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
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