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 <mellyd...@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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