Influence of early through late fusion on pancreas segmentation from imperfectly registered multimodal magnetic resonance imaging.

Purpose: Combining different types of medical imaging data, through multimodal fusion, promises better segmentation of anatomical structures, such as the pancreas. Strategic implementation of multimodal fusion could improve our ability to study diseases such as diabetes. However, where to perform fusion in deep learning models is still an open question. It is unclear if there is a single best location to fuse information when analyzing pairs of imperfectly aligned images or if the optimal fusion location depends on the specific model being used. Two main challenges when using multiple imaging modalities to study the pancreas are (1) the pancreas and surrounding abdominal anatomy have a deformable structure, making it difficult to consistently align the images and (2) breathing by the individual during image collection further complicates the alignment between multimodal images. Even after using state-of-the-art deformable image registration techniques, specifically designed to align abdominal images, multimodal images of the abdomen are often not perfectly aligned. We examine how the choice of different fusion points, ranging from early in the image processing pipeline to later stages, impacts the segmentation of the pancreas on imperfectly registered multimodal magnetic resonance (MR) images. Approach: Our dataset consists of 353 pairs of T2-weighted (T2w) and T1-weighted (T1w) abdominal MR images from 163 subjects with accompanying pancreas segmentation labels drawn mainly based on the T2w images. Because the T2w images were acquired in an interleaved manner across two breath holds and the T1w images on one breath hold, there were three different breath holds impacting the alignment of each pair of images. We used deeds, a state-of-the-art deformable abdominal image registration method to align the image pairs. Then, we trained a collection of basic UNets with different fusion points, spanning from early to late layers in the model, to assess how early through late fusion influenced segmentation performance on imperfectly aligned images. To investigate whether performance differences on key fusion points are generalized to other architectures, we expanded our experiments to nnUNet. Results: The single-modality T2w baseline using a basic UNet model had a median Dice score of 0.766, whereas the same baseline on the nnUNet model achieved 0.824. For each fusion approach, we analyzed the differences in performance with Dice residuals, by subtracting the baseline score from the fusion score for each datapoint. For the basic UNet, the best fusion approach was from early/mid fusion and occurred in the middle of the encoder with a median Dice residual of Conclusions: Fusion in specific blocks can improve performance, but the best blocks for fusion are model-specific, and the gains are small. In imperfectly registered datasets, fusion is a nuanced problem, with the art of design remaining vital for uncovering potential insights. Future innovation is needed to better address fusion in cases of imperfect alignment of abdominal image pairs. The code associated with this project is available here https://github.com/MASILab/influence_of_fusion_on_pancreas_segmentation.