Using --t2 and --bold will always give identical results. If there is not much G/W contrast in the MRA (and there probably isn't), then you can try using the pial surface instead (maybe more GM/CSF contrast). Use --surf pial --t1. Use --t1 here because the GM will probably be brighter than CSF.
doug
On 08/20/2014 04:54 PM, SHAHIN NASR wrote:
Hi Surfers I want to use bbregister to register my MRA scans to the structural scans. The first attempts by using these parameters came out OK but not perfect:
bbregister --s <Subject_ID> --mov MRA.nii --init-fsl --reg register.dat --bold
However, there are obvious problems around frontal areas.
I have to admit that one of the reasons for this imperfect registration may be that MRA scans do not cover the whole brain. However, they still cover a large portion of it. I was wondering if there is any argument in bbregister command that may help me improve the quality. It is very fine if it increases the registration time.
Regards
P.S.: using --t2 in bbregister (instead of --bold) generated the same outcome but --t1 was completely off. -- Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School