Re: [Freesurfer] qdec contrast and data extraction

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:

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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." <DGREVE@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-37a4-1be9-2252-0bccc833a218@mgh.harvard.edu>
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 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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 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: jomaximo@uabmc.edu<mailto:jomaximo@uabmc.edu>

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