Prieto, Claudia
MR imaging in the low-field: Leveraging the power of machine learning
Kofler, Andreas, Si, Dongyue, Schote, David, Botnar, Rene M, Kolbitsch, Christoph, Prieto, Claudia
Magnetic Resonance Imaging (MRI) is an essential tool for the early detection, risk stratification, prognosis, treatment selection, and monitoring of many diseases, including cancer, cardiovascular disease, metabolic, musculoskeletal, and brain disorders, among many others. Its ability to produce multi-contrast and multi-parametric images of soft tissues, coupled with its non-invasive and radiation-free nature, makes it a highly valuable tool in clinical practice. Over the past five decades, the technology behind MRI has undergone significant advancements, especially in terms of the magnetic field strengths used for imaging. Early MRI systems operated at low field strengths (0.15 T to 0.35 T) [1-3], and while they offered important diagnostic insights, they were limited by low signal-to-noise ratio (SNR) and image resolution. Over time, several advancements led to the development of systems operating at higher field strengths, such as 1.5 T and 3 T, which are now considered the clinical standard due to their superior SNR and image quality [4, 5]. Recent developments have even pushed field strengths to ultra-high levels ( 3 T), including 5 T, 7 T and beyond, further enhancing the spatial and temporal resolution of MRI [4, 6, 7]. However, high-field MRI has its challenges [8].
PISCO: Self-Supervised k-Space Regularization for Improved Neural Implicit k-Space Representations of Dynamic MRI
Spieker, Veronika, Eichhorn, Hannah, Huang, Wenqi, Stelter, Jonathan K., Catalan, Tabita, Braren, Rickmer F., Rueckert, Daniel, Costabal, Francisco Sahli, Hammernik, Kerstin, Karampinos, Dimitrios C., Prieto, Claudia, Schnabel, Julia A.
Neural implicit k-space representations (NIK) have shown promising results for dynamic magnetic resonance imaging (MRI) at high temporal resolutions. Yet, reducing acquisition time, and thereby available training data, results in severe performance drops due to overfitting. To address this, we introduce a novel self-supervised k-space loss function $\mathcal{L}_\mathrm{PISCO}$, applicable for regularization of NIK-based reconstructions. The proposed loss function is based on the concept of parallel imaging-inspired self-consistency (PISCO), enforcing a consistent global k-space neighborhood relationship without requiring additional data. Quantitative and qualitative evaluations on static and dynamic MR reconstructions show that integrating PISCO significantly improves NIK representations. Particularly for high acceleration factors (R$\geq$54), NIK with PISCO achieves superior spatio-temporal reconstruction quality compared to state-of-the-art methods. Furthermore, an extensive analysis of the loss assumptions and stability shows PISCO's potential as versatile self-supervised k-space loss function for further applications and architectures. Code is available at: https://github.com/compai-lab/2025-pisco-spieker
Subspace Implicit Neural Representations for Real-Time Cardiac Cine MR Imaging
Huang, Wenqi, Spieker, Veronika, Xu, Siying, Cruz, Gastao, Prieto, Claudia, Schnabel, Julia, Hammernik, Kerstin, Kuestner, Thomas, Rueckert, Daniel
Conventional cardiac cine MRI methods rely on retrospective gating, which limits temporal resolution and the ability to capture continuous cardiac dynamics, particularly in patients with arrhythmias and beat-to-beat variations. To address these challenges, we propose a reconstruction framework based on subspace implicit neural representations for real-time cardiac cine MRI of continuously sampled radial data. This approach employs two multilayer perceptrons to learn spatial and temporal subspace bases, leveraging the low-rank properties of cardiac cine MRI. Initialized with low-resolution reconstructions, the networks are fine-tuned using spoke-specific loss functions to recover spatial details and temporal fidelity. Our method directly utilizes the continuously sampled radial k-space spokes during training, thereby eliminating the need for binning and non-uniform FFT. This approach achieves superior spatial and temporal image quality compared to conventional binned methods at the acceleration rate of 10 and 20, demonstrating potential for high-resolution imaging of dynamic cardiac events and enhancing diagnostic capability.
Self-Supervised k-Space Regularization for Motion-Resolved Abdominal MRI Using Neural Implicit k-Space Representation
Spieker, Veronika, Eichhorn, Hannah, Stelter, Jonathan K., Huang, Wenqi, Braren, Rickmer F., Rückert, Daniel, Costabal, Francisco Sahli, Hammernik, Kerstin, Prieto, Claudia, Karampinos, Dimitrios C., Schnabel, Julia A.
