Purpose Decision support to assist in target vertebra localization could provide a useful aid to safe and effective spine surgery. Previous solutions have shown 3D-2D registration of preoperative CT to intraoperative radiographs to reliably annotate vertebral labels for assistance during level localization. We present an algorithm (referred to as MR-LevelCheck) to perform 3D-2D registration based on a preoperative MRI to accommodate the increasingly common clinical scenario in which MRI is used instead of CT for preoperative planning. Methods Straightforward adaptation of gradient/intensity-based methods appropriate to CT-to-radiograph registration is confounded by large mismatch and noncorrespondence in image intensity between MRI and radiographs. The proposed method overcomes such challenges with a simple vertebrae segmentation step using vertebra centroids as seed points (automatically defined within existing workflow). Forwards projections are computed using segmented MRI and registered to radiographs via gradient orientation (GO) similarity and the CMA-ES (Covariance-Matrix-Adaptation Evolutionary-Strategy) optimizer. The method was tested in an IRB-approved study involving 10 patients undergoing cervical, thoracic, or lumbar spine surgery following preoperative MRI. Results The method successfully registered each preoperative MRI to intraoperative radiographs and maintained desirable properties of robustness against image content mismatch and large capture range. Robust registration performance was achieved with projection distance error (PDE) (median ± iqr) = 4.3 ± 2.6 mm (median ± iqr) and 0% failure rate. Segmentation accuracy for the continuous max-flow method yielded Dice coefficient = 88.1 ± 5.2, Accuracy = 90.6 ± 5.7, RMSE = 1.8 ± 0.6 mm, and contour affinity ratio (CAR) = 0.82 ± 0.08. Registration performance was found to be robust for segmentation methods exhibiting RMSE < 3 mm and CAR > 0.50. Conclusion The MR-LevelCheck method provides a potentially valuable extension to a previously developed decision support tool for spine surgery target localization by extending its utility to preoperative MRI while maintaining characteristics of accuracy and robustness.