I guess if you all you’re interested in are the fibres within the subplate, your approach would be fine. I was assuming you were interested in fibres specifically connecting cortical to ventricular regions… In which case you’d use one ROI as the seed region, and the other as the include region.
However, you clearly still have issues with your gradient directions. Have you tried inverting the z-axis as we discussed a while back…?
As far as dwi2fod goes, you should use a brain mask for that - or no mask if you don’t mind the longer runtime. The mask for dwi2fod is just to restrict the computation to the brain to speed things up, it’s not actually a requirement. The masks you use for tractography are there to specify regions of interest, and as such have nothing to do with the mask used in dwi2fod…