There are great variations in how different technologists create the different imaging planes that can make a precise comparison of computed tomography and magnetic resonance imaging difficult. We aimed to identify a reference line for the coronal images on a computed tomography topography parallel to the posterior borderline of the brainstem (PB), matching standard coronal magnetic resonance imaging planes. We retrospectively reviewed computed tomography topography images of 80 consecutive patients to determine a computed tomography plane to match the PB on magnetic resonance imaging. These included the tuberculum sella (TS)-anterior arch of the C1 vertebra (C1), TS-tip of dens axis (D), dorsum sellae (DS)-C1 and DS-D. We compared these methods of prescribing the coronal computed tomography plane to coronal magnetic resonance imaging planes by measuring the angles between TS-C1 and PB, TS-M and PB, DS-C1 and PB, DS-D and PB on midsagittal brain magnetic resonance images. Bland-Altman plots were created to assess intra-observer reliability. The angles between the PB line and each topogram-determined line are as follows: TS-C1, 10.40° ± 4.86°; TS-D, 22.46° ± 5.23°; DS-C1, 3.01° ± 3.16°; and DS-D, 11.53° ± 4.10°. The mean angles between the DS-C1 and the PB lines were significantly smaller than the mean angle between any other line (DS-D, TS-C1, or TS-D, all P < 0.001). Intra-observer agreement regarding the angular position of the reformatted coronal images on the lateral scout image was excellent (intraclass correlation coefficient >0.900, P < 0.05). The DS-C1 is almost parallel to the PB and easily identifiable on the lateral scout topography of brain computed tomography. Utilising the DS-C1 line as the baseline for brain computed tomography could allow better corroboration with coronal magnetic resonance imaging angulation.