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Wu C, Hormuth DA, Easley T, Eijkhout V, Pineda F, Karczmar GS, Yankeelov TE. An in silico validation framework for quantitative DCE-MRI techniques based on a dynamic digital phantom. Med Image Anal 2021; 73:102186. [PMID: 34329903 PMCID: PMC8453106 DOI: 10.1016/j.media.2021.102186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
Quantitative evaluation of an image processing method to perform as designed is central to both its utility and its ability to guide the data acquisition process. Unfortunately, these tasks can be quite challenging due to the difficulty of experimentally obtaining the "ground truth" data to which the output of a given processing method must be compared. One way to address this issue is via "digital phantoms", which are numerical models that provide known biophysical properties of a particular object of interest. In this contribution, we propose an in silico validation framework for dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) acquisition and analysis methods that employs a novel dynamic digital phantom. The phantom provides a spatiotemporally-resolved representation of blood-interstitial flow and contrast agent delivery, where the former is solved by a 1D-3D coupled computational fluid dynamic system, and the latter described by an advection-diffusion equation. Furthermore, we establish a virtual simulator which takes as input the digital phantom, and produces realistic DCE-MRI data with controllable acquisition parameters. We assess the performance of a simulated standard-of-care acquisition (Protocol A) by its ability to generate contrast-enhanced MR images that separate vasculature from surrounding tissue, as measured by the contrast-to-noise ratio (CNR). We find that the CNR significantly decreases as the spatial resolution (SRA, where the subscript indicates Protocol A) or signal-to-noise ratio (SNRA) decreases. Specifically, with an SNRA / SRA = 75 dB / 30 μm, the median CNR is 77.30, whereas an SNRA / SRA = 5 dB / 300 μm reduces the CNR to 6.40. Additionally, we assess the performance of simulated ultra-fast acquisition (Protocol B) by its ability to generate DCE-MR images that capture contrast agent pharmacokinetics, as measured by error in the signal-enhancement ratio (SER) compared to ground truth (PESER). We find that PESER significantly decreases the as temporal resolution (TRB) increases. Similar results are reported for the effects of spatial resolution and signal-to-noise ratio on PESER. For example, with an SNRB / SRB / TRB = 5 dB / 300 μm / 10 s, the median PESER is 21.00%, whereas an SNRB / SRB / TRB = 75 dB / 60 μm / 1 s, yields a median PESER of 0.90%. These results indicate that our in silico framework can generate virtual MR images that capture effects of acquisition parameters on the ability of generated images to capture morphological or pharmacokinetic features. This validation framework is not only useful for investigations of perfusion-based MRI techniques, but also for the systematic evaluation and optimization new MRI acquisition, reconstruction, and image processing techniques.
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Affiliation(s)
- Chengyue Wu
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, 201 E 24th St, Austin, TX 78712, United States.
| | - David A Hormuth
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, 201 E 24th St, Austin, TX 78712, United States; Livestrong Cancer Institutes, United States
| | - Ty Easley
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, United States
| | | | - Federico Pineda
- Department of Radiology, The University of Chicago, Chicago, IL 60637, United States
| | - Gregory S Karczmar
- Department of Radiology, The University of Chicago, Chicago, IL 60637, United States
| | - Thomas E Yankeelov
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, 201 E 24th St, Austin, TX 78712, United States; Livestrong Cancer Institutes, United States; Departments of Biomedical Engineering, United States; Departments of Diagnostic Medicine, United States; Departments of Oncology, The University of Texas at Austin, Austin, TX 78712, United States; Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX 77030, United States
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Sun W, Wang W, Zhu K, Chen CZ, Wen XX, Zeng MS, Rao SX. Feasibility of compressed sensing technique for isotropic dynamic contrast-enhanced liver magnetic resonance imaging. Eur J Radiol 2021; 139:109729. [PMID: 33905976 DOI: 10.1016/j.ejrad.2021.109729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE To investigate whether an isotropic T1-weighted gradient echo (T1-GRE) sequence using a compressed sensing (CS) technique during liver magnetic resonance imaging (MRI) can improve the image quality compared to that using a standard parallel imaging (PI) technique in patients with hepatocellular carcinoma (HCC). METHODS Forty-nine patients with single pathologically confirmed HCC were included in the prospective study, who underwent a 3.0 T MRI including the two T1-GRE sequences (CS and PI). Qualitative analysis including the relative contrast (RC) of liver-to-lesion, liver-to-portal vein and liver-to-hepatic vein on pre-contrast and postcontrast (delayed phase) images were calculated. Respiratory motion artifact, gastrointestinal motion artifact and overall image quality were scored by using a 4-point scale. RESULTS RC of liver-to-lesion, liver-to-portal vein and liver-to-hepatic vein measured on both pre-contrast and postcontrast phase images were significantly higher for CS than for PI. The scores of overall image quality was comparable between PI and CS (3.98 ± 0.10vs 3.96 ± 0.13, P = 0.083 for pre-contrast; 3.96 ± 0.16 vs 3.93 ± 0.17, P = 0.132 for postcontrast, respectively). The scores of gastrointestinal motion artifact was significantly higher for PI than for CS (3.92 ± 0.21 vs 3.69 ± 0.33 for pre-contrast; 3.86 ± 0.21 vs 3.59 ± 0.30 for postcontrast, P < 0.001 for both). The scores of respiratory motion artifact was significantly higher for PI only in pre-contrast sequence (3.97±0.11 vs 3.89 ± 0.22, P = 0.002 for pre-contrast; 3.95 ± 0.18 vs 3.90 ± 0.22, P = 0.083 for postcontrast, respectively). CONCLUSIONS Compared to the standard PI sequence, the CS technique can provide greater contrast in displaying HCCs and hepatic vessels in MRI without compromise of overall image quality.
