Hi Melinda
The eleventh column age should be age-at-baseline so it's a time-independent covariate.
If you have only two time-points then you should use the vertex-wise lme model with a single random effect for the intercept term:
1-Read your label eg.: lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with a random effect for the intercept term eg.: lhstats = lme_mass_fit_vw(X, [1], lhY, ni, lhcortex);
4-Perform vertex-wise inference eg.: CM.C = [your contrast matrix];
F_lhstats = lme_mass_F(lhstats, CM);
5-Save results eg.: fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');
Best -Jorge
De: melinda dora mellydora@outlook.com Para: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Enviado: Viernes 27 de junio de 2014 9:45 Asunto: [Freesurfer] freesurfer lme matlab tools
Dear Free-surfer Group, I am currently attempting to use the lme
matlab tools for my longitudinal analysis. My dataset consists of two time-points, and I am interested in the group by time interaction for my dataset.
I am attempting to follow the wiki instructions, but are finding them hard at times. I have reached the stage where, for the mass-univariate analysis", it says to do
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3);
May I just ask if its correct to fit the model with two random effects when I only have two time-points. Furthermore, this command is currently running, and it keeps saying, over and over,
Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 7.100165e-19.
In lme_mass_fit_EMinit>(parfor body) at 98
In parallel_function>make_general_channel/channel_general at 907 In remoteParallelFunction at 28
Has anybody else recieved this error? Is there a simpler method whereby to fit my model and the matrix, ie is there actually something wrong with my design matrix? It is as follows:
intercept time hr+ 3xtime hr- 5xtime hc 7xtime hrill 9xtime age First column, all ones (intercept)
Second column; time
third column; group1
fourth column; group1*time
fifth column; group 2 You can just use the
vertex-wise lme with a single random effect for the intercept term:
sixth column; group2*time
seventh column; group three
eighth column; group three*time
nineth column; group4
tenth column; group4*time
eleventh column; age
Does this look correct? Can anyone please advise me on the error I am getting?
Cheers,
Melinda
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