Attenuation Coefficient Estimation for PET/MRI With Bayesian Deep Learning pseudo-CT and Maximum Likelihood Estimation of Activity and Attenuation
Andrew P. Leynes, Sangtae P. Ahn, Kristen A. Wangerin, Sandeep S. Kaushik, Florian Wiesinger, Thomas A. Hope, Peder E. Z. Larson
备注：
Accepted to the IEEE Transactions on Radiation and Plasma Medical Sciences on October 3, 2021. To be published under open access Creative Commons Attribution License (CC BY)
发表信息：
IEEE Transactions on Radiation and Plasma Medical Sciences, Early access, 2021
A major remaining challenge for magnetic resonance-based attenuation correction methods (MRAC) is their susceptibility to sources of MRI artifacts (e.g. implants, motion) and uncertainties due to the limitations of MRI contrast (e.g. accurate bone delineation and density, and separation of air/bone). We propose using a Bayesian deep convolutional neural network that, in addition to generating an initial pseudo-CT from MR data, also produces uncertainty estimates of the pseudo-CT to quantify the limitations of the MR data. These outputs are combined with MLAA reconstruction that uses the PET emission data to improve the attenuation maps. With the proposed approach (UpCT-MLAA), we demonstrate accurate estimation of PET uptake in pelvic lesions and show recovery of metal implants. In patients without implants, UpCT-MLAA had acceptable but slightly higher RMSE than Zero-echo-time and Dixon Deep pseudo-CT when compared to CTAC. In patients with metal implants, MLAA recovered the metal implant; however, anatomy outside the implant region was obscured by noise and crosstalk artifacts. Attenuation coefficients from the pseudo-CT from Dixon MRI were accurate in normal anatomy; however, the metal implant region was estimated to have attenuation coefficients of air. UpCT-MLAA estimated attenuation coefficients of metal implants alongside accurate anatomic depiction outside of implant regions.
Attenuation and scatter correction (AC) is crucial for quantitative Positron Emission Tomography (PET) imaging. Recently, direct application of AC in the image domain using deep learning approaches has been proposed for the hybrid PET/MR and dedicated PET systems that lack accompanying transmission or anatomical imaging. This study set out to investigate deep learning-based AC in the image domain using different input settings.
To reconstruct a radioactive tracer distribution with positron emission tomography (PET), the background attenuation correction is needed to eliminate image artifacts. Recent research shows that time-of-flight (TOF) PET data determine the attenuation sinogram up to a constant, and its gradient can be computed using an analytic algorithm. In this paper, we study a direct estimation of the sinogram only from TOF PET data. First, the gradient of the attenuation sinogram is estimated using the aforementioned algorithm. Then, a relationship is established to link the differential attenuation sinogr…
Quantitative PET attenuation correction (AC) for combined cardiac PET/MR is a challenging problem. We propose and evaluate an AC approach that uses coincidences from a relatively weak and physically fixed sparse external source, in combination with that from the patient, to correct for PET attenuation based on physics principles alone. The low 30 ml volume of the source makes it easy to fill and place, and the method does not use prior image data or attenuation map assumptions. Our supplemental transmission aided maximum likelihood reconstruction of attenuation and activity (sTX-MLAA) algorith…
Yale University（耶鲁大学）；Yale New Haven Hospital（耶鲁纽黑文医院）
In PET/CT imaging, CT is used for PET attenuation correction (AC). Mismatch between CT and PET due to patient body motion results in AC artifacts. In addition, artifact caused by metal, beam-hardening and count-starving in CT itself also introduces inaccurate AC for PET. Maximum likelihood reconstruction of activity and attenuation (MLAA) was proposed to solve those issues by simultaneously reconstructing tracer activity ($λ$-MLAA) and attenuation map ($μ$-MLAA) based on the PET raw data only. However, $μ$-MLAA suffers from high noise and $λ$-MLAA suffers from large bias as compared to the rec…
