Closed 0todd0000 closed 4 years ago
I think it would be fine to average within-subjects, then conduct a two-sample t test. Averaging only discards within-subject variability, but this variability is largely irrelevant to the two-group comparison.
As an aside, note that multiple measurements per subject does not necessarily imply repeated measures. "Repeated measures" only exist if the same subject performs multiple tasks or conditions. The experiment you describe sounds like a multilevel design, and not a repeated measures design. Here is a relevant discussion: Which stats method for multivariate repeated measures with multiple trials?
Currently, spm1d does not directly support multilevel designs. However, it indirectly supports multilevel (hierarchical, random effects) modeling as described here: Overview of random effects analysis in spm1d For the experiment you describe above, multilevel modeling can be achieved by (1) estimating subject means, then (2) conducting a two-sample test, exactly as you suggest.
Todd
(Copied from a previously closed issue: #2}