Pulling a skull from MR

[lassoan (Andras Lasso)]

I woild recommend the HDBrainExtraction extension for skull stripping. See some more details in this recent discussion:

Brain Segmentation in MR

It looks like you correctly created a brain mask segmentation in white, and a new skull-stripped volume. The green segment looks like it is from a different segmentation node created from threshold of the image before skull stripping. If you go back to the data view, you can turn off the node named ‘Segmentation’ with the green head label to see only the brain mask label in white.