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Magnetic Resonance Fingerprinting (MRF) is a time-efficient approach to quantitative MRI, enabling the mapping of multiple tissue properties from a single, accelerated scan. However, achieving accurate reconstructions remains challenging, particularly in highly accelerated and undersampled acquisitions, which are crucial for reducing scan times. While deep learning techniques have advanced image reconstruction, the recent introduction of diffusion models offers new possibilities for imaging tasks, though their application in the medical field is still emerging. Notably, diffusion models have not yet been explored for the MRF problem. In this work, we propose for the first time a conditional diffusion probabilistic model for MRF image reconstruction. Qualitative and quantitative comparisons on in-vivo brain scan data demonstrate that the proposed approach can outperform established deep learning and compressed sensing algorithms for MRF reconstruction. Extensive ablation studies also explore strategies to improve computational efficiency of our approach., Comment: 12 pages, 5 figures, 2 algorithms

Magnetic Resonance Fingerprinting (MRF) is a time-efficient approach to quantitative MRI for multiparametric tissue mapping. The reconstruction of quantitative maps requires tailored algorithms for removing aliasing artefacts from the compressed sampled MRF acquisitions. Within approaches found in the literature, many focus solely on two-dimensional (2D) image reconstruction, neglecting the extension to volumetric (3D) scans despite their higher relevance and clinical value. A reason for this is that transitioning to 3D imaging without appropriate mitigations presents significant challenges, including increased computational cost and storage requirements, and the need for large amount of ground-truth (artefact-free) data for training. To address these issues, we introduce StoDIP, a new algorithm that extends the ground-truth-free Deep Image Prior (DIP) reconstruction to 3D MRF imaging. StoDIP employs memory-efficient stochastic updates across the multicoil MRF data, a carefully selected neural network architecture, as well as faster nonuniform FFT (NUFFT) transformations. This enables a faster convergence compared against a conventional DIP implementation without these features. Tested on a dataset of whole-brain scans from healthy volunteers, StoDIP demonstrated superior performance over the ground-truth-free reconstruction baselines, both quantitatively and qualitatively., Comment: 10 pages, 2 figures, 1 table, 1 algorithm

The estimation of multi-parametric quantitative maps from Magnetic Resonance Fingerprinting (MRF) compressed sampled acquisitions, albeit successful, remains a challenge due to the high underspampling rate and artifacts naturally occuring during image reconstruction. Whilst state-of-the-art DL methods can successfully address the task, to fully exploit their capabilities they often require training on a paired dataset, in an area where ground truth is seldom available. In this work, we propose a method that combines a deep image prior (DIP) module that, without ground truth and in conjunction with a Bloch consistency enforcing autoencoder, can tackle the problem, resulting in a method faster and of equivalent or better accuracy than DIP-MRF., Comment: 4 pages, 3 figures 1 table, presented at ISBI 2024

Monitoring diseases that affect the brain's structural integrity requires automated analysis of magnetic resonance (MR) images, e.g., for the evaluation of volumetric changes. However, many of the evaluation tools are optimized for analyzing healthy tissue. To enable the evaluation of scans containing pathological tissue, it is therefore required to restore healthy tissue in the pathological areas. In this work, we explore and extend denoising diffusion models for consistent inpainting of healthy 3D brain tissue. We modify state-of-the-art 2D, pseudo-3D, and 3D methods working in the image space, as well as 3D latent and 3D wavelet diffusion models, and train them to synthesize healthy brain tissue. Our evaluation shows that the pseudo-3D model performs best regarding the structural-similarity index, peak signal-to-noise ratio, and mean squared error. To emphasize the clinical relevance, we fine-tune this model on data containing synthetic MS lesions and evaluate it on a downstream brain tissue segmentation task, whereby it outperforms the established FMRIB Software Library (FSL) lesion-filling method.

