Hi Greg,

this will depend on your
design matrix. If column 1 models patients and column 2 models controls,
then [1 -1] will test the alternative hypotheses that control are lower
than patients. The opposite hypothesis will be tested for [-1 1].

This sign of the t-statistics will depend on your design matrix and contrast. 

As
a sanity check, you can also consider one of the edges in the
significant network and check that the average connectivity in each
groups for that edge is in the right direction.

Andrew