On Sat, 14 Aug 2004, Alex Fornito wrote:
> Hi all,
> I have axially acquired epis that I'm trying to register to the template
> via coronally acquired T1 structurals (via FLIRT in FEAT) and have a
> couple of questions:
> 1 - I'm using a wholehead epi acquired during the same session as the
> initial highres. This is because, although our task epis were supposed to
> be wholehead acquisitions, some of the superior-most slices appear to be
> chopped off. Should I use 3 or 6 DOF?
Assuming that the time series EPI data is a subset of the whlehead epi,
and that there is no chance of rotation between them then DOF=3, i.e,
translation only. However it sounds like you have a reasonable
field-of-view with the time series data, so if there is any rotation, then
DOF=6 should work ok.
> 2 - I've used mricro to change the orientation of the coronal T1
> structural to be the same as the axial epi. However, I've noticed the
> FLIRT FAQ page says the following:
> "Check that the input image looks fine and that the voxel size is correct
> by (a) looking at the images with slices (none of the views should look
> squashed or stretched) and (b) checking the voxel dimensions (pixdim) with
> avwhd (Note: voxel size can be fixed using avwchpixdim)".
> If I view my epis and T1s as they are, the sagittal and cornoal views are
> compressed in the epis, and the axial and sagittal views are compressed in
> the T1s. Does this mean that I need to re-slice the epis and T1s into
> cubic voxels before registering them?
If either of the images looks "compressed" in any axis compared with the
othe axes then that means that your voxel dimensions are wrong - it is
important to fix this in the header before proceeding with registrations.
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