Heavy ion-beam therapy is a highly precise radiation therapy exploiting the characteristic interaction of ions with matter. The steep dose gradient of the Bragg curve allows the irradiation of targets with high-dose and a narrow dose penumbra around the target, in contrast to photon irradiation. This, however, makes heavy ion-beam therapy very sensitive to minor changes in the range calculation of the treatment planning system, as it has a direct influence on the outcome of the treatment. Our previous study has shown that ion radiography with an amorphous silicon flat-panel detector allows the measurement of the water equivalent thickness (WET) of an imaging object with good accuracy and high spatial resolution. In this study, the developed imaging technique is used to measure the WET distribution of a patient-like phantom, and these results are compared to the WET calculation of the treatment planning system. To do so, a measured two-dimensional map of the WET of an anthropomorphic phantom was compared to WET distributions based on x-ray computed tomography images as used in the treatment planning system. It was found that the WET maps agree well in the overall shape and two-dimensional distribution of WET values. Quantitatively, the ratio of the two-dimensional WET maps shows a mean of 1.004 with a standard deviation of 0.022. Differences were found to be concentrated at high WET gradients. This could be explained by the Bragg-peak degradation, which is measured in detail by ion radiography with the flat-panel detector, but is not taken into account in the treatment planning system. Excluding pixels exhibiting significant Bragg-peak degradation, the mean value of the ratio was found to be 1.000 with a standard deviation of 0.012. Employment of the amorphous silicon flat-panel detector for WET measurements allows us to detect uncertainties of the WET determination in the treatment planning process. This makes the investigated technique a very helpful tool to study the WET determination of critical and complex phantom cases.