Look  in the *.y.ocn.dat file.

 From mri_glmfit-sim --help

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.



On 9/3/2019 5:16 PM, Maximo, Jose Omar wrote:
>          External Email - Use Caution
>
> Hi,
>
> Which specific file should I load? I see cluster.mgh, cluster.summary, 
> sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat.
>
> How can I extract the values from fsaverage space?
>
> Basically, what is the correct way to extract values from these significant 
> clusters?
>
> Many thanks,
> Omar
>
>      Date: Tue, 3 Sep 2019 15:15:02 +0000
>      From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
>      Subject: Re: [Freesurfer] qdec contrast and data extraction
>      To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>      Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a...@mgh.harvard.edu>
>      Content-Type: text/plain; charset="utf-8"
>      
>      You might have done something wrong along the way. When you run the 
> montecarlo correction, it will create a file with the thickness values in it 
> for each cluster. the first thing to do is to load that and see if you see 
> the expected differences. The other thing is to not go back into native space 
> to extract the numbers. There are several operations that happen as it moves 
> into fsaverage space and in preparation for group analysis (interpolation, 
> and smoothing); sometimes these make a big difference. if the ROI is small, 
> it may not map accurately back into the native space (and you should not need 
> to draw it in the first place)
>      
>      On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:
>      
>              External Email - Use Caution
>      Hi,
>      
>      I have a question:
>      
>      My design is 2 groups (HC and Patients in that respective order) and 2 
> nuisance factors (age and eTIV). When I look at the average volume difference 
> between the 2 groups, I get blue and red clusters. I presume the color coding 
> is where each group is greater than the other (Blue = Patients > HC and Red = 
> HC > Patients).
>      
>      Then, I processed to extract individual values from each cluster in 
> order to plot them. When I extract data from the blue clusters and plot them, 
> the two groups show no difference in thickness at all, whereas when I look at 
> volume, HC show more than patients in blue clusters (see attached figure). I 
> would assume that both figures would show patients > HC based on the negative 
> statistic.
>      
>      Am I interpreting the colors wrong? Or am I doing something wrong?
>      
>      These are my steps 1) After applying montecarlo correction, I drew my 
> ROIs to extract the data from; 2) map it onto every single subject; and then 
> 3) used mris_anatomical_stats to extract the data from each subject.
>      
>      Any suggestions are welcome.
>      
>      Best,
>      Omar
>      
>      Jose O. Maximo, Ph.D. | Postdoctoral Fellow
>      Department of Psychiatry & Behavioral Neurobiology
>      UAB School of Medicine
>      University of Alabama at Birmingham
>      Cell Phone: (619) 252-3492
>      Email: jomax...@uabmc.edu<mailto:jomax...@uabmc.edu>
>      
>      
>
>
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