Accurate image registration is pivotal in biomedical image analysis, where selecting suitable registration algorithms demands careful consideration. While numerous algorithms are available, the evaluation metrics to assess their performance have remained relatively static. This study addresses this challenge by introducing a novel evaluation metric termed Landmark Hit Rate (HitR), which focuses on the clinical relevance of image registration accuracy. Unlike traditional metrics such as Target Registration Error, which emphasize subresolution differences, HitR considers whether registration algorithms successfully position landmarks within defined confidence zones. This paradigm shift acknowledges the inherent annotation noise in medical images, allowing for more meaningful assessments. To equip HitR with label-noise-awareness, we propose defining these confidence zones based on an Inter-rater Variance analysis. Consequently, hit rate curves are computed for varying landmark zone sizes, enabling performance measurement for a task-specific level of accuracy. Our approach offers a more realistic and meaningful assessment of image registration algorithms, reflecting their suitability for clinical and biomedical applications.

Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the visible blood vessels is a common first step when extracting quantitative biomarkers from these images. Classical segmentation algorithms based on thresholding are strongly affected by image artifacts and limited signal-to-noise ratio. The use of modern, deep learning-based segmentation methods has been inhibited by a lack of large datasets with detailed annotations of the blood vessels. To address this issue, recent work has employed transfer learning, where a segmentation network is trained on synthetic OCTA images and is then applied to real data. However, the previously proposed simulations fail to faithfully model the retinal vasculature and do not provide effective domain adaptation. Because of this, current methods are unable to fully segment the retinal vasculature, in particular the smallest capillaries. In this work, we present a lightweight simulation of the retinal vascular network based on space colonization for faster and more realistic OCTA synthesis. We then introduce three contrast adaptation pipelines to decrease the domain gap between real and artificial images. We demonstrate the superior segmentation performance of our approach in extensive quantitative and qualitative experiments on three public datasets that compare our method to traditional computer vision algorithms and supervised training using human annotations. Finally, we make our entire pipeline publicly available, including the source code, pretrained models, and a large dataset of synthetic OCTA images., Comment: Currently under review

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space.The BraTS-METS 2023 challenge successfully curated well-annotated, diverse datasets and identified common errors, facilitating the translation of BM segmentation across varied clinical environments and providing personalized volumetric reports to patients undergoing BM treatment.

Gliomas are the most common type of primary brain tumors. Although gliomas are relatively rare, they are among the deadliest types of cancer, with a survival rate of less than 2 years after diagnosis. Gliomas are challenging to diagnose, hard to treat and inherently resistant to conventional therapy. Years of extensive research to improve diagnosis and treatment of gliomas have decreased mortality rates across the Global North, while chances of survival among individuals in low- and middle-income countries (LMICs) remain unchanged and are significantly worse in Sub-Saharan Africa (SSA) populations. Long-term survival with glioma is associated with the identification of appropriate pathological features on brain MRI and confirmation by histopathology. Since 2012, the Brain Tumor Segmentation (BraTS) Challenge have evaluated state-of-the-art machine learning methods to detect, characterize, and classify gliomas. However, it is unclear if the state-of-the-art methods can be widely implemented in SSA given the extensive use of lower-quality MRI technology, which produces poor image contrast and resolution and more importantly, the propensity for late presentation of disease at advanced stages as well as the unique characteristics of gliomas in SSA (i.e., suspected higher rates of gliomatosis cerebri). Thus, the BraTS-Africa Challenge provides a unique opportunity to include brain MRI glioma cases from SSA in global efforts through the BraTS Challenge to develop and evaluate computer-aided-diagnostic (CAD) methods for the detection and characterization of glioma in resource-limited settings, where the potential for CAD tools to transform healthcare are more likely., Comment: arXiv admin note: text overlap with arXiv:2107.02314

