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Scholand N, Graf C, Mackner D, Holme HCM, Uecker M. Rational Approximation of Golden Angles for Simple and Reproducible Radial Sampling. ArXiv 2024:arXiv:2401.02892v1. [PMID: 38259342 PMCID: PMC10802672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
PURPOSE To develop a generic radial sampling scheme that combines the advantages of golden ratio sampling with simplicity of equidistant angular patterns. The irrational angle between consecutive spokes in golden ratio based sampling schemes enables a flexible retrospective choice of temporal resolution, while preserving good coverage of k-space for each individual bin. Nevertheless, irrational increments prohibit precomputation of the point-spread function (PSF), can lead to numerical problems, and require more complex processing steps. To avoid these problems, a new sampling scheme based on a rational approximation of golden angles (RAGA) is developed. METHODS The theoretical properties of RAGA sampling are mathematically derived. Sidelobe-to-peak ratios (SPR) are numerically computed and compared to the corresponding golden ratio sampling schemes. The sampling scheme is implemented in the BART toolbox and in a radial gradient-echo sequence. Feasibility is shown for quantitative imaging in a phantom and a cardiac scan of a healthy volunteer. RESULTS RAGA sampling can accurately approximate golden ratio sampling and has almost identical PSF and SPR. In contrast to golden ratio sampling, each frame can be reconstructed with the same equidistant trajectory using different sampling masks, and the angle of each acquired spoke can be encoded as a small index, which simplifies processing of the acquired data. CONCLUSION RAGA sampling provides the advantages of golden ratio sampling while simplifying data processing, rendering it a valuable tool for dynamic and quantitative MRI.
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Wang X, Rosenzweig S, Roeloffs V, Blumenthal M, Scholand N, Tan Z, Holme HCM, Unterberg-Buchwald C, Hinkel R, Uecker M. Free-breathing myocardial T 1 mapping using inversion-recovery radial FLASH and motion-resolved model-based reconstruction. Magn Reson Med 2023; 89:1368-1384. [PMID: 36404631 PMCID: PMC9892313 DOI: 10.1002/mrm.29521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 09/22/2022] [Accepted: 10/20/2022] [Indexed: 11/22/2022]
Abstract
PURPOSE To develop a free-breathing myocardialT 1 $$ {\mathrm{T}}_1 $$ mapping technique using inversion-recovery (IR) radial fast low-angle shot (FLASH) and calibrationless motion-resolved model-based reconstruction. METHODS Free-running (free-breathing, retrospective cardiac gating) IR radial FLASH is used for data acquisition at 3T. First, to reduce the waiting time between inversions, an analytical formula is derived that takes the incompleteT 1 $$ {\mathrm{T}}_1 $$ recovery into account for an accurateT 1 $$ {\mathrm{T}}_1 $$ calculation. Second, the respiratory motion signal is estimated from the k-space center of the contrast varying acquisition using an adapted singular spectrum analysis (SSA-FARY) technique. Third, a motion-resolved model-based reconstruction is used to estimate both parameter and coil sensitivity maps directly from the sorted k-space data. Thus, spatiotemporal total variation, in addition to the spatial sparsity constraints, can be directly applied to the parameter maps. Validations are performed on an experimental phantom, 11 human subjects, and a young landrace pig with myocardial infarction. RESULTS In comparison to an IR spin-echo reference, phantom results confirm goodT 1 $$ {\mathrm{T}}_1 $$ accuracy, when reducing the waiting time from 5 s to 1 s using the new correction. The motion-resolved model-based reconstruction further improvesT 1 $$ {\mathrm{T}}_1 $$ precision compared to the spatial regularization-only reconstruction. Aside from showing that a reliable respiratory motion signal can be estimated using modified SSA-FARY, in vivo studies demonstrate that dynamic myocardialT 1 $$ {\mathrm{T}}_1 $$ maps can be obtained within 2 min with good precision and repeatability. CONCLUSION Motion-resolved myocardialT 1 $$ {\mathrm{T}}_1 $$ mapping during free-breathing with good accuracy, precision and repeatability can be achieved by combining inversion-recovery radial FLASH, self-gating and a calibrationless motion-resolved model-based reconstruction.
