The SnPM online manual is somewhat out of date. In your SnPM results,
you should look at the column under p_FWE-corr for corrected p-values
for clusters.
The lines you uncommented are probably from the previous version of
SnPM, producing texts for the table heading. Uncommenting these lines
doesn't do much in terms of actual statistical calculation.
-Satoru
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Rajeev Raizada
Sent: Monday, August 25, 2008 11:35 AM
To: [log in to unmask]
Subject: [SPM] Q: Show P(Kmax>=k) in SnPM results figure?
Dear SPM list,
I am using SnPM to perform multiple-comparisons correction,
by calculating the p-val of getting the observed
maximum suprathreshold cluster size.
I would like to display this corrected p-val in the output figure.
According to the SnPM online help, this can be done:
http://www.sph.umich.edu/ni-stat/SnPM/man.html
* P(Kmax>=k): P-value (corrected) for the suprathreshold cluster size.
This is the probability (conditional on the data) of the experiment
giving a suprathreshold cluster of size as or more extreme anywhere
in the statistic image. This is the proportion of the permutation
distribution of the maximal suprathreshold cluster size exceeding
(or equalling) the observed size of the current cluster. This
field is only shown when assessing "spatial extent".
However, in the actual snpm_pp.m code,
the only lines containing 'P(K_{max}>= k)' are all commented out.
This seems to be true both for snpm3 and snpm5.
Simply uncommenting those lines of code doesn't seem to do the trick,
as the extra text that now shows up doesn't fit in with the rest
of the results-window formatting, and seems to have the text-strings
but none of the actual stats numbers.
Any help greatly appreciated,
Many thanks,
Raj
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