The overall amount of helium in the atmosphere is still more than enough for the foreseeable future, and it could be extracted (albeit at high energy cost) by augmenting existing air separation units (ASU's). Of course natural gas wells currently provide an easier to extract source, seeing as the concentration there is way higher.

Helium is only 5ppm in the atmosphere. Extracting useful quantities of it that way will probably never be economically viable. In other words, if for some reason we can no longer get helium from natural gas wells then it will be cheaper to just let patients die instead of doing cryogenic distillation of helium from the atmosphere to run MRI machines.