Hi Jordi

You have implicitlyincluded the reference group in your statistical model by includingan intercept term and a time variable: group0 intercept: ß1group0 time: ß2group1 intercept:ß1+ß3group1 time: ß2+ß4group2 intercept:ß1+ß5group2 time: ß2+ß6

From here you canquickly see that your proposed contrast for the

differences inthe mean response over time between group1 and group2 is correct. Finally the regiongrowing estimation method should yield more precise (lower variance)estimates for the ßs but I think it’s (might be) too complicatedto setup with the current scripts. The vw method will produce goodestimates too. So I recommend the vw estimation method if things gettoo 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,