No problem at all, Golrokh.

1) In setup/Covariates 2nd level you can define as many covariates as you want. For example, you can define 3 covariates such WMFT_Pre, WMFT_Post and WMFT_Difference and, examine each separately via calculator.

2) As for missing values, you can either replace them with the median or, perform the analysis with the discarded data/subject. Up to you!

3) As far as I know that should not be the case. Did not you possibly import them 2 times? can you try removing them (they are specified with their coordinates) from the calculator and import again?

Please correct me if I did not understand your questions correctly! 

Cheers,
V.