Skull strip with FSL

Hi, everyone!

A small portion of cortex in a superior part in axial and coronal view is removed my T1 and T1-gd datasets after done a skull stripping with FSL. I tried to improve the BET quality through manipulating a coordination, fractional intensity and vertical gradient, but still I can’t recover the small portion of cortex. I applied a brain mask from the T2 imaging with a good quality of BET to both T1 and T1-gd imaging, and this method seems to work. However, this method seems not recommendable as T2 and T1 have a different modalities.

Therefore, Is there other method to improve the BET quality of both T1 and T1-gd imaging in FSL?

Hi there, welcome to Neurostars!

If your T2 image is coregistered to your T1 images, I don’t think that it is bad to use the mask calculated from the T2w image if it looks good.

Here are other suggestions to improve skull stripping:

  • try to correct your input images for bias, with FSL-fast for instance, or N4BiasCorrection from ANTs. This can have a dramatic effect on the brain extraction with BET.

Other options than BET:

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