What is the optimal brain mask?


Hello ,
As I am a really new player in DTI image processing, I have a very simple question : what is the optimal brain mask that I should obtain ? Do I have to exclude eyeballs even if I want to asses optical nerves ? Could I expect to analyse some facial nerves with “classic” DTI acquisition (i.e. ~32 dir).
Thanks for your help.


Well, ideally it’s the selection of voxels that contain tissue of interest. How that is defined is actually relatively vague, but generally understood to include the brain (both cerebellar hemispheres, cerebellum and brain stem) and ventricles.

The main point of the brain mask in the initial stages of processing is actually primarily to restrict the amount of time spent processing non-brain regions. So I’d say the ‘optimal’ mask should contain all the tissue you’re interested in analysing, even if that means including a lot more than just brain. There are however some steps that can be adversely influenced by a poor mask, like dwi2response for example. So it’s worth getting it right.

But even then, the notion of ‘optimality’ is loosely defined. How much tissue does a voxel need to contain to be eligible for inclusion? This would influence which voxels at the edge of the brain are included. And then there is the target application, which in your case clearly influences the masking.

Well, you can’t assess the tissue in voxels where the analysis has not been performed. In your case, you clearly need to make sure the mask includes all portions of the optic nerves that you’re interested in. This may require manual editing. Whether you include the eyeballs is up to you – maybe you want to look at the retina too? But there’s no reason to include them if you’re not going to look at them.

That depends entirely on what you’re trying to do, which relates to your research question, which is a much deeper issue than we can address here, based on the information provided. You can certainly do some analyses with 32 directions (I assume b=1000 s/mm²?), but you probably won’t have the power to do some of the more advanced stuff…