Hi again,
> 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)?
Yes
> Do
> I need to fill
> the rest of the brain and give that a value of zero?
No
> Or if there's
> no mask, does FSL assume that everything else
> outside of the filled
> ROI is zero?
By default in fslview, when you're creating a mask, it
generates an image of the same dimension than the
image of interest you're working on filled with 0
value.
Cheers,
Gwenaelle
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