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Affiliation(s)
- Wei Sun
- Department of Radiology, Zhongshan Hospital, Fudan University, China
| | - Wentao Wang
- Department of Radiology, Zhongshan Hospital, Fudan University, China; Shanghai Medical Imaging Institute, Shanghai, China
| | - Kai Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cai-Zhong Chen
- Department of Radiology, Zhongshan Hospital, Fudan University, China
| | - Xi-Xi Wen
- United Imaging Healthcare, Shanghai, China
| | - Meng-Su Zeng
- Department of Radiology, Zhongshan Hospital, Fudan University, China; Shanghai Medical Imaging Institute, Shanghai, China
| | - Sheng-Xiang Rao
- Department of Radiology, Zhongshan Hospital, Fudan University, China; Shanghai Medical Imaging Institute, Shanghai, China.
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Chieh SW, Kaveh M, Akçakaya M, Moeller S. Self-calibrated interpolation of non-Cartesian data with GRAPPA in parallel imaging. Magn Reson Med 2019; 83:1837-1850. [PMID: 31722128 DOI: 10.1002/mrm.28033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 09/17/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE To develop a non-Cartesian k-space reconstruction method using self-calibrated region-specific interpolation kernels for highly accelerated acquisitions. METHODS In conventional non-Cartesian GRAPPA with through-time GRAPPA (TT-GRAPPA), the use of region-specific interpolation kernels has demonstrated improved reconstruction quality in dynamic imaging for highly accelerated acquisitions. However, TT-GRAPPA requires the acquisition of a large number of separate calibration scans. To reduce the overall imaging time, we propose Self-calibrated Interpolation of Non-Cartesian data with GRAPPA (SING) to self-calibrate region-specific interpolation kernels from dynamic undersampled measurements. The SING method synthesizes calibration data to adapt to the distinct shape of each region-specific interpolation kernel geometry, and uses a novel local k-space regularization through an extension of TT-GRAPPA. This calibration approach is used to reconstruct non-Cartesian images at high acceleration rates while mitigating noise amplification. The reconstruction quality of SING is compared with conjugate-gradient SENSE and TT-GRAPPA in numerical phantoms and in vivo cine data sets. RESULTS In both numerical phantom and in vivo cine data sets, SING offers visually and quantitatively similar reconstruction quality to TT-GRAPPA, and provides improved reconstruction quality over conjugate-gradient SENSE. Furthermore, temporal fidelity in SING and TT-GRAPPA is similar for the same acceleration rates. G-factor evaluation over the heart shows that SING and TT-GRAPPA provide similar noise amplification at moderate and high rates. CONCLUSION The proposed SING reconstruction enables significant improvement of acquisition efficiency for calibration data, while matching the reconstruction performance of TT-GRAPPA.
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Affiliation(s)
- Seng-Wei Chieh
- Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Mostafa Kaveh
- Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Mehmet Akçakaya
- Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota.,Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | - Steen Moeller
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
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Krämer M, Herzau B, Reichenbach JR. Segmentation and visualization of the human cranial bone by T2* approximation using ultra-short echo time (UTE) magnetic resonance imaging. Z Med Phys 2019; 30:51-59. [PMID: 31277935 DOI: 10.1016/j.zemedi.2019.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/08/2019] [Accepted: 06/03/2019] [Indexed: 11/19/2022]
Abstract
Segmentation of the human cranial bone from MRI data is challenging, because compact bone is characterized by very short transverse relaxation times and typically produces no signal when using conventional magnetic resonance imaging (MRI) sequences. In this work, we propose a fully automated segmentation algorithm, which uses dual-echo, ultra-short echo-time (UTE) MRI data. The segmentation was initialized by interval thresholding of approximated T2* relaxation time maps in the range of 1ms<T2*<3ms. This parameter range was derived from a manual region-of-interest analysis of high resolution data of the cranial layers, resulting in average T2* relaxation times of 1.7±0.3ms in the lamina externa, 2.5±0.3ms in the diploe and 1.7±0.2ms in the lamina interna. Segmentations were performed based on data of 8 healthy volunteers that were acquired with different acquisition parameters and spatial resolutions to test the stability of the algorithm. Comparison with computed tomography data demonstrated close agreement with the segmented UTE MRI data. Visualization of the segmented cranial bone was performed by volumetric rendering and by using the approximated T2* values for color coding, clearly visualizing the cranial sutures as well as their intersections.
