The stalker has the following ability
Murderous Insight (Su): The stalker designates his combat senses towards ending the lives of his opponents and gains momentary flashes of insight in how to best accomplish this. The stalker can activate this ability by spending one point of ki as a swift action; for a number of rounds equal to 1 + his stalker initiation modifier, he can roll twice on a single attack roll each round and take the higher value.
To find out if it’s a critical hit, you immediately make an attempt to “confirm” the critical hit—another attack roll with all the same modifiers as the attack roll you just made.
So would you be allowed to roll twice during the confirm part or roll once?