In my study I am analyzing the fibers connections between Pedunculopontine Nucleus (PPN) and others GM locations. Therefore I created a my atlas with 12 ROIs that I used to have the connectivity matrices for all my subjects. I decided to run the tractography by using the PPN (left and right) as seeds locations. After, I used tcksift2 algorithm with the 5tt file. I have only a doubt: tcksift2 works correctly with my tractography that used as initial seeds locations only the PPN and not the whole brain or WM, or it is better that I run the tractography by using, for example, the border of GM/WM as seeds locations and than use my atlas with my 12 ROIs.
I hope that my question is clear.