- I, not he am doing the project.
- They, not he are the criminals.
- I, not he, am doing the project.
- They, not he, are the criminals.
ooo... comma rules can get a bit grey with your particular flavour of English but in this case I think everyone stands united. Well at least in theory.
Have a look at rule 5 here. The "not he" is an optional element (we could put parenthesis around it) so needs commas front and back