Comparing to zero

Tom Holroyd tomh at KURAGE.NIMH.NIH.GOV
Thu Jun 23 16:18:43 CEST 2005

> What would be the best way to find clusters that are significally
> different from zero?

One way is to to a group analysis using AFNI.  I'm using that for
coherences---here's a snippet.

[source] = sourceanalysis(cfg, freq);
[source] = sourcedescriptives([], source);

brikname = 'blah';
[err, errmsg, info] = writesourcebrik(source, source.avg.coh, brikname);
if err

I've attached writesourcebrik.m, which sets things up to write a brik in a
format that is compatible with CTF datasets, although that's not really
important.  It uses a function called WriteBrik.m from the AFNI library, you can
get that from the same website where you get AFNI.  Once you have a set of
datasets in BRIK format, you can do the test using 3dttest.  You have to first
warp all your datasets to some common space such as Talairach or MNI (AFNI is
more at home with Talairach), using adwarp.  Then something like

3dttest -prefix outname -base1 0 -set2 subj1+tlrc subj2+tlrc ... subN+tlrc

will do the test.  There's a randpermute function that does the non-parametric
correction on our website, too, at

Dr. Tom Holroyd
"A man of genius makes no mistakes. His errors are volitional and
are the portals of discovery." -- James Joyce
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