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Affiliation(s)
- Xiaoqing Wang
- Institute of Biomedical Imaging, Graz University of Technology, Graz, Austria
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Sebastian Rosenzweig
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Volkert Roeloffs
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
| | - Moritz Blumenthal
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
| | - Nick Scholand
- Institute of Biomedical Imaging, Graz University of Technology, Graz, Austria
| | - Zhengguo Tan
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | | | - Christina Unterberg-Buchwald
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Rabea Hinkel
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
- Laboratory Animal Science Unit, Leibniz Institute for Primate Research, Deutsches Primatenzentrum GmbH, Göttingen, Germany
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behavior, University of Veterinary Medicine, Hannover, Germany
| | - Martin Uecker
- Institute of Biomedical Imaging, Graz University of Technology, Graz, Austria
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
- Cluster of “Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
- BioTechMed-Graz, Graz, Austria
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Blumenthal M, Luo G, Schilling M, Holme HCM, Uecker M. Deep, deep learning with BART. Magn Reson Med 2023; 89:678-693. [PMID: 36254526 PMCID: PMC10898647 DOI: 10.1002/mrm.29485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/26/2022] [Accepted: 09/20/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE To develop a deep-learning-based image reconstruction framework for reproducible research in MRI. METHODS The BART toolbox offers a rich set of implementations of calibration and reconstruction algorithms for parallel imaging and compressed sensing. In this work, BART was extended by a nonlinear operator framework that provides automatic differentiation to allow computation of gradients. Existing MRI-specific operators of BART, such as the nonuniform fast Fourier transform, are directly integrated into this framework and are complemented by common building blocks used in neural networks. To evaluate the use of the framework for advanced deep-learning-based reconstruction, two state-of-the-art unrolled reconstruction networks, namely the Variational Network and MoDL, were implemented. RESULTS State-of-the-art deep image-reconstruction networks can be constructed and trained using BART's gradient-based optimization algorithms. The BART implementation achieves a similar performance in terms of training time and reconstruction quality compared to the original implementations based on TensorFlow. CONCLUSION By integrating nonlinear operators and neural networks into BART, we provide a general framework for deep-learning-based reconstruction in MRI.
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Affiliation(s)
- Moritz Blumenthal
- Institute for Diagnostic and Interventional Radiology,
University Medical Center Göttingen, Göttingen, Germany
| | - Guanxiong Luo
- Institute for Diagnostic and Interventional Radiology,
University Medical Center Göttingen, Göttingen, Germany
| | - Martin Schilling
- Institute for Diagnostic and Interventional Radiology,
University Medical Center Göttingen, Göttingen, Germany
| | | | - Martin Uecker
- Institute for Diagnostic and Interventional Radiology,
University Medical Center Göttingen, Göttingen, Germany
- Institute of Biomedical Imaging, Graz University of
Technology, Graz, Austria
- German Centre for Cardiovascular Research (DZHK),Partner
Site Göttingen, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from
Molecular Machines to Networks of Excitable Cells” (MBExC), University of
Göttingen, Germany
- BioTechMed-Graz, Graz, Austria
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Wang X, Rosenzweig S, Scholand N, Holme HCM, Uecker M. Model-based reconstruction for simultaneous multi-slice T1 mapping using single-shot inversion-recovery radial FLASH. Magn Reson Med 2021; 85:1258-1271. [PMID: 32936487 PMCID: PMC10409492 DOI: 10.1002/mrm.28497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 01/17/2023]
