Dear all,
I am sorry to be sending this again, but I really want to find out
the answer to this problem. I think this could be addressed by
someone who has detailed knowledge of the SPM2 machinery.
I am trying to run the SPM GLM on native space BOLD images as
follows: I created an anatomical ROI on native space anatomical image
first. Then I applied this ROI as a mask to all my BOLD images, thus
creating partial brain BOLD volumes in native (i.e. non-normalized) space.
Now I want to run the GLM on these partial brain images to obtain the
beta parameter estimates. When I check the results, I see that the
resultant analysis mask (mask.img) looks very much like the
anatomical mask that I used in the first place, which is good.
However, when I look at the beta images, I notice that most of the
voxels within the mask (defined by mask.img) have NaN values. I
thought that all voxels within the space defined by the mask should
have non-zero beta values.
That's a problem as I need to get a beta value for every voxel that
is inside the mask. Does anyone have any ideas or suggestions? How do
I fill the whole ROI with beta values? Does this have anything to do
with the fact that I am not using smoothing and normalization?
Please advise. Thank you,
Martin
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