Dear Freesurfer Experts,

Hope this finds you well

I am following the LME tutorial running LME Univariate analysis. I was wondering if someone would kindly check my steps below? I wanted to make sure specially that my matrix (X) and and contrast (C) were designed accordingly to assess group*time interaction.

Study design:

Two groups: 0 = control, 1 = intervention

Time: 0 = baseline, 1 = 6-month follow-up

Outcome of interest: Change in hippocampal volume

Co-Variate: Estimated ICV

 

Here are the steps I took in Matlab:

# Loading into Matlab Qdec table with 7 columns in this exact order:  fsid, fsid-base, time, group, Righ.Hipp, Left.Hipp, estimated_ICV:

Qdec = fReadQdec('qdec-aseg.table.dat');

Qdec = rmQdecCol(Qdec,1);

sID = Qdec(2:end,1);

Qdec = rmQdecCol(Qdec,1);

M = Qdec2num(Qdec);

Y = M(:,3:4);

M = M(:,[1:2 5]); # Here I loaded estimated ICV already into M (as the third column), as it will be treated as a covariate later.

# Sorting data according to time

[M,Y,ni] = sortData(M,1,Y,sID);

# Building design matrix X from M, for a simple time by group interaction. Note that here, I have the slope column as 1, then I add time and group columns via: M(:,1:2), then a column for group*time via: M(:,1).*M(:,2), and finally a column for estimated ICV, as the final column in the matrix via: M(:,3). I wonder if this is correct?

X = [ones(length(M),1) [M(:, 1:2) M(:,1).*M(:,2) M(:,3)]];

# Determining model parameters, for total hippocampal volume, Left.Hipp, and Right.Hipp. Here, since my sample is small (N = 15), I am using 1 random effect only.

hipp_vol_stats_tot = lme_fit_FS(X,[1],Y(:,1)+Y(:,2),ni);

hipp_vol_stats_left = lme_fit_FS(X,[1],Y(:,1),ni);

hipp_vol_stats_right = lme_fit_FS(X,[1],Y(:,2),ni);

# Creating contrast (C) matrix for simple group*time interaction controlling for estimated ICV. Does this look correct, considering that the last 0 would control for estimated ICV?

C = [ 0 0 0 1 0];

# Finally, F test for total, left and right hippocampal volumes

F_C_tot = lme_F(hipp_vol_stats_tot,C);

F_C_left = lme_F(hipp_vol_stats_left,C);

F_C_right = lme_F(hipp_vol_stats_right,C);