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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 

Many thanks,

    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:
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    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 
    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.
    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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