The integration of positron emission tomography (PET) and magnetic resonance imaging (MRI) has been an ongoing research topic for the last 20 years. This paper gives an overview of the different developments and the technical problems associated with combining PET and MRI in one system. After explaining the different detector concepts for integrating PET-MRI and minimising interference the limitations and advantages of different solutions for the detector and system are described for preclinical and clinical imaging systems. The different integrated PET-MRI systems are described in detail. Bes…
Recent developments in artificial intelligence technology have enabled new developments that can improve attenuation and scatter correction in PET and SPECT. These technologies will enable the use of accurate and quantitative imaging without the need to acquire a CT image, greatly expanding the capability of PET/MRI, PET-only, and SPECT-only scanners. The use of AI to aid in scatter correction will lead to improvements in image reconstruction speed, and improve patient throughput. This paper outlines the use of these new tools, surveys contemporary implementation, and discusses their limitatio…
University of California, San Francisco（加州大学旧金山分校）；University of California, Berkeley（加州大学伯克利分校）；University of Colorado（科罗拉多大学）
In this paper, we review physics- and data-driven reconstruction techniques for simultaneous positron emission tomography (PET) / magnetic resonance imaging (MRI) systems, which have significant advantages for clinical imaging of cancer, neurological disorders, and heart disease. These reconstruction approaches utilize priors, either structural or statistical, together with a physics-based description of the PET system response. However, due to the nested representation of the forward problem, direct PET/MRI reconstruction is a nonlinear problem. We elucidate how a multi-faceted approach accom…
Purpose: To develop bone material analogues that can be used in construction of phantoms for simultaneous PET/MRI systems. Methods: Plaster was used as the basis for the bone material analogues tested in this study. It was mixed with varying concentrations of an iodinated CT contrast, a gadolinium-based MR contrast agent, and copper sulfate to modulate the attenuation properties and MRI properties (T1 and T2*). Attenuation was measured with CT and 68Ge transmission scans, and MRI properties were measured with quantitative ultrashort echo time pulse sequences. A proof-of-concept skull was creat…
University of California, San Francisco（加州大学旧金山分校）
Positron Emission Tomography (PET) is a functional imaging modality widely used in neuroscience studies. To obtain meaningful quantitative results from PET images, attenuation correction is necessary during image reconstruction. For PET/MR hybrid systems, PET attenuation is challenging as Magnetic Resonance (MR) images do not reflect attenuation coefficients directly. To address this issue, we present deep neural network methods to derive the continuous attenuation coefficients for brain PET imaging from MR images. With only Dixon MR images as the network input, the existing U-net structure wa…
We propose a magnetic resonance (MR)-based method for estimation of continuous linear attenuation coefficients (LAC) in positron emission tomography (PET) using a physical compartmental model and ultrashort echo time (UTE)/multi-echo Dixon (mUTE) acquisitions. Specifically, we propose a three-dimensional (3D) mUTE sequence to acquire signals from water, fat, and short-T2 components (e.g., bones) simultaneously in a single acquisition. The proposed mUTE sequence integrates 3D UTE with multi-echo Dixon acquisitions and uses sparse radial trajectories to accelerate imaging speed. Errors in the ra…
University of California, San Francisco（加州大学旧金山分校）；University of New Mexico（新墨西哥大学）；Washington University（华盛顿大学）；University of Iowa（爱荷华大学）；University of Washington（华盛顿大学）
Historically, patient datasets have been used to develop and validate various reconstruction algorithms for PET/MRI and PET/CT. To enable such algorithm development, without the need for acquiring hundreds of patient exams, in this paper we demonstrate a deep learning technique to generate synthetic but realistic whole-body PET sinograms from abundantly-available whole-body MRI. Specifically, we use a dataset of 56 $^{18}$F-FDG-PET/MRI exams to train a 3D residual UNet to predict physiologic PET uptake from whole-body T1-weighted MRI. In training we implemented a balanced loss function to gene…
King’s College London（伦敦国王学院）；University College London（伦敦大学学院）
