Hi Gwenaelle,
>> 1) load the mean_FA_skeleton into FSLview (or should
>> I use the MNI152?)
> I would recommend the mean_FA_skeleton on top of
> mean_FA so you can draw *grossly* a mask of the
> cerebellum and/or the brainstem white matter, and then
> mask it with the mean_FA_skeleton (fslmaths
> mycerebellum_mask -mas mean_FA_skeleton_mask
> myfinal_mask).
Can I ask you a question about drawing the mask in FSLview. I've set
the pen value to 1 and filled the cerebellum. Is this the same as
ascribing a value of 1 to the brain (as in BET)? Do I need to fill
the rest of the brain and give that a value of zero? Or if there's
no mask, does FSL assume that everything else outside of the filled
ROI is zero?
Thanks
Suzanna
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