I’m looking at tracking fibres between the superior colliculus (SC) and the pulvinar. Normally I would use a white matter mask to identify seed locations and the white matter/grey matter boundary for fibre termination. When including the SC this is not possible. What I want to know is can I use a whole brain mask (minus CSF) to specify seed/fibre locations and if I do is probabilistic tracking likely to behave appropriately?
Thanks in advance