Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed