Hi,
I am running a patient of ours with some cortical degeneration through the recon process and have run across an interesting problem. It appears as if the intensity normalization process is missing a large portion of the cortex, resulting in an almost straight line through the middle of his head, with the center portion looking like the intensity normalization worked, but the cortex portion is very dark. The white matter in the cortex hasn't been normalized, and some of the gray matter looks as if it has been washed out or stripped away (that may just be due to the degeneration though). I have been going through and attempting to pick out control points to run -autorecon2-cp, but we wanted to check in and see if that was the best course of action for this particular subject before I got too far into it.
The data can be found in /autofs/space/dinah_001/users/balaji/ SUBJECTS_DIR/subjects/ and the subject ID is amcg_anat
Any advice would be greatly appreciated.
Thanks!
-Garth