> Continuing my investigation of my data using the spm_orientations code,
> I've run across something very confusing to me.
>
> Using the display function, I checked my raw data and my normalized data
> (for both structurals and functionals).  For the structurals, using the
> display function I see that the voxel value changes correspond with the
> output from spm_orientations.  For example, before normalization, using
> SPM2's display function:
> x increases as I move from Anterior to Posterior  (A)
> y increases as I move from Superior to Inferior   (S)
> z increases as I move from Left to Right          (L)
> Correspondingly, the output for spm_orientations indicates my data is Right
> handed, (A,S,L) After Normalization, the structurals are Right handed
> (LPI).  This matches exactly with the T1 template which was the
> normalization target.

So you are working with flip=0.  The handedness of the spatially normalised
images should be the same as that indicated by the flip setting, rather than
that of the template image.

>
> So far, so good.
>
> However...
> When I look at my functional data, there is a discrepancy between what
> happens to my voxel values in Display and what spm_orientations returns.

Look again using the Display button.  If you move the crosshairs to voxel
1,1,1 then you'll find that it is in a different position when you display
using voxel space (compared to the position you get when you display the
anatomical images).  This is because displaying is done so that the images
are visualised within a right-handed system - even if the bytes are stored
using a left handed one.

The best way to check is to look for any negative voxel sizes.

> Also, before normalization, spm_orientations runs without warning messages,
> after normalization, it returns an answer preceded by "Warning, can't get
> default Analyze orientation, assuming flipped".

When you start spm, it runs spm_defaults.m , which loads the default settings,
which are stored in the global variable called 'defaults'.  If you run
spm_orientations without first running spm_defaults, then the routines can
not find defaults.analyze.flip .  If this can not be found, then you get the
warning message, which means exactly what it says.  The routines are assuming
that your data are stored left-handed (i.e. defaults.analyze.flip=1) - which
may not be the correct orientation for you.

For any Analyze format image that does not have a .mat file (created by SPM2),
SPM2 can only determine the handedness using the flip parameter.

> Prior to normalization, looking at my input files in display gives results
> that DO MATCH spm_orientations output.
> Left handed (LAS)

Something is wrong.  LAS indicates right-handed storage.

> After normalization, however, using display
> x increases as I move from Left to Right           (L)
> y increases as I move from Posterior to Anterior   (P)
> z increases as I move from Superior to Inferior    (S)
> spm_orientations returns  Right handed, LPI  instead of LPS.
>
> How can this be?

I can't actually think of any reason at all why SPM would reverse the
direction of the slices when displaying an image.  I would expect the storage
of spatially normalised images to be LPI.

>
> If my data are actually LPS, and SPM2 "thinks" they are LPI, then it would
> appear as if the data are left-right flipped, I think.

Left-right flipped and rotated by 180 degrees.  It may be easier to think in
terms of up-down flipped.

>  It's as if instead
> of standing behind my subject as they are lying down (my view is Superior),
> and my left is their left, I am standing at the foot of the gurney (my view
> is Inferior) and my left is their right.
>
> This would explain why the activation I was expecting to find on the left
> (language activity) is instead predominant on the right.
>
> Still - I don't understand why SPM2 "thinks" LPI after normalization, if my
> data are LPS after normalization particularly as up until normalization,
> spm_orientations and Display agreed about my data.  Presumably this has
> something to do with the Warning message, but I'm still not clear on
> exactly what is happening.

Are you sure they are LPS?

>
> Any help is appreciated.  Many thanks to anyone who manages to slog through
> this!

When do you get the warning message?  If you get it during spatial
normalisation or any time when the data are being changed, then it would be
disasterous.  Not having the defaults loaded is not a problem for most people
who have flip set to 1.  It is a problem if flip is set to zero though.  I
really should have written spm_flip_analyze_images so that that was where the
image handedness was set - rather than by doing it in spm_defaults.m .


Bye for now,
-John