Abstract
This work presents the development of an Artificial Intelligence (AI)-based pipeline for patient-specific three-dimensional (3D) reconstruction from oncological magnetic resonance imaging (MRI), leveraging image-derived information to enhance the analysis process. These developments were carried out within the framework of Cella Medical Solutions, forming part of a broader initiative to improve and optimize the company's medical-image processing pipeline. The system integrates automatic MRI sequence classification using a ResNet-based architecture and segmentation of anatomical structures with a modular nnU-Net v2 framework. The classification stage achieved over 90% accuracy and showed improved segmentation performance over prior state-of-the-art pipelines, particularly for contrast-sensitive anatomies such as the hepatic vasculature and pancreas, where dedicated vascular networks showed Dice score differences of approximately 20-22%, and for musculoskeletal structures, where the model outperformed specialized networks in several elements. In terms of computational efficiency, the complete processing of a full MRI case, including sequence classification and segmentation, required approximately four minutes on the target hardware. The integration of sequence-aware information allows for a more comprehensive understanding of MRI signals, leading to more accurate delineations than approaches without such differentiation. From a clinical perspective, the proposed method has the potential to be integrated into surgical planning workflows. The segmentation outputs were converted into a patient-specific 3D model, which was subsequently integrated into Cella's surgical planner as a proof of concept. This process illustrates the transition from voxel-wise anatomical labels to a fully navigable 3D reconstruction, representing a step toward more robust and personalized AI-driven medical-image analysis workflows that leverage sequence-aware information for enhanced clinical utility.