The ability to synthesise Computed Tomography images - commonly known as pseudo CT, or pCT - from MRI input data is commonly assessed using an intensity-wise similarity, such as an L2-norm between the ground truth CT and the pCT. However, given that the ultimate purpose is often to use the pCT as an attenuation map ($μ$-map) in Positron Emission Tomography Magnetic Resonance Imaging (PET/MRI), minimising the error between pCT and CT is not necessarily optimal. The main objective should be to predict a pCT that, when used as $μ$-map, reconstructs a pseudo PET (pPET) which is as close as possibl…
Prostate cancer is the most common disease in men and the second leading cause of death from cancer. Generic large imaging instruments used in cancer diagnosis have sensitivity, spatial resolution, and contrast inadequate for the task of imaging details of a small organ such as the prostate. In addition, multimodality imaging can play a significant role merging anatomical and functional details coming from simultaneous PET and MRI. Indeed, multi-parametric PET/MRI was demonstrated to improve diagnosis, but it suffers from too many false positives. In order to address the above limits of the cu…
Current methods for magnetic resonance-based positron emission tomography attenuation correction (PET-MR AC) are time consuming, and less able than computed tomography (CT)-based AC methods to capture inter-individual variability and skull abnormalities. Deep learning methods have been proposed to produce pseudo-CT from MR images, but these methods have not yet been evaluated in large clinical cohorts. Methods trained on healthy adult data may not work in clinical cohorts where skull morphometry may be abnormal, or in paediatric data where skulls tend to be thinner and smaller. Here, we train …
Standard dual-energy computed tomography (CT) uses two different X-ray energies to obtain energy-dependent tissue attenuation information to allow quantitative material decomposition. The combined use of dual-energy CT and positron emission tomography (PET) may provide a more comprehensive characterization of disease states in cancer and many other diseases. However, the integration of dual-energy CT with PET is not trivial, either requiring costly hardware upgrade or increasing radiation dose. This paper proposes a novel dual-energy CT imaging method that is enabled by the already-available P…
MultiModal Imaging is an innovative technique that consists in the combination of diagnostic exams based on different physical processes, to obtain a unique image with more detailed clinical information. The possibility of a simultaneous use of PET and MRI could be achieved by using a particular radioisotope: 52gMn. The main route to produce this isotope is the reaction 52Cr(p,n)52gMn which is theoretically investigated in this study by means of three nuclear reaction codes. An analysis of the cross sections and a computation of the production rates and time evolution of the produced radioisot…
An efficient approach with theoretical guarantees to simultaneously reconstruct activity and attenuation sinogram for TOF-PET
State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China（数学科学国家重点实验室，数学与系统科学研究院，中国科学院，北京100190，中国）；University of Chinese Academy of Sciences, Beijing 100190, China（中国科学院大学，北京100190，中国）
Patient motion is well-known for degrading image quality during medical imaging. Especially positron emission tomography (PET) is susceptible to motion due to its usually long scan times. In hybrid PET/MRI (magnetic resonance imaging), simultaneously acquired dynamic MRI data can be used to correct for motion. Usually, MRI model-based motion correction approaches are applied to the PET data. However, these approaches may fail for non-predictable, irregular motion. We propose a novel approach for the continuous and real-time tracking of motion using highly accelerated, dynamic MRI for an accura…
Accurate MR-based attenuation correction (MRAC) is essential for quantitative PET/MR imaging of the brain. In this study, we analyze the regional bias caused by MRAC based on Zero-Echo-Time MR images (ZTEAC) compared to CT-based AC (CTAC) in static and dynamic PET imaging. In addition the results are compared to the performance of the current default Atlas-based AC (AtlasAC) implemented in the GE SIGNA PET/MR. Methods: Thirty static [18F]FDG and 11 dynamic [18}F]PE2I acquisitions from a GE SIGNA PET/MR were reconstructed using ZTEAC (using a research tool, GE Healthcare), single-subject AtlasA…
