It is important to create a link between stereotaxic coordinates and head-surface-based positioning systems in order to share data between tomographic and transcranial brain mapping studies. In our previous studies, we established the probabilistic correspondence of the international 10-20 positions to the standard stereotaxic coordinate systems and made a reference database. However, its expansion required the physical marking of the 10-20 positions and the subsequent acquisition of MR images. To avoid such tedious procedures, we developed a virtual 10-20 measurement algorithm that can be applied to re-analyze any structural MR image that covers the whole head. As in the physical 10-20 measurements, with the reference points given, the algorithm automatically determines each 10-20 position step by step. Using the virtual 10-20 measurement method, we re-analyzed the MR images of 17 healthy subjects for whom we had determined 10-20 positions by physical marking in our previous study. The acquired 10-20 positions were normalized to the Montreal Neurological Institute (MNI) stereotactic coordinates and compared with the positions previously determined by physical measurements. 10-20 positions determined using the virtual and physical methods were roughly consistent. Average standard deviations for virtual and physical methods were 7.7 mm and 9.0 mm, respectively. There was a systematic shift in the virtual method, likely due to the absence of hair interference. We corrected the shift with affine transformation. The virtual 10-20 measurement method proved to be an effective alternative to physical marking. This method will serve as an essential tool for expanding the reference database and will further strengthen the link between tomographic and transcranial brain mapping methods.