Neural implicit k-space representations have shown promising results for dynamic MRI at high temporal resolutions. Yet, their exclusive training in k-space limits the application of common image regularization methods to improve the final reconstruction. In this work, we introduce the concept of parallel imaging-inspired self-consistency (PISCO), which we incorporate as novel self-supervised k-space regularization enforcing a consistent neighborhood relationship. At no additional data cost, the proposed regularization significantly improves neural implicit k-space reconstructions on simulated data. Abdominal in-vivo reconstructions using PISCO result in enhanced spatio-temporal image quality compared to state-of-the-art methods.
Unsupervised reconstruction of accelerated cardiac cine MRI using Neural Fields
Catalán, Tabita, Courdurier, Matías, Osses, Axel, Botnar, René, Costabal, Francisco Sahli, Prieto, Claudia
Cardiac cine MRI is the gold standard for cardiac functional assessment, but the inherently slow acquisition process creates the necessity of reconstruction approaches for accelerated undersampled acquisitions. Several regularization approaches that exploit spatial-temporal redundancy have been proposed to reconstruct undersampled cardiac cine MRI. More recently, methods based on supervised deep learning have been also proposed to further accelerate acquisition and reconstruction. However, these techniques rely on usually large dataset for training, which are not always available. In this work, we propose an unsupervised approach based on implicit neural field representations for cardiac cine MRI (so called NF-cMRI). The proposed method was evaluated in in-vivo undersampled golden-angle radial multi-coil acquisitions for undersampling factors of 26x and 52x, achieving good image quality, and comparable spatial and improved temporal depiction than a state-of-the-art reconstruction technique.
LAPNet: Non-rigid Registration derived in k-space for Magnetic Resonance Imaging
Küstner, Thomas, Pan, Jiazhen, Qi, Haikun, Cruz, Gastao, Gilliam, Christopher, Blu, Thierry, Yang, Bin, Gatidis, Sergios, Botnar, René, Prieto, Claudia
Physiological motion, such as cardiac and respiratory motion, during Magnetic Resonance (MR) image acquisition can cause image artifacts. Motion correction techniques have been proposed to compensate for these types of motion during thoracic scans, relying on accurate motion estimation from undersampled motion-resolved reconstruction. A particular interest and challenge lie in the derivation of reliable non-rigid motion fields from the undersampled motion-resolved data. Motion estimation is usually formulated in image space via diffusion, parametric-spline, or optical flow methods. However, image-based registration can be impaired by remaining aliasing artifacts due to the undersampled motion-resolved reconstruction. In this work, we describe a formalism to perform non-rigid registration directly in the sampled Fourier space, i.e. k-space. We propose a deep-learning based approach to perform fast and accurate non-rigid registration from the undersampled k-space data. The basic working principle originates from the Local All-Pass (LAP) technique, a recently introduced optical flow-based registration. The proposed LAPNet is compared against traditional and deep learning image-based registrations and tested on fully-sampled and highly-accelerated (with two undersampling strategies) 3D respiratory motion-resolved MR images in a cohort of 40 patients with suspected liver or lung metastases and 25 healthy subjects. The proposed LAPNet provided consistent and superior performance to image-based approaches throughout different sampling trajectories and acceleration factors.
A Survey on Deep Learning and Explainability for Automatic Image-based Medical Report Generation
Messina, Pablo, Pino, Pablo, Parra, Denis, Soto, Alvaro, Besa, Cecilia, Uribe, Sergio, andía, Marcelo, Tejos, Cristian, Prieto, Claudia, Capurro, Daniel
Research over the last five years shows a clear improvement in computer-aided detection (CAD), specifically in disease prediction from medical images [36, 61, 105, 130, 134] as well as from Electronic Health Records (EHR) [113], by using deep neural networks (DNN) and treating the problem as supervised classification or segmentation tasks. Recently, Topol [129] indicates that the need for diagnosis and reporting from image-based examinations far exceeds the current medical capacity of physicians in the US. This situation promotes the development of automatic image-based diagnosis as well as automatic reporting. Furthermore, the lack of specialist physicians is even more critical in resource-limited countries [111], and therefore the expected impacts of this technology would become even more relevant. However, the elaboration of high-quality medical reports from medical images, such as chest X-rays, computed tomography (CT) or magnetic resonance (MRI) scans, is a task that requires a trained radiologist with years of experience.