Dear Christine,
On 2005-05-26 (Thu) at 20:00:44 +0100, Christine Cox <[log in to unmask]> wrote:
>
> This does not, however, seem to be a MarsBaR-specific problem since plotting
> the contrast estimates in SPM yields similarly high values.
>
I have encountered a similar problem earlier and I suspect that Marsbar
renders c'*beta as a plot (SPM's plot button does this for sure). Thus,
what you see in the plots is a scaled version of your parameter
estimate, NOT the real values from the images. In some case, the
effects of interest contrast matrix contains some unreasonably high
values in the range of several hunderds to tousands. Will Penny has
once explained to a collegue of mine this could be an effect of
a "non-settled" non-spericity correction and suggested that to
re-estimate the design without correction for non-spherical errors.
So, I suggest that you have a look at the contrast matrix of the
contrast that you are plotting against (usually an effects of interest).
The contrast matrix of the effects of interest is stored in
SPM.xCon(1).c. If you find very high value there, they a most likely
causing these high contrast values that you are see.
In order to access the real values of your parameter estimates, try the
following:
xyzmm = [-10 3 24]'; % your coordinates in a 3x1 matrix in world space (mm)
% convert your mm-coordinates to voxel coordinates (you will find the
% function mm2vox.m in the attachment)
xyzvx = mm2vox(xyzmm,SPM.xY.VY(1).mat)
beta = spm_get_data(SPM.xY.VY,xyzvx)
Good luck,
Jan
--
Jan Gläscher NeuroImage Nord
+49-40-42803-7890 (office) Institute for Systems Neuroscience, Bldg S10
+49-40-42803-9955 (fax) University Medical Center Hamburg-Eppendorf
[log in to unmask] Martinistr. 52
20246 Hamburg
Germany
http://www.uke.uni-hamburg.de/kliniken/neurologie/index_16969.php
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GnuPG/PGP key id: FEC4B55C
fingerprint: 5A36 1EF6 8472 117E 805A F240 3146 A410 FEC4 B55C
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function cp = mm2vox(mm,mat);
cp = inv(mat)*[mm; ones(1,size(mm,2))];
cp = cp(1:3,:);
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