Dear Ben,

In essence, what you can do is that you can preprocess subjects from one center at a time, allowing you to set a different slice timing (and other preprocessing parameters). Just make sure you normalize to the same space, using the same template and with the same smoothing.

For my own studies, I use SPM directly, so what I do is that I place the subjects images of one center in one folder, and images from another center in other folder, etc. And then I run one preprocessing per folder/center, so that I can specify a different slice timing for each.

I think you can do the same in CONN GUI, just make sure in the preprocessing window to uncheck "Run for all subjects", and you select only subjects from one center, run the preprocessing (it will ask you for the slice timing parameters), then when it's done you redo the same for subjects of the second center, etc. until you are completely done.

Hope it helps,
Stephen