Hi,

Those coordinates are the midpoints of the given images, so they also incorporate deviations coming from where/how the tissue sample is located/oriented on the slide. Unfortunately it's not easy to see where they point to: when you launch QuickNII, but don't load an image series, hovering the mouse over the values and control box makes a crosshair appear, that's where the coordinates come from.

Anyway, assuming that part is okay for your use case, yes, it's straightforward to create a utility that produces those coordinates. Would you mind naming the atlas in question, and if you have a preferred set of the transformations (some atlases have many of them)?

Best regards,

Gergely Csucs