Dear Freesurfer experts,

I have three groups g0, g1, and g2.

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+ …

The slope of g0 : 0 1 0 0 0 0

The slope of g1: 0 1 0 1 0  0

The slope of g2: 0 1 0 0 0 1

The slope difference between  g0 and g1: 0 0 0 1 0 0

The slope difference between  g0 and g2: 0 0 0 0 0 1

The slope difference between  g1 and g2: 0 0 0 -1 0 1

1) Is this contrast matrix correct to observe pairwise slope difference?

In the tutorial the contrast matrix   C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)]

2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial?

If so, my contrast matrix can be  C=[0 0 0 1 0 0; 0 0 0 -1 0 1]

3) How can we interpret the  result for this contrast matrix?

4) How can I obtain B1, B2, … ?

[sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,...

                                                         dr,pw,alpha,gr_pr)                                 

5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)?

With regards

Getaneh