Hi John,
Thanks for that helpful bit of code. I am still trying to figure out exactly what I've got and I
have one more question for you at the moment - if you have time.
You wrote:
> 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.
When it spm_orientations reports back is it telling me what my data actually is, or what SPM
"assumes" it to be?
Thanks,
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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