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Affiliation(s)
- Martin Krämer
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Germany.
| | - Benedikt Herzau
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Germany
| | - Jürgen R Reichenbach
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Germany
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Lo WC, Chen Y, Jiang Y, Hamilton J, Grimm R, Griswold M, Gulani V, Seiberlich N. Realistic 4D MRI abdominal phantom for the evaluation and comparison of acquisition and reconstruction techniques. Magn Reson Med 2018; 81:1863-1875. [PMID: 30394573 DOI: 10.1002/mrm.27545] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/24/2018] [Accepted: 08/30/2018] [Indexed: 12/22/2022]
Abstract
PURPOSE This work presents a 4D numerical abdominal phantom, which includes T1 and T2 relaxation times, proton density fat fraction, perfusion, and diffusion, as well as respiratory motion for the evaluation and comparison of acquisition and reconstruction techniques. METHODS The 3D anatomical mesh models were non-rigidly scaled and shifted by respiratory motion derived from an in vivo scan. A time series of voxelized 3D abdominal phantom images were obtained with contrast determined by the tissue properties and pulse sequence parameters. Two example simulations: (1) 3D T1 mapping under breath-hold and free-breathing acquisition conditions and (2) two different reconstruction techniques for accelerated 3D dynamic contrast-enhanced MRI, are presented. The source codes can be found at https://github.com/SeiberlichLab/Abdominal_MR_Phantom. RESULTS The proposed 4D abdominal phantom can successfully simulate images and MRI data with nonrigid respiratory motion and specific contrast settings and data sampling schemes. In example 1, the use of a numerical 4D abdominal phantom was demonstrated to aid in the comparison between different approaches for volumetric T1 mapping. In example 2, the average arterial fraction over the healthy hepatic parenchyma as calculated with spiral generalized autocalibrating partial parallel acquisition was closer to that from the fully sampled data than the arterial fraction from conjugate gradient sensitivity encoding, although both are elevated compared to the gold-standard reference. CONCLUSION This realistic abdominal MR phantom can be used to simulate different pulse sequences and data sampling schemes for the comparison of acquisition and reconstruction methods under controlled conditions that are impossible or prohibitively difficult to perform in vivo.
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Affiliation(s)
- Wei-Ching Lo
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Yong Chen
- Department of Radiology, UH Cleveland Medical Center, Cleveland, Ohio
| | - Yun Jiang
- Department of Radiology, UH Cleveland Medical Center, Cleveland, Ohio
| | - Jesse Hamilton
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | | | - Mark Griswold
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio.,Department of Radiology, UH Cleveland Medical Center, Cleveland, Ohio
| | - Vikas Gulani
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio.,Department of Radiology, UH Cleveland Medical Center, Cleveland, Ohio
| | - Nicole Seiberlich
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio.,Department of Radiology, UH Cleveland Medical Center, Cleveland, Ohio
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Hamilton J, Franson D, Seiberlich N. Recent advances in parallel imaging for MRI. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 101:71-95. [PMID: 28844222 PMCID: PMC5927614 DOI: 10.1016/j.pnmrs.2017.04.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/09/2017] [Accepted: 04/17/2017] [Indexed: 05/22/2023]
Abstract
Magnetic Resonance Imaging (MRI) is an essential technology in modern medicine. However, one of its main drawbacks is the long scan time needed to localize the MR signal in space to generate an image. This review article summarizes some basic principles and recent developments in parallel imaging, a class of image reconstruction techniques for shortening scan time. First, the fundamentals of MRI data acquisition are covered, including the concepts of k-space, undersampling, and aliasing. It is demonstrated that scan time can be reduced by sampling a smaller number of phase encoding lines in k-space; however, without further processing, the resulting images will be degraded by aliasing artifacts. Nearly all modern clinical scanners acquire data from multiple independent receiver coil arrays. Parallel imaging methods exploit properties of these coil arrays to separate aliased pixels in the image domain or to estimate missing k-space data using knowledge of nearby acquired k-space points. Three parallel imaging methods-SENSE, GRAPPA, and SPIRiT-are described in detail, since they are employed clinically and form the foundation for more advanced methods. These techniques can be extended to non-Cartesian sampling patterns, where the collected k-space points do not fall on a rectangular grid. Non-Cartesian acquisitions have several beneficial properties, the most important being the appearance of incoherent aliasing artifacts. Recent advances in simultaneous multi-slice imaging are presented next, which use parallel imaging to disentangle images of several slices that have been acquired at once. Parallel imaging can also be employed to accelerate 3D MRI, in which a contiguous volume is scanned rather than sequential slices. Another class of phase-constrained parallel imaging methods takes advantage of both image magnitude and phase to achieve better reconstruction performance. Finally, some applications are presented of parallel imaging being used to accelerate MR Spectroscopic Imaging.
