Great question: what Yin Yoga practice helps the brain? Well, before I answer that, first a huge caveat. Someone with a significant brain injury should not be taking medical advice from yoga teachers! Make sure his doctor knows what he wants to do and is okay with it.
From a meridian perspective the one that goes deeply into the brain is the
Urinary Bladder. The poses that stress the Urinary Bladder are flexions of the spine such as Caterpillar, Butterfly, Snail as well as a few others. I would NOT recommend Snail as an inversion could put too much pressure into the brain: in fact any inversions may be contra-indicated now, unless the doctor says otherwise and the student's own experience shows that they are safe. For this reason I would also exclude Dangling. Stick with Butterfly, Half Butterfly and Caterpillar for now. Since these are flexions of the spine, the counterposes would be extensions but keep them easy too: Sphinx with the head supported may be all he needs: just hang out there for more time than normal to allow the full counterpose effect to develop.
For a more complete Meridian assessment your student should go see a qualified acupuncturist. She (he) can advise which Meridians really do need stimulation because, while the UB line does pass through the brain, healing involves the whole body. The Kidney meridians may also need stimulation to send their universal energy to the brain and all other organs. (Sphinx will help with stimulating the Kidneys.) Again, a yoga teacher is not the best one to give such unique and detailed advice.
I hope this helps.
Bernie