Joint Reconstruction of Activity and Attenuation in PET by Diffusion Posterior Sampling in Wavelet Coefficient Space
LaTIM, Inserm UMR 1101, Université de Bretagne Occidentale（洛里昂医学成像与组织实验室，法国国家健康与医学研究院 UMR 1101，布列塔尼西部大学）；CentraleSupélec, IETR, CNRS UMR 6164（中央苏佩莱克高等学院，IETR，法国国家科学研究中心 UMR 6164）；Inria Monc, Université de Bordeaux, Bordeaux INP, CNRS（法国国家信息与自动化研究所蒙彼利埃中心，波尔多大学，波尔多国立理工学院，法国国家科学研究中心）；Nuclear Medicine Department, Poitiers University Hospital（核医学科，普瓦捷大学医院）
The integration of PET into MRI to form a hybrid system requires often compromises for both subsystems. For example, the integration might come at the cost of a reduced PET detector height or a reduced MRI examination volume diameter. Here, we propose a so-called shared-volume concept to use the volume required for both subsystems more efficiently, in which the MR transparency of the scintillator is exploited by integrating the RF shielding into the scintillator of the PET detector. Semi-monolithic scintillator prototypes (PVC slabs) of 7 mm and 12 mm height with integrated copper foil between…
University College London（伦敦大学学院）；King's College London（伦敦国王学院）
Attenuation correction is an essential requirement of positron emission tomography (PET) image reconstruction to allow for accurate quantification. However, attenuation correction is particularly challenging for PET-MRI as neither PET nor magnetic resonance imaging (MRI) can directly image tissue attenuation properties. MRI-based computed tomography (CT) synthesis has been proposed as an alternative to physics based and segmentation-based approaches that assign a population-based tissue density value in order to generate an attenuation map. We propose a novel deep fully convolutional neural ne…
Hyperion-IID is a positron emission tomography (PET) insert which allows simultaneous operation in a clinical magnetic resonance imaging (MRI) scanner. To read out the scintillation light of the employed LYSO crystal arrays with a pitch of 1 mm pitch and 12 mm in height, digital silicon photomultipliers (DPC 3200-22, Philips Digital Photon Counting) (DPC) are used. The basic PET performance in terms of energy resolution, coincidence resolution time (CRT) and sensitivity as a function of operating parameters, such as the operating temperature, the applied overvoltage, activity and configuration…
Organ-specific, targeted Field-of-View (FoV) Positron Emission Tomography (PET)/Magnetic Resonance Imaging (MRI) inserts are viable solutions for a number of imaging tasks where whole-body PET/MRI systems lack the necessary sensitivity and resolution. To meet the required PET detector performance of these systems, high count-rates and effective spatial resolutions on the order of a few mm, a novel two-axis patterned reflector foil pixelated scintillator crystal array design is developed and its proof-of-concept illustrated in-silico with the Monte Carlo radiation transport modelling toolkit Ge…
Multi-modality imaging hardware can be integrated in a single gantry to collect diverse datasets for complementary information and spatiotemporal correlation, with excellent examples including PET-CT and PET-MRI. However, there is no CT-MRI prototype up to today due to technical challenges and associated cost-benefit considerations. Thanks to the rapid development of medical imaging, it becomes feasible now to integrate cost-effective CT and MRI imagers together for portability, popularity, and point of care. In this paper, we present the top-level design of the first portable CT-MRI system an…
Arizona State University（亚利桑那州立大学）；Banner Alzheimer’s Institute（班纳阿尔茨海默病研究所）；Children’s Hospital Los Angeles（洛杉矶儿童医院）；Mayo Clinic Arizona（梅奥诊所亚利桑那分院）；University of Southern California（南加州大学）
Background: Beta-amyloid (A$β$) plaques and tau protein tangles in the brain are the defining 'A' and 'T' hallmarks of Alzheimer's disease (AD), and together with structural atrophy detectable on brain magnetic resonance imaging (MRI) scans as one of the neurodegenerative ('N') biomarkers comprise the ''ATN framework'' of AD. Current methods to detect A$β$/tau pathology include cerebrospinal fluid (CSF; invasive), positron emission tomography (PET; costly and not widely available), and blood-based biomarkers (BBBM; promising but mainly still in development). Objective: To develop a non-invasiv…
Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Zhejiang University（浙江大学）
Positron emission tomography (PET) is widely used for clinical diagnosis. As PET suffers from low resolution and high noise, numerous efforts try to incorporate anatomical priors into PET image reconstruction, especially with the development of hybrid PET/CT and PET/MRI systems. In this work, we proposed a novel 3D structural convolutional sparse coding (CSC) concept for penalized-likelihood PET image reconstruction, named 3D PET-CSC. The proposed 3D PET-CSC takes advantage of the convolutional operation and manages to incorporate anatomical priors without the need of registration or supervise…
In phase-contrast magnetic resonance imaging (PC-MRI), spin velocity contributes to the phase measured at each voxel. Therefore, estimating velocity from potentially wrapped phase measurements is the task of solving a system of noisy congruence equations. We propose Phase Recovery from Multiple Wrapped Measurements (PRoM) as a fast, approximate maximum likelihood estimator of velocity from multi-coil data with possible amplitude attenuation due to dephasing. The estimator can recover the fullest possible extent of unambiguous velocities, which can greatly exceed twice the highest venc. The est…
Arizona State University（亚利桑那州立大学）；Banner Alzheimer’s Institute（班纳阿尔茨海默病研究所）；Southeast University（东南大学）；Children’s Hospital Los Angeles（洛杉矶儿童医院）；Mayo Clinic Arizona（梅奥诊所亚利桑那分院）；University of Southern California（南加州大学）
Biomarker-assisted diagnosis and intervention in Alzheimer's disease (AD) may be the key to prevention breakthroughs. One of the hallmarks of AD is the accumulation of tau plaques in the human brain. However, current methods to detect tau pathology are either invasive (lumbar puncture) or quite costly and not widely available (Tau PET). In our previous work, structural MRI-based hippocampal multivariate morphometry statistics (MMS) showed superior performance as an effective neurodegenerative biomarker for preclinical AD and Patch Analysis-based Surface Correntropy-induced Sparse coding and ma…
Two algorithms for solving misalignment issues in penalized PET/CT reconstruction using anatomical priors are proposed. Both approaches are based on a recently published joint motion estimation and image reconstruction method. The first approach deforms the anatomical image to align it with the functional one while the second approach deforms both images to align them with the measured data. Our current implementation alternates between image reconstruction and alignment estimation. To evaluate the potential of these approaches, we have chosen Parallel Level Sets (PLS) as a representative anat…
Physics-Constrained Diffusion Reconstruction with Posterior Correction for Quantitative and Fast PET Imaging
Beijing Normal University（北京师范大学）；Beijing Friendship Hospital, Capital Medical University（首都医科大学北京友谊医院）；The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China（中国科学技术大学生命科学与医学部附属第一医院）；Jiangnan University（江南大学）；University of Melbourne（墨尔本大学）
University Medical Center Utrecht（乌得勒支大学医学中心）；DKFZ German Cancer Research Center（德国癌症研究中心）；Heidelberg University（海德堡大学）
Recently, deep learning (DL)-based methods for the generation of synthetic computed tomography (sCT) have received significant research attention as an alternative to classical ones. We present here a systematic review of these methods by grouping them into three categories, according to their clinical applications: I) To replace CT in magnetic resonance (MR)-based treatment planning. II) Facilitate cone-beam computed tomography (CBCT)-based image-guided adaptive radiotherapy. III) Derive attenuation maps for the correction of positron emission tomography (PET). Appropriate database searching …
Combined use of PET and dual-energy CT provides complementary information for multi-parametric imaging. PETenabled dual-energy CT combines a low-energy x-ray CT image with a high-energy &γ&-ray CT (GCT) image reconstructed from time-of-flight PET emission data to enable dual-energy CT material decomposition on a PET/CT scanner. The maximumlikelihood attenuation and activity (MLAA) algorithm has been used for GCT reconstruction but suffers from noise. Kernel MLAA exploits an x-ray CT image prior through the kernel framework to guide GCT reconstruction and has demonstrated substantial improvemen…