Abstract
PURPOSE To develop a single-shot multi-slice T 1 mapping method by combing simultaneous multi-slice (SMS) excitations, single-shot inversion-recovery (IR) radial fast low-angle shot (FLASH), and a nonlinear model-based reconstruction method. METHODS SMS excitations are combined with a single-shot IR radial FLASH sequence for data acquisition. A previously developed single-slice calibrationless model-based reconstruction is extended to SMS, formulating the estimation of parameter maps and coil sensitivities from all slices as a single nonlinear inverse problem. Joint-sparsity constraints are further applied to the parameter maps to improve T 1 precision. Validations of the proposed method are performed for a phantom and for the human brain and liver in 6 healthy adult subjects. RESULTS Phantom results confirm good T 1 accuracy and precision of the simultaneously acquired multi-slice T 1 maps in comparison to single-slice references. In vivo human brain studies demonstrate the better performance of SMS acquisitions compared to the conventional spoke-interleaved multi-slice acquisition using model-based reconstruction. Aside from good accuracy and precision, the results of 6 healthy subjects in both brain and abdominal studies confirm good repeatability between scan and re-scans. The proposed method can simultaneously acquire T 1 maps for 5 slices of a human brain ( 0.75 × 0.75 × 5 mm 3 ) or 3 slices of the abdomen ( 1.25 × 1.25 × 6 mm 3 ) within 4 seconds. CONCLUSIONS The IR SMS radial FLASH acquisition together with a nonlinear model-based reconstruction enable rapid high-resolution multi-slice T 1 mapping with good accuracy, precision, and repeatability.
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Affiliation(s)
- Xiaoqing Wang
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Sebastian Rosenzweig
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Nick Scholand
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - H. Christian M. Holme
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Martin Uecker
- Institute for Diagnostic and Interventional Radiology of the University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Göttingen, Germany
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Rosenzweig S, Scholand N, Holme HCM, Uecker M. Cardiac and Respiratory Self-Gating in Radial MRI Using an Adapted Singular Spectrum Analysis (SSA-FARY). IEEE Trans Med Imaging 2020; 39:3029-3041. [PMID: 32275585 DOI: 10.1109/tmi.2020.2985994] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cardiac Magnetic Resonance Imaging (MRI) is time-consuming and error-prone. To ease the patient's burden and to increase the efficiency and robustness of cardiac exams, interest in methods based on continuous steady-state acquisition and self-gating has been growing in recent years. Self-gating methods extract the cardiac and respiratory signals from the measurement data and then retrospectively sort the data into cardiac and respiratory phases. Repeated breathholds and synchronization with the heart beat using some external device as required in conventional MRI are then not necessary. In this work, we introduce a novel self-gating method for radially acquired data based on a dimensionality reduction technique for time-series analysis (SSA-FARY). Building on Singular Spectrum Analysis, a zero-padded, time-delayed embedding of the auto-calibration data is analyzed using Principle Component Analysis. We demonstrate the basic functionality of SSA-FARY using numerical simulations and apply it to in-vivo cardiac radial single-slice bSSFP and Simultaneous Multi-Slice radiofrequency-spoiled gradient-echo measurements, as well as to Stack-of-Stars bSSFP measurements. SSA-FARY reliably detects the cardiac and respiratory motion and separates it from noise. We utilize the generated signals for high-dimensional image reconstruction using parallel imaging and compressed sensing with in-plane wavelet and (spatio-)temporal total-variation regularization.
