Try using the data in the csdbase.y.ocn.dat file rather than transferring the clusters back into the individual space. What are you using to do the ROI-based analysis? You have to make sure that the design matrix and contrasts are exactly the same. You can do this in matlab with FS commmands, eg,

X = load('Xg.dat'); % Xg.dat created by qdec

[beta rvar] = fast_glmfit(y,X); % y is the vector of average areas, one row for each subject, one column for each cluster

C = load('contrastfolder/C.dat'); % Created by qdec

[F p] = fast_fratio(beta,X,rvar,C);

p will be a vector of p-values

On 11/24/2016 04:43 AM, Yaakub, Siti Nurbaya wrote:

Dear Experts,

I'm looking at differences in area between two groups of subjects in FreeSurfer using qdec. I've delineated an ROI based on a cluster that showed significant differences in surface area between the two groups (taking gender into account, and with age and ICV as nuisance covariates). As a sanity check, I extracted the total surface area values for that ROI for each subject in native space (using mri_label2label and mris_anatomical_stats) When I plot these values (and do an ANCOVA with the same covariates, or even just a simple t-test) there is almost no difference between the groups. Did I do something wrong? How do I get the average surface area values for each subject (in that ROI that shows a difference) so I can see the spread of values in each group?

Thanks, Siti

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