K-space data processing for Magnetic Resonance Elastography (MRE)

International audienceObject: Magnetic Resonance Elastography (MRE) requires substantial data processing based on phase image reconstruction, wave enhancement and inverse problem solving. The objective of this study is to propose a new, fast MRE method based on MR raw data processing, particularly adapted to applications requiring fast MRE measurement or high elastogram update rate.Material and Methods: The proposed method allows measuring tissue elasticity directly from raw data without prior phase image reconstruction and without phase unwrapping. Experimental feasibility is assessed both in a gelatin phantom and in the liver of a porcine model in vivo. Elastograms are reconstructed with the raw MRE method and compared to those obtained using conventional MRE. In a third experiment, changes in elasticity are monitored in real-time in a gelatin phantom during its solidification by using both conventional MRE and raw MRE.Results: The raw MRE method shows promising results by providing similar elasticity values to the ones obtained with conventional MRE methods while decreasing the number of processing steps and circumventing the delicate step of phase unwrapping. Limitations of the proposed method are the influence of the magnitude on the elastogram and the requirement for a minimum number of phase offsets.Conclusion: This study demonstrates the feasibility of directly reconstructing elastograms from raw data

QUARCH: A New Quasi-Affine Reconstruction Stratum From Vague Relative Camera Orientation Knowledge

International audienceWe present a new quasi-affine reconstruction of a scene and its application to camera self-calibration. We refer to this reconstruction as QUARCH (QUasi-Affine Reconstruction with respect to Camera centers and the Hodographs of horopters). A QUARCH can be obtained by solving a semidefinite programming problem when, (i) the images have been captured by a moving camera with constant intrinsic parameters, and (ii) a vague knowledge of the relative orientation (under or over 120°) between camera pairs is available. The resulting reconstruction comes close enough to an affine one allowing thus an easy upgrade of the QUARCH to its affine and metric counterparts. We also present a constrained Levenberg-Marquardt method for nonlinear optimization subject to Linear Matrix Inequality (LMI) constraints so as to ensure that the QUARCH LMIs are satisfied during optimization. Experiments with synthetic and real data show the benefits of QUARCH in reliably obtaining a metric reconstruction

QUARCH: A New Quasi-Affine Reconstruction Stratum From Vague Relative Camera Orientation Knowledge

International audienceWe present a new quasi-affine reconstruction of a scene and its application to camera self-calibration. We refer to this reconstruction as QUARCH (QUasi-Affine Reconstruction with respect to Camera centers and the Hodographs of horopters). A QUARCH can be obtained by solving a semidefinite programming problem when, (i) the images have been captured by a moving camera with constant intrinsic parameters, and (ii) a vague knowledge of the relative orientation (under or over 120°) between camera pairs is available. The resulting reconstruction comes close enough to an affine one allowing thus an easy upgrade of the QUARCH to its affine and metric counterparts. We also present a constrained Levenberg-Marquardt method for nonlinear optimization subject to Linear Matrix Inequality (LMI) constraints so as to ensure that the QUARCH LMIs are satisfied during optimization. Experiments with synthetic and real data show the benefits of QUARCH in reliably obtaining a metric reconstruction

Inverse real-time Finite Element simulation for robotic control of flexible needle insertion in deformable tissues

International audienceThis paper introduces a new method for automatic robotic needle steering in deformable tissues. The main contribution relies on the use of an inverse Finite Element (FE) simulation to control an articulated robot interacting with deformable structures. In this work we consider a flexible needle, embedded in the end effector of a 6 arm Mitsubishi RV1A robot, and its insertion into a silicone phantom. Given a trajectory on the rest configuration of the silicone phantom, our method provides in real-time the displacements of the articulated robot which guarantee the permanence of the needle within the predefined path, taking into account any undergoing deformation on both the needle and the trajectory itself. A forward simulation combines i) a kinematic model of the robot, ii) FE models of the needle and phantom gel iii) an interaction model allowing the simulation of friction and puncture force. A Newton-type method is then used to provide the displacement of the robot to minimize the distance between the needle's tip and the desired trajectory. We validate our approach with a simulation in which a virtual robot can successfully perform the insertion while both the needle and the trajectory undergo significant deformations

Using spatial-temporal ensembles of convolutional neural networks for lumen segmentation in ureteroscopy

