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." <[email protected]> > Subject: Re: [Freesurfer] qdec contrast and data extraction > To: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > 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: [email protected]<mailto:[email protected]> > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
