A study of why we need to reassess full reference image quality assessment with medical images

Image quality assessment (IQA) is not just indispensable in clinical practice to ensure high standards, but also in the development stage of novel algorithms that operate on medical images with reference data. This paper provides a structured and comprehensive collection of examples where the two most common full reference (FR) image quality measures prove to be unsuitable for the assessment of novel algorithms using different kinds of medical images, including real-world MRI, CT, OCT, X-Ray, digital pathology and photoacoustic imaging data. In particular, the FR-IQA measures PSNR and SSIM are known and tested for working successfully in many natural imaging tasks, but discrepancies in medical scenarios have been noted in the literature. Inconsistencies arising in medical images are not surprising, as they have very different properties than natural images which have not been targeted nor tested in the development of the mentioned measures, and therefore might imply wrong judgement of novel methods for medical images. Therefore, improvement is urgently needed in particular in this era of AI to increase explainability, reproducibility and generalizability in machine learning for medical imaging and beyond. On top of the pitfalls we will provide ideas for future research as well as suggesting guidelines for the usage of FR-IQA measures applied to medical images.

Neural Orientation Distribution Fields for Estimation and Uncertainty Quantification in Diffusion MRI

Inferring brain connectivity and structure \textit{in-vivo} requires accurate estimation of the orientation distribution function (ODF), which encodes key local tissue properties. However, estimating the ODF from diffusion MRI (dMRI) signals is a challenging inverse problem due to obstacles such as significant noise, high-dimensional parameter spaces, and sparse angular measurements. In this paper, we address these challenges by proposing a novel deep-learning based methodology for continuous estimation and uncertainty quantification of the spatially varying ODF field. We use a neural field (NF) to parameterize a random series representation of the latent ODFs, implicitly modeling the often ignored but valuable spatial correlation structures in the data, and thereby improving efficiency in sparse and noisy regimes. An analytic approximation to the posterior predictive distribution is derived which can be used to quantify the uncertainty in the ODF estimate at any spatial location, avoiding the need for expensive resampling-based approaches that are typically employed for this purpose. We present empirical evaluations on both synthetic and real in-vivo diffusion data, demonstrating the advantages of our method over existing approaches.

SlicerTMS: Interactive Real-time Visualization of Transcranial Magnetic Stimulation using Augmented Reality and Deep Learning

Transcranial magnetic stimulation (TMS) is a non-invasive neuromodulation approach that effectively treats various brain disorders. One of the critical factors in the success of TMS treatment is accurate coil placement, which can be challenging, especially when targeting specific brain areas for individual patients. Calculating the optimal coil placement and the resulting electric field on the brain surface can be expensive and time-consuming. We introduce SlicerTMS, a simulation method that allows the real-time visualization of the TMS electromagnetic field within the medical imaging platform 3D Slicer. Our software leverages a 3D deep neural network, supports cloud-based inference, and includes augmented reality visualization using WebXR. We evaluate the performance of SlicerTMS with multiple hardware configurations and compare it against the existing TMS visualization application SimNIBS. All our code, data, and experiments are openly available: \url{https://github.com/lorifranke/SlicerTMS}