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Dear Freesurfer Experts,
I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools.
I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3).
I am trying to use LME model with random effects y-int and time from the base line.
Based on the LME tutorial and the questions and answers from Freesurfer support list:
Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ....
To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools
C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)];
Based on the tutorial I run the following functions.
rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig');
nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end;
rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh');
[detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0);
fs_write_Y(sided_pval,rhmri1,'spval.mgh');
When I view sig.mgh using tksurfer I see regions with red and blue color.
1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is larger than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file?
With regards
Getaneh