Based on this nistats example we saw I believe the second-level contrast should be
1 0 0 0 ... 0
0 1 0 0 ... 0
0 0 1 0 ... 0
(3 rows, 3 + n_subjects columns). but the docstrings of FirstLevelModel and SecondLevelModel give no information about 2-dimensional contrast vectors (for “F” stat type, as used in the example)