help > RE: QCistern missing occipital regions when using T1 + Brainmask
Oct 28, 2019  07:10 AM | Martin Styner
RE: QCistern missing occipital regions when using T1 + Brainmask
Correct assessment. In this case, the processing is too aggressive in getting rid of small islands. This is part of the final cleanup steps, which consists of several steps (heuristically determined) to clean up the segmentation. 

Several possibilities:
a) if this is a common occurrence in your data and the MID002 image is of sufficient quality for the EACSF label, you could use that image instead of the QCistern label. 
b) advanced: you could edit the script and run the last steps manually, leaving out that connected component step.
c) You can even skip the final cleanup altogether if the segmentation quality is fine.

Whichever you choose, the main thing is that you would do that for ALL images of a study so that you are not introducing a different methodological bias for some images.

In our studies, we find that manual post-processing to remove small unwanted CSF parts (islands) with a tool like ITK-SNAP is super efficient and reliable, but adding missed CSF parts into the segmentation is time consuming and unreliable. Thus, using the output prior to the final cleanup (the segmentation after the ventricle removal) can be optimal (depending on the data). We are applying the tool for infants (a few weeks old), where it seems that such too aggressive clean up is rare. On the other hand in young adults, this can be an issue.

Martin

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