A myriad of algorithms for the automatic analysis of brain MR images is available to support clinicians in their decision-making. For brain tumor patients, the image acquisition time series typically starts with an already pathological scan. This poses problems, as many algorithms are designed to analyze healthy brains and provide no guarantee for images featuring lesions. Examples include, but are not limited to, algorithms for brain anatomy parcellation, tissue segmentation, and brain extraction. To solve this dilemma, we introduce the BraTS inpainting challenge. Here, the participants explore inpainting techniques to synthesize healthy brain scans from lesioned ones. The following manuscript contains the task formulation, dataset, and submission procedure. Later, it will be updated to summarize the findings of the challenge. The challenge is organized as part of the ASNR-BraTS MICCAI challenge., Comment: 14 pages, 6 figures

Even though simultaneous optimization of similarity metrics is a standard procedure in the field of semantic segmentation, surprisingly, this is much less established for image registration. To help closing this gap in the literature, we investigate in a complex multi-modal 3D setting whether simultaneous optimization of registration metrics, here implemented by means of primitive summation, can benefit image registration. We evaluate two challenging datasets containing collections of pre- to post-operative and pre- to intra-operative MR images of glioma. Employing the proposed optimization, we demonstrate improved registration accuracy in terms of TRE on expert neuroradiologists' landmark annotations.

Optical coherence tomography angiography (OCTA) can non-invasively image the eye's circulatory system. In order to reliably characterize the retinal vasculature, there is a need to automatically extract quantitative metrics from these images. The calculation of such biomarkers requires a precise semantic segmentation of the blood vessels. However, deep-learning-based methods for segmentation mostly rely on supervised training with voxel-level annotations, which are costly to obtain. In this work, we present a pipeline to synthesize large amounts of realistic OCTA images with intrinsically matching ground truth labels; thereby obviating the need for manual annotation of training data. Our proposed method is based on two novel components: 1) a physiology-based simulation that models the various retinal vascular plexuses and 2) a suite of physics-based image augmentations that emulate the OCTA image acquisition process including typical artifacts. In extensive benchmarking experiments, we demonstrate the utility of our synthetic data by successfully training retinal vessel segmentation algorithms. Encouraged by our method's competitive quantitative and superior qualitative performance, we believe that it constitutes a versatile tool to advance the quantitative analysis of OCTA images., Comment: Accepted at MICCAI 2022

Novel multimodal imaging methods are capable of generating extensive, super high resolution datasets for preclinical research. Yet, a massive lack of annotations prevents the broad use of deep learning to analyze such data. So far, existing generative models fail to mitigate this problem because of frequent labeling errors. In this paper, we introduce a novel generative method which leverages real anatomical information to generate realistic image-label pairs of tumours. We construct a dual-pathway generator, for the anatomical image and label, trained in a cycle-consistent setup, constrained by an independent, pretrained segmentor. The generated images yield significant quantitative improvement compared to existing methods. To validate the quality of synthesis, we train segmentation networks on a dataset augmented with the synthetic data, substantially improving the segmentation over baseline.

This paper presents a novel yet efficient defense framework for segmentation models against adversarial attacks in medical imaging. In contrary to the defense methods against adversarial attacks for classification models which widely are investigated, such defense methods for segmentation models has been less explored. Our proposed method can be used for any deep learning models without revising the target deep learning models, as well as can be independent of adversarial attacks. Our framework consists of a frequency domain converter, a detector, and a reformer. The frequency domain converter helps the detector detects adversarial examples by using a frame domain of an image. The reformer helps target models to predict more precisely. We have experiments to empirically show that our proposed method has a better performance compared to the existing defense method.

Designing of a cranial implant needs a 3D understanding of the complete skull shape. Thus, taking a 2D approach is sub-optimal, since a 2D model lacks a holistic 3D view of both the defective and healthy skulls. Further, loading the whole 3D skull shapes at its original image resolution is not feasible in commonly available GPUs. To mitigate these issues, we propose a fully convolutional network composed of two subnetworks. The first subnetwork is designed to complete the shape of the downsampled defective skull. The second subnetwork upsamples the reconstructed shape slice-wise. We train the 3D and 2D networks together end-to-end, with a hierarchical loss function. Our proposed solution accurately predicts a high-resolution 3D implant in the challenge test case in terms of dice-score and the Hausdorff distance.

