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 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. 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".
Prior to normalization, looking at my input files in display gives results that DO MATCH
spm_orientations output.
Left handed (LAS)
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?
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. 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.
Any help is appreciated. Many thanks to anyone who manages to slog through this!
Best,
Juliana
On Wed, 25 May 2005 12:53:26 +0000
John Ashburner <[log in to unmask]> wrote:
>
>> I have data for which I confirmed that the left, posterior, inferior corner
>> had the lowest values and were all positive (voxel [1 1 1] was off screen).
>> This means, I think, that my data are right handed
>
> If your data are stored axially, so that the fastest changing direction (i.e.
> the first element of the voxel coordinate) in the file is left->right, the
> middle (second element of voxel coordinate) is posterior->anterior and the
> slowest (third element) is inferior->superior.
>
>> and therefore the
>> defaults.analyze.flip value should be set to 0.
>
> Is all your data in this orientation or just this particular case? Does
> everybody you share data with (now and in the future) have the same
> value set for flip?
>
> If this dataset is just a one-off, then you should ensure that it is all in
> the correct orientation before you do anything at all to it, where correct is
> defined by the value you have for defaults.analyze.flip.
>
> Note that defaults.analyze.flip only has an effect on Analyze files that have
> no .mat file associated with them. SPM should know the correct orientation
> for all other files. I have attached a small .m file that should help. Once
> it is somewhere in your path, then all you need to do is type:
>
> spm_orientations
>
> and then select the files that you want to check. It will then report whether
> SPM assumes that your data are stored with a right or left handed system, the
> position of the first voxel, and the ordering of the data.
>
>> The raw images I was
>> loading in and checking for LPI voxel values were .mnc files. I also
>> confirmed that the analyzed results had the low value voxels in the LPI
>> corner.
>>
>> However, after analyzing the data, I am finding language activation
>> bilaterally, but stronger on the right (i.e. on the right in the glass
>> brain). The subjects are children, and the task was somewhat difficult for
>> them so it is remotely possible, though not likely, that these results are
>> accurate. More likely, however, I am making some mistake and the images
>> are either not right handed or there is some other kind of problem.
>>
>> If anyone has any suggestions for how I can further test to be sure that my
>> data are indeed right handed and/or can spot where I'm making a mistake
>> either in setting the default to 0, or in reading the results, that would
>> be much appreciated.
>
> I hope the function will help you.
>
> Best regards,
> -John
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