afni.nimh.nih.gov

> I have 35 subjects that have undergone 2 different scans in which they have completed a task following 2 different conditions

These 2 conditions are Ex and Rest? What are those 2 different scans?

> The input file is the activity of contrast 1 - 2

What are 1 and 2?

> I would like to identify this with 3dLME

Cond, Order, and Hand are all within-subject factors? I suggest that you use 3dMVM instead of 3dLME unless you have missing data.

Gang