Dear Jesper,
Thank you for your reply.
I still get the same error message when I try to use "--subsamp=8,4,2,2"
even if I also use "--warpres=10,10,12". I.e. "Exception thrown with
message: St9bad_alloc". Is there something else I should try?
This also brings up another point. As you say, EPI warping occurs mainly in
the phase-encoding direction, and only a little bit in the
frequency-encoding direction. I'm confident that there's no significant
warping at all in the z direction (i.e. between slices). So, if I assign a
very high warp resolution in the z-direction, will that save any execution
time by constraining fnirt's search in that direction? Or will these
dimensional constraints have to wait for the new version of fnirt that you
mention is in development?
Your point about choosing more isotropic voxels is well-taken. This
protocol is designed to have slices that match those of other sequences in
our clinical protocols, but I shall try to have more isotropic voxels in our
next iteration.
Thanks again,
William
|