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

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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