Dear Dianne,
>Hello All,
>
>I seem to have confused myself about left and right...so I need to touch base
>with some experts.
>
>Here's the scenario:
>We collect a functional spiral file and T1 in radiological orientation.
>
>
left is right
>However, we collect our high resolution spgrs in neurological orientation.
>
>
left is left
>We use the default defaults.analyze.flip=1 for spm2 because the functional and
>T1 are indeed radiological.
>
>
right (will flip the data)
>However, we L-R flip the spgr so that it will be in radiological orientation as
>well....this flipping is, of course, recorded in the mat file.
>
>
right
>Now, when spm2 displays any of our images, it will look at the
>defaults.analyze.flip=1
>and it will display everything in neurological orientation (flipped)...
>
>
right
>
>BUT, doesn't spm2 also know that we have flipped the spgr L-R? If so, what are
>it's assumptions in displaying that image?
>
>Possibility 1) It displays the image correctly because it reads
>defaults.analyze.flip=1....assumes the image is radiological (which it is now),
>and flips the display into neurological. End of Story.
>
>Possibility 2) It tries to be clever...assumes we started with the spgr in
>radiological, that we flipped it into neurological and now it does NOT flip
>again when it displays. (If this is the case, then we see the wrong thing
>because it now displays the spgr in neurological orientation.
>
>
I don't know how SPM does it, but it does! (sure that someone will
answer that ;-) , maybe flips 2 times the image). It will show you the
spgr in neurological orientation. Note that SPM does not really flip the
image, it's only stored in the .mat file. If you're not sure, I suggest
you to flip your images with MRIcro (or other soft) and compare the
results ...
Hope it helps,
cyril
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