Dear Doug,

I don't know if I am doing something wrong but when I run the simulation under QDEC I am not getting the  csdbase.y.ocn.dat file. The only files that I get under after running the  simulation under QDEC are:
mc-z.abs.th20.sig.cluster.summary, mc-z.abs.th20.sig.ocn.annot,mc-z.abs.th20.sig.ocn.mgh while QDEC output file are: Contrasts, lh_Avg-Intercept-thickness, lh_Avg-thickness-Age-Cor. In the last two files I have sig.mgh so I am not sure on what file should I run the simulation and why Monte Carlo does not give me as an output the file I want as a .dat.

Because I want to do a study and eliminate age, I choose as a Continuous Variable: Age and as a Discrete Variable: Class and I highlight them in QDEC in the Design window. What if I my discrete variable is not highlighted? Also, Age is coming under Nuisance Factors but do I need to highlight this?

Thank you very much for your help.
Antonella

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, September 26, 2011 11:19 AM
Subject: Re: [Freesurfer] QDEC stats table output

You can run mri_glmfit-sim on the QDEC output directory. Or you can run
the simulation from within QDEC. Both will give you this output file.
doug

Antonella Kis wrote:
> Dear Doug,
>
> I got this results while I was running the GLM simulation but I wonder
> if there is a way to get under QDEC (when I run QDEC from the
> interface) and I am using the FDR and Monte Carlo simulation. In this
> case I am not getting any output as in GLM from which I got the
> csdbase.y.ocn.dat.
> While using QDEC I can get the thickness on the graph which is one
> point in the cluster, not the mean of the cluster.
> Is there a way to change the cluster into binary data (I am not sure)
> and then extract the mean thickness of that cluster or how I can get
> under QDEC the average thickness of the clusters?
>
>
> Many thanks,
> Antonella
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* Antonella Kis <atorok9@yahoo.com>
> *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Monday, September 26, 2011 10:23 AM
> *Subject:* Re: [Freesurfer] QDEC stats table output
>
> Will this work (this is from running mri_glmfit-sim --help, which has
> even more info):
>
> csdbase.y.ocn.dat - this is a summary of the input (y) over each
> cluster. It has a column for each cluster. Each row is a subject. The
> value is the average of the input (y) in each cluster. This is a
> simple text file.
>
>
> Antonella Kis wrote:
> >
> >
> > Hi,
> > After running QDEC, I would like to  output in a table the average
> > value for the cortical thickness within each clusters. I know this is
> > a dependent variable and I can see the values on the plot but is there
> > a way that I can get this values in a table ?
> > Thanks,
> > Antonella
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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