Paul Fischer

Paul Fischer, Thomas Küstner, Christian F. Baumgartner

MRI reconstruction techniques based on deep learning have led to unprecedented reconstruction quality especially in highly accelerated settings. However, deep learning techniques are also known to fail unexpectedly and hallucinate structures. This is particularly problematic if reconstructions are directly used for downstream tasks such as real-time treatment guidance or automated extraction of clinical paramters (e.g. via segmentation). Well-calibrated uncertainty quantification will be a key ingredient for safe use of this technology in clinical practice. In this paper we propose a novel probabilistic reconstruction technique (PHiRec) building on the idea of conditional hierarchical variational autoencoders. We demonstrate that our proposed method produces high-quality reconstructions as well as uncertainty quantification that is substantially better calibrated than several strong baselines. We furthermore demonstrate how uncertainties arising in the MR econstruction can be propagated to a downstream segmentation task, and show that PHiRec also allows well-calibrated estimation of segmentation uncertainties that originated in the MR reconstruction process.

Paul Fischer, Hannah Willms, Moritz Schneider et al.

Cancer remains a leading cause of death, highlighting the importance of effective radiotherapy (RT). Magnetic resonance-guided linear accelerators (MR-Linacs) enable imaging during RT, allowing for inter-fraction, and perhaps even intra-fraction, adjustments of treatment plans. However, achieving this requires fast and accurate dose calculations. While Monte Carlo simulations offer accuracy, they are computationally intensive. Deep learning frameworks show promise, yet lack uncertainty quantification crucial for high-risk applications like RT. Risk-controlling prediction sets (RCPS) offer model-agnostic uncertainty quantification with mathematical guarantees. However, we show that naive application of RCPS may lead to only certain subgroups such as the image background being risk-controlled. In this work, we extend RCPS to provide prediction intervals with coverage guarantees for multiple subgroups with unknown subgroup membership at test time. We evaluate our algorithm on real clinical planing volumes from five different anatomical regions and show that our novel subgroup RCPS (SG-RCPS) algorithm leads to prediction intervals that jointly control the risk for multiple subgroups. In particular, our method controls the risk of the crucial voxels along the radiation beam significantly better than conventional RCPS.

Paul Fischer, Jan Nikolas Morshuis, Thomas Küstner et al.

Magnetic Resonance Imaging (MRI) offers unparalleled soft-tissue contrast but is fundamentally limited by long acquisition times. While deep learning-based accelerated MRI can dramatically shorten scan times, the reconstruction from undersampled data introduces ambiguity resulting from an ill-posed problem with infinitely many possible solutions that propagates to downstream clinical tasks. This uncertainty is usually ignored during the acquisition process as acceleration factors are often fixed a priori, resulting in scans that are either unnecessarily long or of insufficient quality for a given clinical endpoint. This work introduces a dynamic, uncertainty-aware acquisition framework that adjusts scan time on a per-subject basis. Our method leverages a probabilistic reconstruction model to estimate image uncertainty, which is then propagated through a full analysis pipeline to a quantitative metric of interest (e.g., patellar cartilage volume or cardiac ejection fraction). We use conformal prediction to transform this uncertainty into a rigorous, calibrated confidence interval for the metric. During acquisition, the system iteratively samples k-space, updates the reconstruction, and evaluates the confidence interval. The scan terminates automatically once the uncertainty meets a user-predefined precision target. We validate our framework on both knee and cardiac MRI datasets. Our results demonstrate that this adaptive approach reduces scan times compared to fixed protocols while providing formal statistical guarantees on the precision of the final image. This framework moves beyond fixed acceleration factors, enabling patient-specific acquisitions that balance scan efficiency with diagnostic confidence, a critical step towards personalized and resource-efficient MRI.