[Freesurfer] FSL to FsFast: registration problem

Hi

I used both FSL and FsFast to process a set of fMRI data. after using FSL, I used "reg-feat2anat --feat xxxx.feat --subject xxxx" to check the fMRI to T1 registration in FSL. for some reason, I cannot get the FSL registration to come close to the one done by FsFast (please look at figure at http://web.mit.edu/paymon/www/regis.pdf)

the left most figure, shows the fMRI to t1epi to T1 registration done entirely in FsFast using "autoreg-sess".

the two right most figures, show registrations done in FSL followed by "reg-feat2anat --feat xxxx.feat --subject xxxx".

Visually, the registration done with FsFast looks much better than the ones done with FSL and then transformed to FsFast.

here is my question: should I be suspicious of the my registration process in FSL, or am I not applying reg-feat2anat correctly, and hence causing a poor fMRI to T1 registration.

I am using FSL 3.3.7, and FsFast under nmrenv.

thanks a lot for your help, paymon