We're having a problem where some of our subjects show insula volumes in the aparc.stats file, but others do not show insula but show unknown and corpus callosum volumes in the file. All subjects were run in Freesurfer 5.1. We did some testing on our dataset and found that in cases where the insula was missing and unknown was present, the unknown is much larger. We also understand that the unknown volume is more than just the insula, so a simple substitution is not possible. We want to know a few things:

1) In cases where Freesurfer cannot allocate to the insula, is that volume automatically added to the 'unknown' volume?

1) If there's a way to somehow force volumes to go to these labels consistently throughout our data set (i.e. to each of insula, CC and unknown rather than only to some of them.)

2) If that' s not possible (i.e. if there's no way to maintain consistency in output) then will measures from the other regions (everything besides insula, CC or unknown) will be affected by the difference?

Thanks,

Neeraj