Hi Eileen,

my answer is quite dependent on your FD measures. Did you do as Alfonso suggested and aggregate your first level single subject FD values to one per subject? If so, in my understanding it is fine to enter one 'big' covariate, containing each one value per subject. If you then want to control for this covariate, in the between-subject contrast you should select 'All' and 'FD' and enter the contrast [1 0].

I hope that helps. 

Best,
Julia