John Ashburner wrote:
>In SPM2, the defaults.analyze.flip is only used when working out the
>orientations of images without a .mat file (or a .mat file created with
>SPM99). If there is a .mat file, then defaults.analyze.flip, the origin
>field, and the voxel sizes are all ignored.
>
>If you use the DICOM conversion in SPM2, then images should be created with a
>.mat file (unless they are exactly axial and the origin is at the exact
>centre of a voxel). The conversion routine will take the value of the flip
>in order to figure out whether the order that the voxels are stored in should
>be left- or right- handed. The values in the .mat file are set so that
>images are displayed using a right-handed system.
>
I'm still confused.
For example, the data for the FIAC contest is in SPM ANALYZE format, with
accompanying .mat files. According to what I read above, and what I read in
the SPM Data format page, that should clearly define all three axes'
orientations.
And yet, for some reason the FIAC contest description then contains the
following
sentence:"With these 'mat' files, the images are considered in the
radiological
convention (Left is Right)."
Would the average SPM user, despite SPM's clear definition of axis
orders and
orientations via the mat file, assume this means that instead of L-R,P-A,I-S
axes, you actually have R-L,P-A,I-S axes after applying the transformation
in the matrix?
We've already asked JBP for clarification specifically about this
contest data,
but I see this terminology a lot when I'm supporting SPM users, and
would like
to know how it is intended to be. Can you offer any additional
clarification?
rich
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