and the cancer outline (red) was mapped onto MRI ( \[fig:ResultsQualitativeC2\] Columns 3-4). The public dataset includes the cancer annotation (blue) for this subject, which was obtained using a landmark-based registration [@singanamalli_identifying_2016]. The cancer annotations obtained via RAPSODI overlaps well with the labels provided by the dataset authors, with a dice overlap of 0.58 and a Hausdorff Distance of 2.71 mm. The relatively low overlap indicated by the dice coefficient may be accounted by the relatively small size of the tumor, and the misalignment of the regions in the apex slice ( \[fig:ResultsQualitativeC2\] Row 1).]{}

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Quantitative Results {#quantitative-results .unnumbered}
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An improvement in the alignment of the histopathology images and the T2w MRI can be observed across the different steps of our framework ( \[fig:ResultsQuantitative\]). Statistically significant differences in Dice coefficients and Hausdorff distances were found between the input and the results of the registration performed using RAPSODI(Mann-Whitney test is statistically significant for $\alpha<0.05$). [ These statistically significant differences were observed both between the input and the affine registration in step 2 as well as between 