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);
Thanks so much for your help!
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon