In "Unimatrix Zero (aspect 1)", it was so the Doctor could track her REM slumber and test to alleviate her nightmares about Unimatrix Zero. In "Imperfection", it was to observe the effectiveness of her malfunctioning cortical node. Given that Voyager was stranded in the Delta Quadrant as a end result of Janeway's actions, whatever the motives guiding them, this could be a scenario of her getting "kicked upstairs." It can be seen either way.