Osteoporotic vertebral fractures have a severe impact on patients' overall well-being but are severely under-diagnosed. These fractures present themselves at various levels of severity measured using the Genant's grading scale. Insufficient annotated datasets, severe data-imbalance, and minor difference in appearances between fractured and healthy vertebrae make naive classification approaches result in poor discriminatory performance. Addressing this, we propose a representation learning-inspired approach for automated vertebral fracture detection, aimed at learning latent representations efficient for fracture detection. Building on state-of-art metric losses, we present a novel Grading Loss for learning representations that respect Genant's fracture grading scheme. On a publicly available spine dataset, the proposed loss function achieves a fracture detection F1 score of 81.5%, a 10% increase over a naive classification baseline., Comment: To be presented at MICCAI 2020

The treatment of degenerative spinal disorders requires an understanding of the individual spinal anatomy and curvature in 3D. An upright spinal pose (i.e. standing) under natural weight bearing is crucial for such bio-mechanical analysis. 3D volumetric imaging modalities (e.g. CT and MRI) are performed in patients lying down. On the other hand, radiographs are captured in an upright pose, but result in 2D projections. This work aims to integrate the two realms, i.e. it combines the upright spinal curvature from radiographs with the 3D vertebral shape from CT imaging for synthesizing an upright 3D model of spine, loaded naturally. Specifically, we propose a novel neural network architecture working vertebra-wise, termed \emph{TransVert}, which takes orthogonal 2D radiographs and infers the spine's 3D posture. We validate our architecture on digitally reconstructed radiographs, achieving a 3D reconstruction Dice of $95.52\%$, indicating an almost perfect 2D-to-3D domain translation. Deploying our model on clinical radiographs, we successfully synthesise full-3D, upright, patient-specific spine models for the first time.

Robust localization of organs in computed tomography scans is a constant pre-processing requirement for organ-specific image retrieval, radiotherapy planning, and interventional image analysis. In contrast to current solutions based on exhaustive search or region proposals, which require large amounts of annotated data, we propose a deep reinforcement learning approach for organ localization in CT. In this work, an artificial agent is actively self-taught to localize organs in CT by learning from its asserts and mistakes. Within the context of reinforcement learning, we propose a novel set of actions tailored for organ localization in CT. Our method can use as a plug-and-play module for localizing any organ of interest. We evaluate the proposed solution on the public VISCERAL dataset containing CT scans with varying fields of view and multiple organs. We achieved an overall intersection over union of 0.63, an absolute median wall distance of 2.25 mm, and a median distance between centroids of 3.65 mm., Comment: Accepted paper in MIDL 2020

Magnetic Resonance Fingerprinting (MRF) enables the simultaneous quantification of multiple properties of biological tissues. It relies on a pseudo-random acquisition and the matching of acquired signal evolutions to a precomputed dictionary. However, the dictionary is not scalable to higher-parametric spaces, limiting MRF to the simultaneous mapping of only a small number of parameters (proton density, T1 and T2 in general). Inspired by diffusion-weighted SSFP imaging, we present a proof-of-concept of a novel MRF sequence with embedded diffusion-encoding gradients along all three axes to efficiently encode orientational diffusion and T1 and T2 relaxation. We take advantage of a convolutional neural network (CNN) to reconstruct multiple quantitative maps from this single, highly undersampled acquisition. We bypass expensive dictionary matching by learning the implicit physical relationships between the spatiotemporal MRF data and the T1, T2 and diffusion tensor parameters. The predicted parameter maps and the derived scalar diffusion metrics agree well with state-of-the-art reference protocols. Orientational diffusion information is captured as seen from the estimated primary diffusion directions. In addition to this, the joint acquisition and reconstruction framework proves capable of preserving tissue abnormalities in multiple sclerosis lesions.