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Affiliation(s)
- Jesse Hamilton
- Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Dominique Franson
- Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Nicole Seiberlich
- Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA; Radiology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
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Krämer M, Motaal AG, Herrmann KH, Löffler B, Reichenbach JR, Strijkers GJ, Hoerr V. Cardiac 4D phase-contrast CMR at 9.4 T using self-gated ultra-short echo time (UTE) imaging. J Cardiovasc Magn Reson 2017; 19:39. [PMID: 28359292 PMCID: PMC5374606 DOI: 10.1186/s12968-017-0351-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 03/02/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Time resolved 4D phase contrast (PC) cardiovascular magnetic resonance (CMR) in mice is challenging due to long scan times, small animal ECG-gating and the rapid blood flow and cardiac motion of small rodents. To overcome several of these technical challenges we implemented a retrospectively self-gated 4D PC radial ultra-short echo-time (UTE) acquisition scheme and assessed its performance in healthy mice by comparing the results with those obtained with an ECG-triggered 4D PC fast low angle shot (FLASH) sequence. METHODS Cardiac 4D PC CMR images were acquired at 9.4 T in healthy mice using the proposed self-gated radial center-out UTE acquisition scheme (TE/TR of 0.5 ms/3.1 ms) and a standard Cartesian 4D PC imaging sequence (TE/TR of 2.1 ms/5.0 ms) with a four-point Hadamard flow encoding scheme. To validate the proposed UTE flow imaging technique, experiments on a flow phantom with variable pump rates were performed. RESULTS The anatomical images and flow velocity maps of the proposed 4D PC UTE technique showed reduced artifacts and an improved SNR (left ventricular cavity (LV): 8.9 ± 2.5, myocardium (MC): 15.7 ± 1.9) compared to those obtained using a typical Cartesian FLASH sequence (LV: 5.6 ± 1.2, MC: 10.1 ± 1.4) that was used as a reference. With both sequences comparable flow velocities were obtained in the flow phantom as well as in the ascending aorta (UTE: 132.8 ± 18.3 cm/s, FLASH: 134.7 ± 13.4 cm/s) and pulmonary artery (UTE: 78.5 ± 15.4 cm/s, FLASH: 86.6 ± 6.2 cm/s) of the animals. Self-gated navigator signals derived from information of the oversampled k-space center were successfully extracted for all animals with a higher gating efficiency of time spent on acquiring gated data versus total measurement time (UTE: 61.8 ± 11.5%, FLASH: 48.5 ± 4.9%). CONCLUSIONS The proposed self-gated 4D PC UTE sequence enables robust and accurate flow velocity mapping of the mouse heart in vivo at high magnetic fields. At the same time SNR, gating efficiency, flow artifacts and image quality all improved compared to the images obtained using the well-established, ECG-triggered, 4D PC FLASH sequence.
