The problem isn't because of the voxel sizes, but is instead because the
images are in different orientations. Did you reslice then realign, or did
you realign and then reslice? If you realign without reslicing (or reslice
before realigning) then the headers will indicate that the images are all in
different orientations. Try this:
P = spm_get(Inf,'*.img','Select the images in the analysis');
VY = spm_vol(P);
R = zeros(numel(VY),12);
for i=1:numel(VY),
R(i,:) = spm_imatrix(VY(i).mat);
end
figure
plot(R)
A few functions in SPM need all the data to be aligned so that a voxel in one
image exactly corresponds to the same voxel in another image. These
functions do not reslice the data on-the-fly (because it is likely to lead to
problems to do with the boundary condidions used for the smoothing). Because
there is no on-the-fly reslicing, the only option is to crash out, reporting
that the images are not aligned voxel-for-voxel.
Best regards,
-John
On Thursday 01 November 2007 01:45, you wrote:
> John,
>
> We have manual ROIs in native voxel space that I'm attempting to use as
> masks in Marsbar on smoothed, non-normalized functional data (3.75 x 3.75 x
> 3.80 mm voxels). However, I can't get out scripts to estimate the models
> and perform the contrasts due to a orientation/voxel size error message.
> The data were acquired in an interleaved fashion, so were resliced and then
> realigned. Each subjects' three runs have the same bounding box and voxel
> dimensions, so I'm uncertain why I keep getting the error message.
>
> Error using ==> spm_fmri_spm_ui
> images do not all have same orientation & voxel size
>
> I attempted the plot visualization using the brief script code:
>
> P = spm_get(Inf,'*.img','Select the images in the analysis');
> VY = spm_vol(P);
> dims = cat(1,VY.dim);
> figure
> plot(dims(:,1:3));
>
> I receive the attached plot graph, which appears to suggest no outliers
> over the course of the three runs. Not certain what's going on. I've also
> attached a single functional image if it would help ferret out the problem.
> I did notice that the voxel and world space were not the same and that
> there are no .mat files for normalized data. So, is it a problem with SPM
> not liking the presence of files with associated .mat files when attempting
> to construct and estimate a model? Our manual ROIs were constructed to
> match the functional world space, not voxel space.
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