Dear all,
I am just reporting back to let you know that turning off the
analysis threshold took care of my original problem. Thank you all
for your input.
Martin
At 08:04 AM 2/5/2006, Thomas Nichols wrote:
>Sounds like a analysis threshold problem. Turn off the analysis theshold
>mask (ie set it to -Inf) and see if that fixes it (see the fMRI
>thresholding gem 12 here http://www.sph.umich.edu/~nichols/JohnsGems2.html )
>
>Let the list know if this works.
>
>-Tom
>
>
>...... Original Message .......
>On Sun, 5 Feb 2006 06:44:04 -0800 "Martin Zalesak" <[log in to unmask]> wrote:
> > 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
> >
> >
|