Hi FreeSurfer Experts,

I am trying to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates in my permutation analysis.

This is a 3 group analysis with 3 covariates (age, sex, and ICV).

After navigating to the glmdir folder of interest, I ran the following code:

X = load('Xg.dat');

The X matrix was 240x12 (see attached file)

Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3
Column 10: zICV for Group 1 and 0s for Group 2 and 0s for Group 3
Column 11: 0s for Group 1 and zICV for Group 2 and 0s for Group 3
Column 12: 0s for Group 1 and 0s for Group 2 and zICV for Group 3

beta = MRIread('beta.mgh');

betamat = fast_vol2mat(beta);

And I got stuck at this step: yhatmat = X(:,[i j k m n])*betamat([i j k m n],:);

I wasn't sure how to modify the code. Is this correct: yhatmat = X(:,[4 5 6 7 8 9 10 11 12])*betamat([4 6 7 8 9 10 11 12],:);

Once I figure out the above step, I will finish with this code:

yhat = beta;

yhat.vol = fast_mat2vol(yhat,yhat.volsize);