Hi Jordi

You have implicitly included the reference group in your statistical model by including an intercept term and a time variable:

group0 intercept: ß1

group0 time: ß2

group1 intercept: ß1+ß3

group1 time: ß2+ß4

group2 intercept: ß1+ß5

group2 time: ß2+ß6

From here you can quickly see that your proposed contrast for the
differences in the mean response over time between group1 and group2 is correct.

Finally the region growing estimation method should yield more precise (lower variance) estimates for the ßs but I think it’s (might be) too complicated to setup with the current scripts. The vw method will produce good estimates too. So I recommend the vw estimation method if things get too complicated for you with the region-wise method.

Cheers

-Jorge

De: Jordi Pegueroles <jordi@pegueroles.cat>
Para: Freesurfer <freesurfer@nmr.mgh.harvard.edu>; jbernal0019@yahoo.es
Enviado: Lunes 28 de noviembre de 2016 5:11
Asunto: LME: contrast questions

Dear FS experts,

I am trying to run a LME model for three groups (group0, group1 and
group2) and (almost all) with three time points, all processed using the
Longitudinal FS stream.

Our intention is to compare the differences between group0 against
group1 and group0 against group2. I have followed the online LME
tutorial and I have adapted your code to my data. However, I think I
have not well understood the steps and I have few questions that you
will be able to answer me...

i) In the X matrix I put the following columns:

1) intercept
2) time (years from baseline)
3) group1 (binary variable: 1 if belongs to group1)
4) group1.*time
5) group2 (binary variable: 1 if belongs to group2)
6) group2.*time

I don't understand why I do not have to include the reference group
(in my case group0 and group0.*time) in the design matrix. How I can see
the progresion of the reference group if I did not include it in the
design matrix? How I can compare both progressions if the time of the
group0 subjects is not taking into account?

ii) Linked to the previous question, if I want to compare the
differences in time between group1 and group2... Should the contrast be
C = [0 0 0 1 0 -1]?

iii) Finally, between the vw method and the region growing method which
one is more accurate? In other words, which one do you recommend to use?

Thank you,

--
Jordi.