Dear John,
thanks a lot for the prompt and informative reply.
> MI-coregistering followed by coregistering by minimising the sum of
squared
> difference (as in realignment) should hopefully just give you the same
answer
> as if you had just used the realignment.
How can I visualize or check for the additional change of MI-coregistered
images which finally underwent additional realignment? Of course, I could
use your realign.m but is there some more easy way to get an overview?
> the filename of a weighting image. When you say the image intensities
> differ, do you mean that the overall scaling is different?
Yes, a bit.
> As the second pass involves aligning all images to an
> average, do you mean that you want to create some kind of a weighted
everage
> of all the images? This can't be done directly, but if you really wanted
to,
> you could tweek the image scalefactors so that the images were weighted
> appropriately beforehand.
No, I did not intend to do that.
> I'm not sure about the weighted target thing. PET/SPECT realignment is a
two
> pass procedure that realigns all images to the first, then creates a mean
of
> these realigned images to which all images are aligned to again.
The defaults button allows weighting of reference image under realignment.
Selecting it one is prompted with the question "Weight the reference image?"
after having selected the scans (even so in the PET module). If one would be
picking "yes", weight registration is marked and one has to select weight
images for each subject (1 scan per subject). Basicly, I am not sure what is
happining here. spm_realign talks about
PW - a filename of a refertence image (reciprocal of standard deviation)
but I donīt get what all this is about and what it is good for...
Also, would people suggest NaNing Tc99m-HMPAO-SPECT images (before any
spatial preprocessing, smoothing etc.) or using an implicit mask (ignore
zeroīs) in the full monty? How is that handeled outside the full monty -
ignoring zeroīs by default?
Thanks a lot in advance and best regards-
Andreas
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