Dear FSL list,

I'm trying to play around a little bit with FIRST in order to get the best in term on striatum (putamen + caudate, no accumbens) segmentation. One of the things that I thought to try is to include a third registration step in first_flirt using a mask of the striatum.
So I created a mask of the striatum tresholding the Harvard Oxford subcortical atlas (1mm) and I entered this image in first_flirt with the following call

first_flirt ${dirroot}${subject}_T1 ${dirroot}${subject}_firstflirt_p4 -strucweight ${Striatum}

What I obtain can be seen attached: the registrations look totally wrong, in different ways (mainly over-zoomed or strangely rotated).
Have any one an idea of what I'm doing wrong ? Do you think the cost-benefit ratio of applying  the third registration is interesting ?

Thanks in advance and best

Alain



Bad registration 1

Bad registration 2


Striatum mask