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Affiliation(s)
- M. Krämer
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Philosophenweg 3, D-07743 Jena, Germany
| | - A. G. Motaal
- Biomedical NMR, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - K-H. Herrmann
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Philosophenweg 3, D-07743 Jena, Germany
| | - B. Löffler
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - J. R. Reichenbach
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Philosophenweg 3, D-07743 Jena, Germany
- Michael Stifel Center for Data-driven and Simulation Science Jena, Friedrich Schiller University Jena, Jena, Germany
- Abbe School of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Center of Medical Optics and Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - G. J. Strijkers
- Biomedical NMR, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Biomedical Engineering and Physics, Academic Medical Center, Amsterdam, Netherlands
| | - V. Hoerr
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
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Lingala SG, Zhu Y, Lim Y, Toutios A, Ji Y, Lo WC, Seiberlich N, Narayanan S, Nayak KS. Feasibility of through-time spiral generalized autocalibrating partial parallel acquisition for low latency accelerated real-time MRI of speech. Magn Reson Med 2017; 78:2275-2282. [PMID: 28185301 DOI: 10.1002/mrm.26611] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 12/08/2016] [Accepted: 12/27/2016] [Indexed: 12/11/2022]
Abstract
PURPOSE To evaluate the feasibility of through-time spiral generalized autocalibrating partial parallel acquisition (GRAPPA) for low-latency accelerated real-time MRI of speech. METHODS Through-time spiral GRAPPA (spiral GRAPPA), a fast linear reconstruction method, is applied to spiral (k-t) data acquired from an eight-channel custom upper-airway coil. Fully sampled data were retrospectively down-sampled to evaluate spiral GRAPPA at undersampling factors R = 2 to 6. Pseudo-golden-angle spiral acquisitions were used for prospective studies. Three subjects were imaged while performing a range of speech tasks that involved rapid articulator movements, including fluent speech and beat-boxing. Spiral GRAPPA was compared with view sharing, and a parallel imaging and compressed sensing (PI-CS) method. RESULTS Spiral GRAPPA captured spatiotemporal dynamics of vocal tract articulators at undersampling factors ≤4. Spiral GRAPPA at 18 ms/frame and 2.4 mm2 /pixel outperformed view sharing in depicting rapidly moving articulators. Spiral GRAPPA and PI-CS provided equivalent temporal fidelity. Reconstruction latency per frame was 14 ms for view sharing and 116 ms for spiral GRAPPA, using a single processor. Spiral GRAPPA kept up with the MRI data rate of 18ms/frame with eight processors. PI-CS required 17 minutes to reconstruct 5 seconds of dynamic data. CONCLUSION Spiral GRAPPA enabled 4-fold accelerated real-time MRI of speech with a low reconstruction latency. This approach is applicable to wide range of speech RT-MRI experiments that benefit from real-time feedback while visualizing rapid articulator movement. Magn Reson Med 78:2275-2282, 2017. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Sajan Goud Lingala
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California, USA
| | - Yinghua Zhu
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California, USA
| | - Yongwan Lim
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California, USA
| | - Asterios Toutios
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California, USA
| | - Yunhua Ji
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA
| | - Wei-Ching Lo
- Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Nicole Seiberlich
- Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shrikanth Narayanan
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California, USA
| | - Krishna S Nayak
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California, USA
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Sayin O, Saybasili H, Zviman MM, Griswold M, Halperin H, Seiberlich N, Herzka DA. Real-time free-breathing cardiac imaging with self-calibrated through-time radial GRAPPA. Magn Reson Med 2016; 77:250-264. [PMID: 26969611 DOI: 10.1002/mrm.26112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 11/29/2015] [Accepted: 12/12/2015] [Indexed: 12/23/2022]
Abstract
PURPOSE Real-time free-breathing cardiac imaging with highly undersampled radial trajectories has previously been successfully demonstrated using calibrated radial generalized autocalibrating partially parallel acquisition (rGRAPPA). A self-calibrated approach for rGRAPPA is proposed that removes the need for the calibration prescan. METHODS To investigate the effect of various parameters on image quality, a comprehensive imaging study on one normal swine was performed. Root mean squared errors (RMSEs) were computed with respect to gold standard acquisitions, and several acquisition/reconstruction strategies were compared. Additionally, the method was tested on 13 human subjects, and RMSEs relative to standard through-time radial GRAPPA were computed. RESULTS Real-time images with high spatiotemporal resolution were obtained. Image quality was comparable to calibrated through-time rGRAPPA with endocardial and epicardial borders clearly delineated. In the swine, the average RMSE between self-calibrated and gold-standard calibrated images was 5.18 ± 0.84%. In normal human subjects, the average RMSE between self-calibrated and calibrated through-time rGRAPPA was 3.79 ± 0.64%. For lower accelerations rates (R = 6-8) image quality was similar to comparable calibrated scans though RMSE increased for higher degrees of undersampling (R = 12-16). CONCLUSION Highly accelerated real-time imaging with undersampled radial trajectories without additional calibration data is feasible. Image quality was acceptable for real-time cardiac MRI applications demanding high speed. Magn Reson Med 77:250-264, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ozan Sayin
