Hi Han,
Try to find a local statistician to help you with your analysis.
About your matrix: rows need to be number of all time points from all subject. Time 2 should probably not be there. Also columns 7-9 need to be dropped (they are just the negative of the rows before).

On May 21, 2016 3:32 PM, Hanbyul Cho <hanbyul.h.cho@gmail.com> wrote:

Dear FreeSurfer Team,

I processed in MATLAB for Linear Mixed Effects Models Analysis with this X matrix:

X matrix is 'Subjects N X 11', 11 columns are as follow,

1. Intercept (all '1')
2. time (from baseline time point)
3. time2
4. Patients group = 1, Control = 0
5. 4.X time
6. 4.X time2
7. Patients group = 0, Control = 1
8. 7. X time
9. 8. X time2
10. age
11. extra values for covariate

1.
When I process this command,
[lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4)
The MATLAB windows print the warning alarm repeatedly.
" Warning: Matrix is close to singular or badly scaled. Results may be inaccurate."
Is this X matrix something wrong?

2.
After complete 'lme_mass_fit_EMinit' process with the warning, I tried the next command,
[lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95);
This command took a long time to process, and it caused the whole stop MATLAB works.
Is it also because of the X matrix...?

Could you let me know the solution for the X matrix problems ?

Best Wishes,

Han