Hello,
I have a PET dataset where I'm interested in evaluating signal in the skull and meninges. I would like to do a voxelwise group comparison, but I'm finding that normalization to MNI with FNIRT causes a great deal of odd warping in structures outside the brain.
I'm aware that FNIRT is optimized for brain normalization and ideally should be conducted with a skull-stripped image, but I was wondering if there are any FSL tools or options that would preferentially maximize the normalization of the skull to MNI space, rather than brain. Does anyone know of these or has anyone been working on a similar issue?
Any help is greatly appreciated! Thanks,
Dan
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