5 Oct
2015
5 Oct
'15
11:43 a.m.
Dear freesurfer experts,
I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.0). Sometimes the ventricles are not fully filled and the white matter is localized within the remaining gaps. After manually filling the gaps in the wm.mgz (following the wiki - Fixing Common Geometric Inaccuracies in White Matter Surfaces) and rerunning (-autorecon2-wm) I still have the wm surface following the ventricle holes, even though I can see they are filled on wm.mgz. I used freesurfer v.5.1.0 before and didn't have these issues. How would you recommend fixing this?
Thanks a lot, Ana