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - M Muz Zviman
- Department of Medicine, Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Griswold
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Henry Halperin
- Department of Medicine, Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicole Seiberlich
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Daniel A Herzka
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Free-breathing liver perfusion imaging using 3-dimensional through-time spiral generalized autocalibrating partially parallel acquisition acceleration. Invest Radiol 2016; 50:367-75. [PMID: 25946703 DOI: 10.1097/rli.0000000000000135] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The goal of this study was to develop free-breathing high-spatiotemporal resolution dynamic contrast-enhanced liver magnetic resonance imaging using non-Cartesian parallel imaging acceleration, and quantitative liver perfusion mapping. MATERIALS AND METHODS This study was approved by the local institutional review board and written informed consent was obtained from all participants. Ten healthy subjects and 5 patients were scanned on a Siemens 3-T Skyra scanner. A stack-of-spirals trajectory was undersampled in-plane with a reduction factor of 6 and reconstructed using 3-dimensional (3D) through-time non-Cartesian generalized autocalibrating partially parallel acquisition. High-resolution 3D images were acquired with a true temporal resolution of 1.6 to 1.9 seconds while the subjects were breathing freely. A dual-input single-compartment model was used to retrieve liver perfusion parameters from dynamic contrast-enhanced magnetic resonance imaging data, which were coregistered using an algorithm designed to reduce the effects of dynamic contrast changes on registration. Image quality evaluation was performed on spiral images and conventional images from 5 healthy subjects. RESULTS Images with a spatial resolution of 1.9 × 1.9 × 3 mm3 were obtained with whole-liver coverage. With an imaging speed of better than 2 s/vol, free-breathing scans were achieved and dynamic changes in enhancement were captured. The overall image quality of free-breathing spiral images was slightly lower than that of conventional long breath-hold Cartesian images, but it provided clinically acceptable or better image quality. The free-breathing 3D images were registered with almost no residual motion in liver tissue. After the registration, quantitative whole-liver 3D perfusion maps were obtained and the perfusion parameters are all in good agreement with the literature. CONCLUSIONS This high-spatiotemporal resolution free-breathing 3D liver imaging technique allows voxelwise quantification of liver perfusion.
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Fair MJ, Gatehouse PD, DiBella EVR, Firmin DN. A review of 3D first-pass, whole-heart, myocardial perfusion cardiovascular magnetic resonance. J Cardiovasc Magn Reson 2015; 17:68. [PMID: 26231784 PMCID: PMC4522116 DOI: 10.1186/s12968-015-0162-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 06/23/2015] [Indexed: 01/19/2023] Open
Abstract
A comprehensive review is undertaken of the methods available for 3D whole-heart first-pass perfusion (FPP) and their application to date, with particular focus on possible acceleration techniques. Following a summary of the parameters typically desired of 3D FPP methods, the review explains the mechanisms of key acceleration techniques and their potential use in FPP for attaining 3D acquisitions. The mechanisms include rapid sequences, non-Cartesian k-space trajectories, reduced k-space acquisitions, parallel imaging reconstructions and compressed sensing. An attempt is made to explain, rather than simply state, the varying methods with the hope that it will give an appreciation of the different components making up a 3D FPP protocol. Basic estimates demonstrating the required total acceleration factors in typical 3D FPP cases are included, providing context for the extent that each acceleration method can contribute to the required imaging speed, as well as potential limitations in present 3D FPP literature. Although many 3D FPP methods are too early in development for the type of clinical trials required to show any clear benefit over current 2D FPP methods, the review includes the small but growing quantity of clinical research work already using 3D FPP, alongside the more technical work. Broader challenges concerning FPP such as quantitative analysis are not covered, but challenges with particular impact on 3D FPP methods, particularly with regards to motion effects, are discussed along with anticipated future work in the field.
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Affiliation(s)
- Merlin J Fair
- National Heart & Lung Institute, Imperial College London, London, UK.
- Cardiovascular Magnetic Resonance Unit, Royal Brompton Hospital, Sydney Street, London, SW3 6NP, UK.
| | - Peter D Gatehouse
- National Heart & Lung Institute, Imperial College London, London, UK.
- Cardiovascular Magnetic Resonance Unit, Royal Brompton Hospital, Sydney Street, London, SW3 6NP, UK.
| | - Edward V R DiBella
- Utah Center for Advanced Imaging Research, University of Utah, Salt Lake City, UT, USA.
| | - David N Firmin
- National Heart & Lung Institute, Imperial College London, London, UK.
- Cardiovascular Magnetic Resonance Unit, Royal Brompton Hospital, Sydney Street, London, SW3 6NP, UK.
