> I cannot run a paired t-test (since I have an uneven number of subjects in each group)

You have two groups, not two conditions; so it's not a "paired" situation. You should be fine using 3dttest++. However, it would be much easier to set it up in your situation with 3dMVM since you would not have to take care of the dummy coding issue.

> Father's Age is significantly different between the two groups (and I would like to "regress out" the effect of this covariate)

It depends on whether you want to model the interaction between Father's Age and the Group. If yes, it would make sense to properly center Father's Age. If no, you don't have to center this variable.

> Brain Volume is not significantly different between the two groups

Similar to the situation with Father's Age, the impact of centering is on the interpretation of the group difference, not on the covariate effect. Also, it's better to think about how you would like to interpret the difference between the two groups instead of whether the two groups differ in Brain Volume.

Gang