Hi again,
> Wherein lies my confusion. The EPI is a low-res image. The T1 is a hi-res
> image. If scaling is not involved, how can an alignment or an overlap occur,
> especially since the resolution is not changed? It obviously does, so what
> am I understanding wrong here?
I think that your confusion stems from the fact that you assume one can
only match immages voxel-by-voxel. However, you can still minimize the
diffferences (by optimizing the histogram) without matching each voxel
with a corresponding one. Consider a small and a large book lying on a
desk: they will, without scaling, never be the same, but they can be
"much more similar" if they are aligned well. I guess that is a bad
example (as in coregistration, the two images typically cover the same
head but with different resolutions) but I can't think of a better one
right now...
> I do intend to perform all three, realign, coreg and normalize, in that
> order. When would I reslice? Do I reslice at realign and estimate for both
> coreg and normalize or do I estimate for realign and coreg, and
> estimate&reslice for normalize?
The idea is that you refrain from data interpolation as much as
possible. In your case, you would do
realign (estimate only: parameters are stored in the header)
coregister (say, mean EPI to anatomical, specifying all other EPIs as
"other"; the parameters are combined with the previous step and stored
in the header)
normalize (estimate and write; as you cannot implement the non-linear
steps of spatial normalization in the header, you have to write out the
images in this step if you want to do smoothing and statistics; the
parameters from the previous 2 steps are taken into account)
Voila: three steps, one interpolation. Generate results, write paper,
become famous - science can be just great :)
Hope this helps,
Marko
--
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Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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