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12
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Quantitative high-resolution renal perfusion imaging using 3-dimensional through-time radial generalized autocalibrating partially parallel acquisition. Invest Radiol 2015; 49:666-74. [PMID: 24879298 DOI: 10.1097/rli.0000000000000070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) examinations of the kidneys provide quantitative information on renal perfusion and filtration. However, these examinations are often difficult to implement because of respiratory motion and their need for a high spatiotemporal resolution and 3-dimensional coverage. Here, we present a free-breathing quantitative renal DCE-MRI examination acquired with a highly accelerated stack-of-stars trajectory and reconstructed with 3-dimensional (3D) through-time radial generalized autocalibrating partially parallel acquisition (GRAPPA), using half and quarter doses of gadolinium contrast. MATERIALS AND METHODS Data were acquired in 10 asymptomatic volunteers using a stack-of-stars trajectory that was undersampled in-plane by a factor of 12.6 with respect to Nyquist sampling criterion and using partial Fourier of 6/8 in the partition direction. Data had a high temporal (2.1-2.9 seconds per frame) and spatial (approximately 2.2 mm) resolution with full 3D coverage of both kidneys (350-370 mm × 79-92 mm). Images were successfully reconstructed with 3D through-time radial GRAPPA, and interframe respiratory motion was compensated by using an algorithm developed to automatically use images from multiple points of enhancement as references for registration. Quantitative pharmacokinetic analysis was performed using a separable dual-compartment model. RESULTS Region-of-interest (ROI) pharmacokinetic analysis provided estimates (mean (SD)) of quantitative renal parameters after a half dose: 218.1 (57.1) mL/min per 100 mL; plasma mean transit time, 4.8 (2.2) seconds; renal filtration, 28.7 (10.0) mL/min per 100 mL; and tubular mean transit time, 131.1 (60.2) seconds in 10 kidneys. The ROI pharmacokinetic analysis provided estimates (mean (SD)) of quantitative renal parameters after a quarter dose: 218.1 (57.1) mL/min per 100 mL; plasma mean transit time, 4.8 (2.2) seconds; renal filtration, 28.7 (10.0) mL/min per 100 mL; and tubular mean transit time, 131.1 (60.2) seconds in the 10 kidneys. Three-dimensional pixelwise parameter maps were also evaluated. CONCLUSIONS Highly undersampled data were successfully reconstructed with 3D through-time radial GRAPPA to achieve a high-resolution 3-dimensional renal DCE-MRI examination. The acquisition was completely free breathing, and the images were registered to compensate for respiratory motion. This allowed for an accurate high-resolution 3D quantitative renal functional mapping of perfusion and filtration parameters.
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Chen Y, Lee GR, Aandal G, Badve C, Wright KL, Griswold MA, Seiberlich N, Gulani V. Rapid volumetric T1 mapping of the abdomen using three-dimensional through-time spiral GRAPPA. Magn Reson Med 2015; 75:1457-65. [PMID: 25980949 DOI: 10.1002/mrm.25693] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/06/2015] [Accepted: 02/20/2015] [Indexed: 01/09/2023]
Abstract
PURPOSE To develop an ultrafast T1 mapping method for high-resolution, volumetric T1 measurements in the abdomen. METHODS The Look-Locker method was combined with a stack-of-spirals acquisition accelerated using three-dimensional (3D) through-time spiral GRAPPA reconstruction for fast data acquisition. A segmented k-space acquisition scheme was proposed and the time delay between segments for the recovery of longitudinal magnetization was optimized using Bloch equation simulations. The accuracy of this method was validated in a phantom experiment and in vivo T1 measurements were performed with 35 asymptomatic subjects on both 1.5 Tesla (T) and 3T MRI systems. RESULTS Phantom experiments yielded close agreement between the proposed method and gold standard measurements for a large range of T1 values (200 to 1600 ms). The in vivo results further demonstrate that high-resolution T1 maps (2 × 2 × 4 mm(3)) for 32 slices can be achieved in a single clinically feasible breath-hold of approximately 20 s. The T1 values for multiple organs and tissues in the abdomen are in agreement with the published literature. CONCLUSION A high-resolution 3D abdominal T1 mapping technique was developed, which allows fast and accurate T1 mapping of multiple abdominal organs and tissues in a single breath-hold.
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Affiliation(s)
- Yong Chen
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Gregory R Lee
- Pediatric Neuroimaging Research Consortium, Department of Radiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Chaitra Badve
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Katherine L Wright
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark A Griswold
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Nicole Seiberlich
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Vikas Gulani
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
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14
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Cooper MA, Nguyen TD, Xu B, Prince MR, Elad M, Wang Y, Spincemaille P. Patch based reconstruction of undersampled data (PROUD) for high signal-to-noise ratio and high frame rate contrast enhanced liver imaging. Magn Reson Med 2014; 74:1587-97. [PMID: 25483782 DOI: 10.1002/mrm.25551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 11/04/2014] [Accepted: 11/04/2014] [Indexed: 11/08/2022]
Abstract
PURPOSE High spatial-temporal four-dimensional imaging with large volume coverage is necessary to accurately capture and characterize liver lesions. Traditionally, parallel imaging and adapted sampling are used toward this goal, but they typically result in a loss of signal to noise. Furthermore, residual under-sampling artifacts can be temporally varying and complicate the quantitative analysis of contrast enhancement curves needed for pharmacokinetic modeling. We propose to overcome these problems using a novel patch-based regularization approach called Patch-based Reconstruction Of Under-sampled Data (PROUD). THEORY AND METHODS PROUD produces high frame rate image reconstructions by exploiting the strong similarities in spatial patches between successive time frames to overcome the severe k-space under-sampling. To validate PROUD, a numerical liver perfusion phantom was developed to characterize contrast-to-noise ratio (CNR) performance compared with a previously proposed method, TRACER. A second numerical phantom was constructed to evaluate the temporal footprint and lag of PROUD and TRACER reconstructions. Finally, PROUD and TRACER were evaluated in a cohort of five liver donors. RESULTS In the CNR phantom, PROUD, compared with TRACER, improved peak CNR by 3.66 times while maintaining or improving temporal fidelity. In vivo, PROUD demonstrated an average increase in CNR of 60% compared with TRACER. CONCLUSION The results presented in this work demonstrate the feasibility of using a combination of patch based image constraints with temporal regularization to provide high SNR, high temporal frame rate and spatial resolution four dimensional imaging.
