Hi Tiffany,
> mat(:,:,1) =
>
> 4.0000 0 0 -128.0000
> 0 4.0000 0 -156.0000
> 0 0 9.2000 -36.8000
> 0 0 0 1.0000
>
>
> mat(:,:,2) =
>
> -4.0000 0.0000 0 126.5593
> -0.0000 -3.8450 -2.5359 160.4999
> 0 -1.1025 8.8436 4.5491
> 0 0 0 1.0000
[others same as mat(:,:,2)]
This looks as though you have just resliced the first image, the
others have been realigned only, but not resliced, so their mat files
encode rotations.
The flipping you mention may also be related to the value of
defaults.analyze.flip in spm_defaults (which you can change if you
need to, though do be careful...)
If you reslice all of them, then other software should at least get
the right data, though the origin and/or axis labels may be incorrect
(basically, *complete* portability between different software just
isn't possible with the Analzye format; one example is that Analyze
can only store integer origins, so e.g. the translation of -36.8 you
see above would have to be rounded or truncated; another is that
flipping Analyze images seems inconsistently implemented in different
software).
If you can use NIfTI with SPM5, then other NIfTI-aware software (e.g.
MRIcron, FSLview, ...) should orient the files exactly as SPM5 does.
Best,
Ged
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