I would like to use SIENA to estimate volume loss with two scans taken of
the same patient.
There exists already at Time 1 a significant amount of brain atrophy which
may be the reason for some of the difficulty that I am having.
When SIENA uses BET, it misses some portions of the brain, while taking in
the orbits and the neck. I have tried to change the fractional intensity
values (using values <0.5) but this has not helped. Are there other options
that I should use in the command line in SIENA?
Alternatively, should I try to remove non-brain tissue manually from each
image and then submit only brain tissue into SIENA?
Thanks in advance!