Accurate segmentation of tubular, network-like structures, such as vessels, neurons, or roads, is relevant to many fields of research. For such structures, the topology is their most important characteristic; particularly preserving connectedness: in the case of vascular networks, missing a connected vessel entirely alters the blood-flow dynamics. We introduce a novel similarity measure termed centerlineDice (short clDice), which is calculated on the intersection of the segmentation masks and their (morphological) skeleta. We theoretically prove that clDice guarantees topology preservation up to homotopy equivalence for binary 2D and 3D segmentation. Extending this, we propose a computationally efficient, differentiable loss function (soft-clDice) for training arbitrary neural segmentation networks. We benchmark the soft-clDice loss on five public datasets, including vessels, roads and neurons (2D and 3D). Training on soft-clDice leads to segmentation with more accurate connectivity information, higher graph similarity, and better volumetric scores., Comment: * The authors Suprosanna Shit and Johannes C. Paetzold contributed equally to the work

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse., Comment: Challenge report for the VerSe 2019 and 2020. Published in Medical Image Analysis (DOI: https://doi.org/10.1016/j.media.2021.102166)

Novel methods for quantitative, transient-state multiparametric imaging are increasingly being demonstrated for assessment of disease and treatment efficacy. Here, we build on these by assessing the most common Non-Cartesian readout trajectories (2D/3D radials and spirals), demonstrating efficient anti-aliasing with a k-space view-sharing technique, and proposing novel methods for parameter inference with neural networks that incorporate the estimation of proton density. Our results show good agreement with gold standard and phantom references for all readout trajectories at 1.5T and 3T. Parameters inferred with the neural network were within 6.58% difference from the parameters inferred with a high-resolution dictionary. Concordance correlation coefficients were above 0.92 and the normalized root mean squared error ranged between 4.2% - 12.7% with respect to gold-standard phantom references for T1 and T2. In vivo acquisitions demonstrate sub-millimetric isotropic resolution in under five minutes with reconstruction and inference times < 7 minutes. Our 3D quantitative transient-state imaging approach could enable high-resolution multiparametric tissue quantification within clinically acceptable acquisition and reconstruction times., Comment: 43 pages, 12 Figures, 5 Tables

We propose an auto-encoding network architecture for point clouds (PC) capable of extracting shape signatures without supervision. Building on this, we (i) design a loss function capable of modelling data variance on PCs which are unstructured, and (ii) regularise the latent space as in a variational auto-encoder, both of which increase the auto-encoders' descriptive capacity while making them probabilistic. Evaluating the reconstruction quality of our architectures, we employ them for detecting vertebral fractures without any supervision. By learning to efficiently reconstruct only healthy vertebrae, fractures are detected as anomalous reconstructions. Evaluating on a dataset containing $\sim$1500 vertebrae, we achieve area-under-ROC curve of $>$75%, without using intensity-based features., Comment: Accepted at Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2019; JSK and BHM are joint supervising authors

Magnetic resonance imaging (MRI) is a remarkably powerful diagnostic technique: it generates wide-ranging information for the non-invasive study of tissue anatomy and physiology. Complementary data is normally obtained in separate measurements, either as contrast-weighted images, which are fast and simple to acquire, or as quantitative parametric maps, which offer an absolute quantification of underlying biophysical effects, such as relaxation times or flow. Here, we demonstrate how to acquire and reconstruct data in a transient-state with a dual purpose: 1 - to generate contrast-weighted images that can be adjusted to emphasise clinically relevant image biomarkers; exemplified with signal modulation according to flow to obtain angiography information, and 2 - to simultaneously infer multiple quantitative parameters with a single, highly accelerated acquisition. This is a achieved by introducing three novel elements: a model that accounts for flowing blood, a method for sequence design that incorporates both parameter encoding and signal contrast, and the reconstruction of temporally resolved contrast-weighted images. From these images we simultaneously obtain angiography projections and multiple quantitative maps. By doing so, we increase the amount of clinically relevant data without adding measurement time, creating new dimensions for biomarker exploration and adding value to MR examinations for patients and clinicians alike.