help > QCistern missing occipital regions when using T1 + Brainmask
Oct 14, 2019  10:10 AM | cccoleman
QCistern missing occipital regions when using T1 + Brainmask
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:  

Image


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: 


Image 


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

C

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TitleAuthorDate
QCistern missing occipital regions when using T1 + Brainmask
cccoleman Oct 14, 2019
Martin Styner Oct 15, 2019
cccoleman Oct 18, 2019
Martin Styner Oct 28, 2019