MRI from patients with cortical
lesions. The automatic segmentation does not work correctly, so I
edited the wm.mgz manually and filled the missing white matter
according to the tutorial. After this I ran recon-all with the
-autorecon2-wm parameter. In some cases this works fine, but in a few
cases the segmentation is still not correct. The wm surface forms a
hole at the lesion despite the fact that I have manually filled the
wm.mgz at that region. The pial surface forms an even deeper hole at
the same spot, so that the surfaces cross.
I have filled the gap from end to end but still the segmentation does
not work correctly. What would be the correct approach to this problem?
Thanks in advance,
Martti Ilvesmäki
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