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?
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?
Thanks for your help,