Hi Johanna,
> I tried registration straight to highres as you suggested. It seemed
> really good but when I tested by drawing some spots to anatomical landmarks and
> running these spots through the same registration (with the same matrices)
> the spots were misplaced in craniocaudal direction. The displacement was not
> great (about 1 cm) but still so much that it is a problem since I am
> trying to disclose a small anatomical area in my analysis.
This seems odd; in the example that you sent, once I turned off the
initial registration, the general accuracy I would say was way better than
1cm. I'm not sure exactly what steps you are going through to do this
test?
> I guess this happens easily when you try to register an axial epi T2 with
> some distortion to sagittal T1 and have to use many degrees of freedom.
> I would like to be able to control the craniocaudal displacement and slice
> tilting by using the T1 FSE axial volume taken with the same slices as the
> epi-volume as initial highres image and giving only 3 DOF in
> epi2initial_highres phase but I cant get a good registration between
> these two.
I think you are saying that you have some EPI distortion, and are looking
for a way to minimise the effect of this. However, with affine
registration, you cannot correct for local distortion, and attempting to
use various different options such as those that you are suggesting is
unlikely to fix the problem. Maybe I'm missing something, sorry!
> You mentioned that the voxel sizes (22 FOV, 64x64 matrix in epi, 22 FOV,
> 256x256 matrix in initial highres) do not match between epi and initial
> highres. To get around this, I changed the voxel size in initial highres
> to be the same as in epi. Now both volumes have 22cm FOV, 64x64 matrix and
> 28 slices.
Ah, no, I'm saying that the voxel sizes in one or other of the original
images was slightly _wrong_, not that they should be set to be the same!
Ie the true voxel size in one or other image was not exactly what was put
into the header. You will need to use greater than 3DOF to find out what
the right ratio of voxel sizes should be.
Thanks, Steve.
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
|