help > RE: QCistern missing occipital regions when using T1 + Brainmask
Oct 15, 2019  11:10 AM | Martin Styner
RE: QCistern missing occipital regions when using T1 + Brainmask
Not sure what the specific issue is with this processing, likely one of the processing steps is too aggressive and stripped those parts away. 

Do you only see this when you have a particular setup?

Also, the tool maintains all the intermediate steps, so you can look backwards and see the step at which those parts were removed.

I would look at segmentation output in the output folder, sort them by last  created and load the different masks into a visualization tool such as Slicer or itksnap (I use the latter for such quick checkups)

Which is the latest mask that still has those regions? We could then see about the settings for that step and adapt/customize it (likely we need to add an option to the GUI for that).

Best
Martin

Threaded View

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