> Let's say 21 subjects in both the patients and control groups, respectively. However, for the
> patient group, one subject has data missing data for the neutral condition, and two subjects
> have data missing for the positive condition: How can one do pairwise contrasts between pos
> and neutral conditions across the group, when you have missing values in each condition.

The solution is probably not so intuitive: If the missing data can be considered missing at random, 3dLME estimates the effects and their contrasts through optimizing the restricted maximum likelihood function where a balanced structure is not required.

> Also, if I want to include two within subject factors instead of one like in example 3, would I use the option below:
>
> -wsVars cond group

Use

-wsVars "cond,group"

Gang