Hi freesurfer,
We are reprocessing our data from FS version 3.05 with the latest 4.50. We found there are about 20% of the subjects have problem at the ventricle as shown in the attached image. I have tried the method suggested by Doug to remove the wm.mgz and rerun from autorecon2-cp. However, for two subjects I have tried, the method did not help. It will be tedious to manually fill in all the ventricles in wm.mgz. Any other work around?
Thanks, Zheng Hui