Taylor,

> 1) Should we include a 'scan number' variable?

If you don't explicitly model the variable of scans, 3dLME would simply assume that the two scans have the same intercept other than the age effect, which is probably what you want. However, you may want to consider change the random effect specification to

-ranEff "~1+AGE"

> 2) Would we also model SUBJ (as well as -ranEFF "~1 + SUBJ") to indicate all continuous repeated measures within SUBJ?

No, 3dLME automatically assumes that the pivotal unit is subject. You need to change the label 'subj' in the data table to 'Subj'.

A couple of further comments:

1) Make sure to properly center SYMP_SEV and AGE first (https://afni.nimh.nih.gov/sscc/gangc/centering.html), then create another column that is the product of the two. And use the following

-model "SYMP_SEV+AGE + SYMP_AGE + SEX + COV"

2) Make sure that you explicitly declare all the quantitative variables with option -qVars.

Gang



Edited 1 time(s). Last edit at 07/15/2016 10:00AM by Gang.