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Affiliation(s)
- Mitchell A Cooper
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA.,Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Thanh D Nguyen
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Bo Xu
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA.,Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Martin R Prince
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Michael Elad
- Division of Computer Science, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yi Wang
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, USA.,Department of Radiology, Weill Cornell Medical College, New York, New York, USA
| | - Pascal Spincemaille
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
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15
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Barkauskas KJ, Rajiah P, Ashwath R, Hamilton JI, Chen Y, Ma D, Wright KL, Gulani V, Griswold MA, Seiberlich N. Quantification of left ventricular functional parameter values using 3D spiral bSSFP and through-time non-Cartesian GRAPPA. J Cardiovasc Magn Reson 2014; 16:65. [PMID: 25231607 PMCID: PMC4160541 DOI: 10.1186/s12968-014-0065-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 08/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The standard clinical acquisition for left ventricular functional parameter analysis with cardiovascular magnetic resonance (CMR) uses a multi-breathhold multi-slice segmented balanced SSFP sequence. Performing multiple long breathholds in quick succession for ventricular coverage in the short-axis orientation can lead to fatigue and is challenging in patients with severe cardiac or respiratory disorders. This study combines the encoding efficiency of a six-fold undersampled 3D stack of spirals balanced SSFP sequence with 3D through-time spiral GRAPPA parallel imaging reconstruction. This 3D spiral method requires only one breathhold to collect the dynamic data. METHODS Ten healthy volunteers were recruited for imaging at 3 T. The 3D spiral technique was compared against 2D imaging in terms of systolic left ventricular functional parameter values (Bland-Altman plots), total scan time (Welch's t-test) and qualitative image rating scores (Wilcoxon signed-rank test). RESULTS Systolic left ventricular functional values were not significantly different (i.e. 3D-2D) between the methods. The 95% confidence interval for ejection fraction was -0.1 ± 1.6% (mean ± 1.96*SD). The total scan time for the 3D spiral technique was 48 s, which included one breathhold with an average duration of 14 s for the dynamic scan, plus 34 s to collect the calibration data under free-breathing conditions. The 2D method required an average of 5 min 40s for the same coverage of the left ventricle. The difference between 3D and 2D image rating scores was significantly different from zero (Wilcoxon signed-rank test, p < 0.05); however, the scores were at least 3 (i.e. average) or higher for 3D spiral imaging. CONCLUSION The 3D through-time spiral GRAPPA method demonstrated equivalent systolic left ventricular functional parameter values, required significantly less total scan time and yielded acceptable image quality with respect to the 2D segmented multi-breathhold standard in this study. Moreover, the 3D spiral technique used just one breathhold for dynamic imaging, which is anticipated to reduce patient fatigue as part of the complete cardiac examination in future studies that include patients.
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Affiliation(s)
| | - Prabhakar Rajiah
- />Cardiothoracic Imaging, Department of Radiology, University Hospitals Case Medical Center, Cleveland, Ohio USA
| | - Ravi Ashwath
- />Pediatric Cardiology, Rainbow Babies and Children’s Hospital, University Hospitals Case Medical Center, Cleveland, Ohio USA
| | - Jesse I Hamilton
- />Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio USA
| | - Yong Chen
- />Radiology, University Hospitals Case Medical Center, Cleveland, Ohio USA
| | - Dan Ma
- />Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio USA
| | - Katherine L Wright
- />Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio USA
| | - Vikas Gulani
- />Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio USA
- />Radiology, University Hospitals Case Medical Center, Cleveland, Ohio USA
| | - Mark A Griswold
- />Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio USA
- />Radiology, University Hospitals Case Medical Center, Cleveland, Ohio USA
| | - Nicole Seiberlich
- />Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio USA
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