Purpose: Ureteroscopy is an efficient endoscopic minimally invasive technique for the diagnosis and treatment of upper tract urothelial carcinoma (UTUC). During ureteroscopy, the automatic segmentation of the hollow lumen is of primary importance, since it indicates the path that the endoscope should follow. In order to obtain an accurate segmentation of the hollow lumen, this paper presents an automatic method based on Convolutional Neural Networks (CNNs). Methods: The proposed method is based on an ensemble of 4 parallel CNNs to simultaneously process single and multi-frame information. Of these, two architectures are taken as core-models, namely U-Net based in residual blocks($m_1$) and Mask-RCNN($m_2$), which are fed with single still-frames $I(t)$. The other two models ($M_1$, $M_2$) are modifications of the former ones consisting on the addition of a stage which makes use of 3D Convolutions to process temporal information. $M_1$, $M_2$ are fed with triplets of frames ($I(t-1)$, $I(t)$, $I(t+1)$) to produce the segmentation for $I(t)$. Results: The proposed method was evaluated using a custom dataset of 11 videos (2,673 frames) which were collected and manually annotated from 6 patients. We obtain a Dice similarity coefficient of 0.80, outperforming previous state-of-the-art methods. Conclusion: The obtained results show that spatial-temporal information can be effectively exploited by the ensemble model to improve hollow lumen segmentation in ureteroscopic images. The method is effective also in presence of poor visibility, occasional bleeding, or specular reflections

Interventional MR Elastography for MRI-Guided Percutaneous Procedures

International audiencePURPOSE : MRI-guided thermal ablations require reliable monitoring methods to ensure complete destruction of the diseased tissue while avoiding damage to the surrounding healthy tissue. Based on the fact that thermal ablations result in substantial changes in biomechanical properties, interventional MR elastography (MRE) dedicated to the monitoring of MR-guided thermal therapies is proposed here. METHODS : Interventional MRE consists of a needle MRE driver, a fast and interactive gradient echo pulse sequence with motion encoding, and an inverse problem solver in real-time. This complete protocol was tested in vivo on swine and the ability to monitor elasticity changes in real-time was assessed in phantom. RESULTS : Thanks to a short repetition time, a reduction of the number of phase-offsets and the use of a sliding window, one refreshed elastogram was provided every 2.56 s for an excitation frequency of 100 Hz. In vivo elastograms of swine liver were successfully provided in real-time during one breath-hold. Changes of elasticity were successfully monitored in a phantom during its gelation with the same elastogram frame rate. CONCLUSION : This study demonstrates the ability of detecting elasticity changes in real-time and providing elastograms in vivo with interventional MRE that could be used for the monitoring of thermal ablations

Marker-based Registration for Large Deformations -Application to Open Liver Surgery

International audienceThis paper introduces an Augmented Reality (AR) system for open liver surgery. Although open surgery remains the gold-standard for the treatment of complex tumors and central lesions, technological issues actually prevent using AR with sufficient accuracy for clinical use. We propose a markers-based method allowing for the tracking and the deformation of a preoperative model in real-time during the surgery. Markers are manually placed on the surface of the organ after opening the abdominal cavity, and tracked in real-time by a set of infrared cameras. Our framework is composed of both a non-rigid initial registration method, providing an estimation of the location of the markers in the preoperative model, and a real-time tracking algorithm to deform the model during the surgery (even for large deformation or partial occlusion of the organ). The method is validated on both synthetic and ex-vivo samples; in addition, we demonstrate its applicability in the operating room during a liver resection surgery on a human patient. Preliminary studies provided promising results to improve the location of tumors, and to help surgeons into planning the ideal resection intraoperatively

Distortion and instability compensation with deep learning for rotational scanning endoscopic optical coherence tomography

Optical Coherence Tomography (OCT) is increasingly used in endoluminal procedures since it provides high-speed and high resolution imaging. Distortion and instability of images obtained with a proximal scanning endoscopic OCT system are significant due to the motor rotation irregularity, the friction between the rotating probe and outer sheath and synchronization issues. On-line compensation of artefacts is essential to ensure image quality suitable for real-time assistance during diagnosis or minimally invasive treatment. In this paper, we propose a new online correction method to tackle both B-scan distortion, video stream shaking and drift problem of endoscopic OCT linked to A-line level image shifting. The proposed computational approach for OCT scanning video correction integrates a Convolutional Neural Network (CNN) to improve the estimation of azimuthal shifting of each A-line. To suppress the accumulative error of integral estimation we also introduce another CNN branch to estimate a dynamic overall orientation angle. We train the network with semi-synthetic OCT videos by intentionally adding rotational distortion into real OCT scanning images. The results show that networks trained on this semi-synthetic data generalize to stabilize real OCT videos, and the algorithm efficacy is demonstrated on both ex vivo and in vivo data, where strong scanning artifacts are successfully corrected. (c) 2022 The Authors. Published by Elsevier B.V

Domain Decomposition for real time Simulation of needle insertion

International audienceOur goal is to develop robotized needle insertion for drug delivery in small animals. We control the robot with a real-time Finite Element simulation that provides accurate models of the deformable environment. To predict the deformations we need to solve a contact problem which is known to be time consuming. To reduce the computational time we use the domain decomposition method: the FE mesh is split in several domains in order to extract paral-lelism for GPU computing and to concentrate the computation time around the needle