> 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
