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 howgood 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:
- Is there anyway to improve this registration?
- 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