Give him time. He's still adjusting to being indoors and your presence will help him integrate and also get use to you. Always call his name so that he recognizes his own name and also importantly, your voice.
There is this stray cat at who's living below our apartment was quite skittish when she sees me. Each time I see her, I call out her name lovingly and I think I've been doing that for several months and lately, when I call out to her, she'll come running to me meowing.
Whenever you enter the room, call out her name first in a loving manner and once you enter the room, sit on the floor and while still calling him, wave your treat or toy and slowly inch towards him. It may take awhile for him to realized things are going to be different for him. Just make him as comfortable as possible and make him feel safe as possible.
Remember, love, patience and routine rules the day.
