Dear Dr Reinsel,
> I notice that SPM96 prints only a few of the significant locations in a
> given cluster, whereas SPM95 used to print a long list of secondary foci.
> I recall some email from many months ago which said the additional
> significant locations are stored in the XYZ.mat file.
> This is a binary file, however, and since I'm not a matlab maven, I don't
> know how to open it for viewing.
> Do you have a "magic word" to give me?
Sorry to add a third reply to this but it may be worth noting that the
XYZ.mat contains a single matrix, called XYZ, with three rows, (1 = X
coordinate relative to AC, 2 = Y, 3 = Z), and as many columns as there were
voxels remaining in the analysis after application of gray matter and F
threshold. Other matrices contain the results of the analysis in similar
format. In particular, the SPMt.mat file contains a matrix, SPMt, with
one row for each contrast in the analysis, and a column for each voxel, each
value being the Z score for that voxel. Of course the SPM interface will give
you the Z value for a particular voxel, in the results section, if you type
in the coordinates in the boxes provided. Neither this interface nor the
underlying matrices will directly tell you more about 'secondary foci' than
the output you know about already, though. If you wanted to replicate the
SPM results interface to get the Z score, you might try code like this,
to return (and print) the Z value in the variable Z:
coord = [0 0 0]; % coordinates of Z score required
contrast = 1; % contrast of interest
load XYZ
load SPMt
Col = find((XYZ(1, :) == coord(1)) & (XYZ(2, :) == coord(2)) ...
& (XYZ(3, :) == coord(3)));
if isempty(Col)
error('There are no data for these coordinates');
end
Z = SPMt(contrast, Col)
If you wanted the underlying corrected data, as used in the plot function in
SPM, then it may be worth trying my little getvoxdata utility:
ftp://ftp.physiol.ox.ac.uk/pub/matthew.brett/spm96/getvoxdata.m
which should I hope be relatively self-explanatory.
Hope that adds something,
Matthew
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