Dear Krish,
Interesting questions:
[log in to unmask] said:
> 1) Take a set of high-resolution T1 weighted slices in the same plane
> and with the same FOV as the EPI slices. Normalise this to the T1
> template and then apply the normalisation parameters to each EPI
> volume.
> 2) Take a high-resolution multi-shot EPI image, again with exactly the
> same parameters as the single -shot functional EPIs, normalise this to
> the EPI Template and then apply the normalisation parameters to the
> single-shot functional EPIs
> 3) Simply normalise the single-shot functional EPI (usually the mean
> image from the realignment) to the EPI template.
My ill-informed 2 new pence:
1) is obviously dangerous, and more so at higher field, because of the
distortions of EPI relative to the structural. The distortions are much
greater in the phase encode direction, so I guess if your activation is at the
extremes of the brain in that direction (say AP = Y direction), and there is a
reasonable difference in susceptibility between subjects, you will lose
activation by averaging between subjects. The distortions will mean that the
functional images are misregistered with the template.
2) Not easy, as the high resolution is nearly always (as I understand it) a
compromise, as you cannot reproduce exactly the same EPI parameters, as for
the functionals, and get a higher resolution image. So, you usually end up
with intermediate structural functional mismatch
3) A little dangerous - particularly because of the holes in the functional
images, and the dangers are difficult to quantify. A large problem is that you
cannot accurately match the subject's own structural scan to their activation,
but I guess that's a given.
We do 3, for now, and are trying to optimise it as best we can.
I would like to do a variant of 1) i.e. to use some estimate of the EPI
distortions relative to the functional to better match the two images - e.g
using phase maps - a la
P. Jezzard, S. Clare, "Sources of Distortion in Functional MRI Data", Human Brain Mapping, 8, 80-85 (1999),
and we are working on that at the moment.
Perhaps someone who knows more physics than me can clarify / correct? But
that's my understanding...
Cheers,
Matthew
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