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