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Rosenzweig S, Holme HCM, Uecker M. Simple auto‐calibrated gradient delay estimation from few spokes using Radial Intersections (RING). Magn Reson Med 2018; 81:1898-1906. [DOI: 10.1002/mrm.27506] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/02/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Sebastian Rosenzweig
- Institute for Diagnostic and Interventional RadiologyUniversity Medical Center Göttingen Göttingen Germany
| | - H. Christian M. Holme
- Institute for Diagnostic and Interventional RadiologyUniversity Medical Center Göttingen Göttingen Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen Göttingen Germany
| | - Martin Uecker
- Institute for Diagnostic and Interventional RadiologyUniversity Medical Center Göttingen Göttingen Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen Göttingen Germany
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Roeloffs V, Rosenzweig S, Holme HCM, Uecker M, Frahm J. Frequency-modulated SSFP with radial sampling and subspace reconstruction: A time-efficient alternative to phase-cycled bSSFP. Magn Reson Med 2018; 81:1566-1579. [PMID: 30357904 DOI: 10.1002/mrm.27505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/05/2018] [Accepted: 08/03/2018] [Indexed: 11/11/2022]
Abstract
PURPOSE A novel subspace-based reconstruction method for frequency-modulated balanced steady-state free precession (fmSSFP) MRI is presented. In this work, suitable data acquisition schemes, subspace sizes, and efficiencies for banding removal are investigated. THEORY AND METHODS By combining a fmSSFP MRI sequence with a 3D stack-of-stars trajectory, scan efficiency is maximized as spectral information is obtained without intermediate preparation phases. A memory-efficient reconstruction routine is implemented by introducing the low-frequency Fourier transform as a subspace which allows for the formulation of a convex reconstruction problem. The removal of banding artifacts is investigated by comparing the proposed acquisition and reconstruction technique to phase-cycled bSSFP MRI. Aliasing properties of different undersampling schemes are analyzed and water/fat separation is demonstrated by reweighting the reconstructed subspace coefficients to generate virtual spectral responses in a post-processing step. RESULTS A simple root-of-sum-of-squares combination of the reconstructed subspace coefficients yields high-SNR images with the characteristic bSSFP contrast but without banding artifacts. Compared to Golden-Angle trajectories, turn-based sampling schemes were superior in minimizing aliasing across reconstructed subspace coefficients. Water/fat separated images of the human knee were obtained by reweighting subspace coefficients. CONCLUSIONS The novel subspace-based fmSSFP MRI technique emerges as a time-efficient alternative to phase-cycled bSFFP. The method does not need intermediate preparation phases, offers high SNR and avoids banding artifacts. Reweighting of the reconstructed subspace coefficients allows for generating virtual spectral responses with applications to water/fat separation.
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Affiliation(s)
- Volkert Roeloffs
- Biomedizinische NMR Forschungs GmbH am Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - Sebastian Rosenzweig
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), Göttingen, Germany
| | - H Christian M Holme
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), Göttingen, Germany
| | - Martin Uecker
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), Göttingen, Germany
| | - Jens Frahm
- Biomedizinische NMR Forschungs GmbH am Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), Göttingen, Germany
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Holme HCM, Frahm J. Sinogram-based coil selection for streak artifact reduction in undersampled radial real-time magnetic resonance imaging. Quant Imaging Med Surg 2016; 6:552-556. [PMID: 27942475 DOI: 10.21037/qims.2016.10.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Streak artifacts are a common problem in radial magnetic resonance imaging (MRI). We therefore developed a method for automatically excluding receiver coil elements which lead to these artifacts. METHODS The proposed coil selection relates to real-time MRI data based on highly undersampled radial acquisitions. It exploits differences between high- and low-resolution sinograms reconstructed from datasets acquired during preparatory scans. Apart from phantom validations, the performance was assessed for real-time MRI studies of different human organ systems in vivo. RESULTS The algorithm greatly reduces streak artifact strength without compromising image quality in other parts of the image. It is robust with respect to different experimental settings and fast to be included in the online reconstruction pipeline for real-time MRI. CONCLUSIONS The proposed method enables a fast reduction of streak artifacts in radial real-time MRI.
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Affiliation(s)
| | - Jens Frahm
- Max Planck Institute for Biophysical Chemistry, 37070 Göttingen, Germany;; DZHK (German Center for Cardiovascular Research), partner site Göttingen, Göttingen, Germany
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