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 lgreater 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

 

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