Hi
I am having some problems with brain extraction. We have run BET many times using various parameters and can't get it to successfully remove the skull from a T1 Flair image. Whatever we do we always have some fragments of skull left.
Somone suggested creating a mask in fslview and using the eraser to effectively 'rub out' the sections of skull that remain from the BET extracted image by setting their intensity to 0. When I load the flair image in fslview all the voxels have intensity values. However when I select 'create mask' all the intensity values are set to 0. Furthermore I can't seem to get the Eraser tool to do anything. I can highlight areas with it, but it doesn't change the intensity of them, or remove them from the image.
How are you supposed to use the eraser tool?
What is the best way of removing remaining fragments of the skull after using BET?
Thanks
Rob
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