Using the T2w and pathology phantom, we tested three conditions: 1) the influence of the rotation angle when mounting the tissue slice on the glass slide, 2) the influence of shrinkage caused by fixation of the tissue during histology processing, and 3) the influence of imperfect slice correspondences between the MRI and histopathology slices, e.g.,  \[fig:Phantom\]d-e have a perfect correspondence, while  \[fig:Phantom\]d-f are 2mm apart from each other.

To evaluate RAPSODI, we used one or multiple conditions and evaluated different quantitative metrics. Ten experiments were run for each condition to assess the mean and variance in performance of RAPSODI. When a random rotation of $r$ was assigned to the histopathology phantom, it resulted in applying a random angle ranging between $-r$ and $r$ to each slide and running 10 experiments with different noise and random angle conditions. When rotations were applied alone, no translation or scaling were applied. When a shrinkage factor $s$ is applied, all histopathology slices are shrunk by $s$ relative to their original appearance. Moreover, along with shrinking the images, we also apply a random translation of as much as 5% relative to the entire image in either x or y directions. Thereby, the experiments that include 