What are those variables with values of 0 and 1? Are they actually categorical variables (factors)? If so, it's better to explicitly treat them as factors instead of quantitative variables. In addition, center those real quantitative variables properly:
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afni.nimh.nih.gov]
Since there are no within-subject variables in your case, 3dLME is not an ideal program for the situation. Instead use 3dMVM.
Gang