Hi Mark,
>Anyway, I had a look at the mag to spgr registration and there is a huge
>scale difference. It was over 15% which is really pretty big. If these were
>of the same individual then something is wrong. I'd suggest double checking the
>voxel sizes as that is normally what gets set wrong.
You were exactly right. The voxel sizes were wrongly specified during
reconstruction. But, why is that important? That is, during normal registration we
have brains of different shapes and sizes, and flirt scales them all to the standard
brain. It seems to me that all flirt would have to do is scale this brain down by 15% in
one or more dimensions. Clearly, I'm missing something about how flirt works.
>As for fugue, it requires a pair of phase images to calculate the phase
>difference, which is proportional to the field (it needs a 4D analyze
>format - I keep meaning to add alternative input options, but for the moment use
>avwmerge if you have them separately). That's why it is complaining.
I'm confused. The input to fugue is
-i <unwarped-image> -p <unwrapped phase map> -d <swell-to-asym-ratio> -w <
epi-like-result>
Are you saying that the <unwrapped phase map> is really two concatenated
images? I thought the phase map is the result of calculating the phase difference.
jack
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