...
to look at bi-directional effects (fonly), after de-meaning the data (-D), with an F threshold of 3, with cluster-based correction for multiple comparisons.
Note: the *.fts file is only needed for f tests; it can be left out for t tests.
The "-o" indicates the output file name, so you probably want to label this with the test parameters (e.g., -o L_Hipp_vertexMNI_rand_D_F3 for the suggested options).
Example 1: t-tests
To run a t test
[user@localhost temp]$ randomise -i L_Hipp_vertexMNI.nii.gz -m L_Hipp_vertexMNI_mask.nii.gz -o L_Hipp_vertexMNI_rand -d design.mat -t design.con T 2