Dear Douglas,

Thank you for your advice.
It works like magic.
I have one more question.
In qdec gui, I found some small areas in two-group comparision with two discrete variables (diagnosis and gender) and two nuisance variables (ICV, age). 
Then processed monte-carlo simulation with 1.3 abs.
->Finally got three significant areas

Now your code gave me the mean thickness of three areas.
However, When I run stats with SPSS, (independent group t-test, ANCOVA using GLM multivariate), the p-value is far from significant (.05).

Is there any mistake, or I ran wrong stats with SPSS?

Again, Thanks for your advice : )
-June

On Jul 2, 2014, at 11:28 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:


In QDEC, there is not a way to do this, but you can do it from the 
command line. If you cd to where the qdec output is (it might be a 
folder called Untitled in your $SUBJECTS_DIR), then run

mri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 1.3 abs 
--2spaces

This will only take a minute or so to run. In each contrast folder, 
there will be a file called
cache.th13.abs.sig.cluster.summary with a list of clusters and a file 
called cache.th13.abs.y.ocn.dat which
will have a column for each cluster and a row for each subject. You can 
compute statistics from this.

Note that the clusters found this way should be the same as with qdec, 
but might not be if the threshold parameters are not identical.

doug




On 07/02/2014 04:14 AM, June k. wrote:
Dear surfers.
I’ve analyzed 2 group comparison data using qdec gui.
I got some significant clusters after Monte-carlo simulation with 1.3, absolute.
However, I have no idea to get thickness value of each group in the significant areas.

Is there any way to extract mean (and S.D. if possible) thickness of the area shown in gui analysis after monte-carlo simulation?

-Sincerely, June.




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