Everything his companions were saying registered with the Doctor on a subconscious level, but the vast majority of his attention was on the energies in his body. Time Lords were in general physically superior to humans, and one of their more useful traits was the ability to consciously control certain bodily functions that in most species were involuntary. While Galen's ship was busy drawing off the radiation and effecting repairs to the Doctor's body, he was busy isolating those areas where his own regenerative energy was most needed and making certain they healed properly. He'd already had one bad experience with human medicine attempting to fix him and instead killing him; he wasn't about to let it happen again.
From an outside perspective, the Doctor was wreathed in the soft yellow glow of regenerative energy. As he became stronger, he began to slowly redirect that energy into the ship's own systems. Might as well repay Galen for the use of his medical facilities by giving them a fresh charge. The technique certainly worked in place of his handy spare hand.