Dear Jorge,
At 17:09 29/07/99 -0700, Jorge Jovicich wrote:
| with SPM96 I could easily get a display of the distribution of z-
| values for a given contrast (for example, by typing hist(SPMt(1,:))
| for the contrast 1). I would like to do the equivalent thing with
| SPM99b for the t-distribution but I seem to be stuck. I don't seem to
| understand how to access the t-values and I am now a bit confused
| about what is in the SPM.mat, con_xxx.img and spmT_xxx.img files.
| While I keep on reading the help pages, would anyone offer some help?
Note that in SPM94/5/6/7 the SPMt.mat file only contained t-statistics for
those voxels (listed in XYZ.mat) at which the F-test for effects of
interest was significant at the specified F-threshold UFp (default 0.05 for
PET, 0.001 for fMRI). Since these voxels are activated for some contrast,
the histogram of the SPMt.mat for a particular contrast is highly likely to
have much heavier tails than the t-distribution expected under the null
hypothesis, even when the null hypothesis is true.
For SPM99, John (in message
http://www.mailbase.ac.uk/lists/spm/1999-07/0159.html surmised below) has
provided a recipe to get a histogram of the t-statistics in the entire
intracerebral volume (i.e. the volume analysed by SPM, shown in the
mask.img file).
If you really do want a histogram of the filtered SPM{t}, then using the
results section, a histogram of the SPM as currently shown (i.e. filtered
by height and spatial extent, and including any masking and/or
conjunctions) can be obtained by typing:
figure
hist(SPM.Z)
See spm_getSPM.m for further documentation on the data structures (such as
the SPM structure) used in the results section.
----------------
At 14:06 30/07/99 +0100, John Ashburner wrote:
| The attached program should produce the histograms you are after.
| To call it, type:
|
| V = spm_vol(spm_get(1,'*.img','Select image...'));
| [n, x] = histvol(V, 100);
| figure;
| bar(x,n);
|
| I will let someone else explain the contents of the SPM.mat,
| con_xxx.img and spmT_xxx.img files.
The SPM.mat file contains all the design and global (i.e. not
voxel-specific) estimation information after the parameter estimation stage
has been run. SPM.mat is written by program spm_spm.m, where it is
documented.
For each t-contrast, the con_xxxx.img file contains the contrast of the
parameter estimates (e.g. the difference in condition effects). The
spmT_xxxx.img file contains the t-statistic, which has a Student's
t-distribution under the null hypothesis that the contrast is zero, and is
formed by dividing the contrast image by the square root of the variance
image (ResMS.img) and scaling appropriately. Voxels outside the analysis
volume are coded as NaN (hence the "isfinite" command in John's "histvol").
For F-contrasts, the files are ess_xxxx.img & spmF_xxxx.img. The "xxxx"
numbers correspond to the contrast numbers in the contrast manager. These
files are written by spm_getSPM.m, where they will (eventually) be
documented.
----------------
Hope this helps,
-andrew
+- Dr Andrew Holmes ------------------ mailto:[log in to unmask] -+
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