Hi Ahmad,
> Considering the missing data, I think 3dlme is my only option, is that right(I have only one group of subjects)?
Well, you have too much missing data, so I'm not so 1) whether missing-at-random is a reasonable assumption in your case, and 2) whether you have enough data to make robust inferences.
> my hypothesis is there is no differences between runs
Is that your real research hypothesis or is it the straw man for the null hypothesis significance framework?
> -model "1" \
> -ranEff 'Time+Subj' \
These two lines should be
-model "Time" \
-ranEff '~1' \
Gang