We're using T1s and Brainmasks, skipping reorient and skull stripping, then running tissue seg and ventricle masking.  
In some subjects, we got bad-looking results, where whole chuck of csf are 'missing' where there clearly should be csf.   For example:  




Suspecting this was an orientation problem, I reoriented the image using Flirt (using 1year-Average-IBIS-MNI-T1w as ref) and applied the same transform to the brainmask.   Then they were run through AutoEACSF.  

The results were much better, but still have a missing chunk: 


 


Is this to be expected, or a sign something is wrong?   Any ideas on how to fix it? 

C