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