FreeSurfer 6.0.0, issues with CSF

Hi all! I am in the process to implement FreeSurfer 6.0 (previously running 5.0) and it seems to work nicely (I mainly use it to extract volumes of interest that then are used elsewhere). However when I look at the CSF mask I see that in most subject there is no connection between 3:d and 4:th ventricle. The cerebral aqueduct no longer goes the whole way through the midbrain. When I use the -brainstem-structures it finds the aqueduct without problems and also it worked with FreeSurfer 5.0. This is of no big consequense but I worry that it might be indicative of a poorer CSF segmentation or that I have done something wrong in the installing.

Does anyone know if something been changed in the way CSF is segmented betweeb FreeSurfer 5 and 6? Im running FreeSurfer on ubuntu 16.04 LTS

Just following up on this thread as I am noticing the same behavior.
Jonas, did you learn anything that would explain this discrepency?

Sorry no. I noted the same behavior on other computers in our lab and concluded that the problem was not with my machine and stopped there. Still curious as to the cause though. Seems weird that a later version should do a poorer job.

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