For the record, I applied two changes:

1) I used my AAScout scan as --int and it worked.  
2) As you suggested I also used --t2 rather than --t1 this time and it also helped.  

Combination of these two changes worked very well.

Thanks

On Tue, Sep 30, 2014 at 1:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

A couple of suggestions ...

It looks like the new sequence is T2 weighted, so you can try using --t2 with the white surface

It may be that the fsl is not initializing the BBR registration properly. Try using spm (which may still fail because it is partial brain coverage). Do you have a whole-brain volume that was acquired during the same session as the MRA? If not, you should start collecting this. If so, then use that as an intermediate (--int). It will use fsl/spm to register the whole-brain to the anatomical using standard volume reg, then transfer that registration to the partial FoV assuming that the whole and partial share a scanner space (which they will if acquired at the same time). The intermediate can be anything, eg, fMRI, anatomical, B0 map, low-b DTI volume.

doug






On 09/30/2014 12:41 PM, SHAHIN NASR wrote:
Hi Doug,
    Sorry for interrupting you again with this topic but recently we changed couple of parameters in our MRA to increase our chance or detecting veins.  The problem is that, bbregister can not register the MRA volume to T1 scans anymore.

    As an example, here you can see the old version of our MRA and how good it was when we used T1+pial registeration:

tkregister2 --mov /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/001_nu.nii --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/register_t1_pial.dat --surf

    And here, you can see the new one:

tkregister2 --mov /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/001_nu.nii --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_TOF_2D_500_fa70_cor/018/register_t1_pial.dat --surf

Now I have two questions:
1) Is there anyway to improve this registration?
2) Since I collect both MRA types in one session, can I use the good volume (or registrations) to help registering the second volume?  I  actually used --init-reg but it did not help.

Regards

On Wed, Aug 20, 2014 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:


    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 <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





--
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
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





--
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School