Gang,

Thanks for your response.

We are running a 4 x 3 x 3 model. All within subjects factors.

3 Factors:

Visit: 1, 2, 3 4
Temp: 1 2 3
Trial: 1 2 3

We do have missing data for 1 subject. That subject has missing data from 1 visit. They only have data from 3 out of 4 visits.

In addition to the random effects question, there is something else:

We've run this model without specifying the correlation structure, so it is using compound symmetry, no? Something weird is going on with the output, that doesn't look right compared to when we run 3dMVM with a complete data set. We aren't expecting identical results, but not such a wide disparity.. I don't think it is something with 3dLME because I get the same results using SPSS on extracted data from a voxel. Just wondering if having data missing for an entire visit has substantial effect on the results.

Thanks.

Michael