Dear Valeria:
Actually the thresholds for the masking are set in spm_fmri_spm_ui.m
around the line where is says "Compute Global Covariate." For fMRI an
average is computed for all the voxels in a slice and for voxels to
survive they have to have an intensity that is 100% of that average
or greater. In usual fmri data since you have a whole bunch of 0's
outside the brain (or values close to 0 anyway) it's no problem for
the in-brain voxels to exceed that average. For your data in which
the slices are simulated it's possible that the average (consisting
of noise and signal voxels) has a greater value than your signal
voxels.
You could try changing the value of GM to 0. I don't know what line
it is but it's in spm_fmri_spm_ui.m and the line above it looks like
this.
%-Compute Global variate
%-----------------------------------------------------------------------
GM = 100;
I think that will work, but hopefully John will respond if I'm not correct.
regards,
Darren
>Hi all, we were wondering whether anyone can help us figure out this little
>problem we have.
>
>We are trying to run SPM on a simulated data set, which contains voxels
>with gaussian noise and several actived voxels with an ideal hemodynamic
>response. The dynamic range of data values is between 0 and 32767.
>Whenever we apply fMRI model on the data set in SPM99, it gives us the
>following error messages:
>
>-----------------------------------------------------------------------
>Warning: No inmask voxels - empty analysis!
> > In /home/wilkin/spm_spm.m at line 1076
> In /software/spm99/spm_fmri_spm_ui.m at line 619
>Design parameters : ...intrinsic autocorrelation
>Warning: Divide by zero.
>-----------------------------------------------------------------------
>
>We have tried several different setting and still get the same error. It
>appears that SPM99 applies some kind of scaling during the preprocessing
>steps. As the results, there is not voxel survive from the masking
>operation done by the script of "spm_spm.m".
>
>any suggestions of what can be causing this problem?
>
>thanks a lot
>Wilkin Chau
>Valeria Della Maggiore
Darren R. Gitelman, M.D.
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