1. A system for associating anatomical information with image data that forms a three-dimensional space, the system comprising: a computer processor configured to: output a graphical user interface (GUI) in which a first two-dimensional image slice of the image data and a second two-dimensional image slice of the image data are simultaneously displayed, wherein the first and second two-dimensional image slices are orthogonal to each other; obtain, via user interaction with the GUI, selection of three points within the three-dimensional space, two of the three points being selected in different respective ones of the first and second two-dimensional image slices, wherein a first point of the three points corresponds to an anterior commissure (AC) and a second point of the three points corresponds to a posterior commissure (PC); record the three points in association with the image data; selecting an alignment point along a line connecting the AC to the PC; aligning the image data with an anatomical atlas by anisotropically scaling the image data using a first scaling factor in an anterior/posterior direction relative to the alignment point and a second scaling factor in a superior/inferior direction relative to the alignment point, wherein the first and second scaling factors are different.