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van der Heide O, van den Berg CAT, Sbrizzi A. GPU-accelerated Bloch simulations and MR-STAT reconstructions using the Julia programming language. Magn Reson Med 2024; 92:618-630. [PMID: 38441315 DOI: 10.1002/mrm.30074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 06/02/2024]
Abstract
PURPOSE MR-STAT is a relatively new multiparametric quantitative MRI technique in which quantitative paramater maps are obtained by solving a large-scale nonlinear optimization problem. Managing reconstruction times is one of the main challenges of MR-STAT. In this work we leverage GPU hardware to reduce MR-STAT reconstruction times. A highly optimized, GPU-compatible Bloch simulation toolbox is developed as part of this work that can be utilized for other quantitative MRI techniques as well. METHODS The Julia programming language was used to develop a flexible yet highly performant and GPU-compatible Bloch simulation toolbox called BlochSimulators.jl. The runtime performance of the toolbox is benchmarked against other Bloch simulation toolboxes. Furthermore, a (partially matrix-free) modification of a previously presented (matrix-free) MR-STAT reconstruction algorithm is proposed and implemented using the Julia language on GPU hardware. The proposed algorithm is combined with BlochSimulators.jl and the resulting MR-STAT reconstruction times on GPU hardware are compared to previously presented MR-STAT reconstruction times. RESULTS The BlochSimulators.jl package demonstrates superior runtime performance on both CPU and GPU hardware when compared to other existing Bloch simulation toolboxes. The GPU-accelerated partially matrix-free MR-STAT reconstruction algorithm, which relies on BlochSimulators.jl, allows for reconstructions of 68 seconds per two-dimensional (2D slice). CONCLUSION By combining the proposed Bloch simulation toolbox and the partially matrix-free reconstruction algorithm, 2D MR-STAT reconstructions can be performed in the order of one minute on a modern GPU card. The Bloch simulation toolbox can be utilized for other quantitative MRI techniques as well, for example for online dictionary generation for MR Fingerprinting.
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Affiliation(s)
- Oscar van der Heide
- Computational Imaging Group for MR Diagnostics and Therapy, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Radiotherapy, Division of Imaging and Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis A T van den Berg
- Computational Imaging Group for MR Diagnostics and Therapy, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Radiotherapy, Division of Imaging and Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alessandro Sbrizzi
- Computational Imaging Group for MR Diagnostics and Therapy, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Radiotherapy, Division of Imaging and Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
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Liu H, van der Heide O, Versteeg E, Froeling M, Fuderer M, Xu F, van den Berg CAT, Sbrizzi A. A three-dimensional Magnetic Resonance Spin Tomography in Time-domain protocol for high-resolution multiparametric quantitative magnetic resonance imaging. NMR IN BIOMEDICINE 2024; 37:e5050. [PMID: 37857335 DOI: 10.1002/nbm.5050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/04/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023]
Abstract
Magnetic Resonance Spin TomogrAphy in Time-domain (MR-STAT) is a multiparametric quantitative MR framework, which allows for simultaneously acquiring quantitative tissue parameters such as T1, T2, and proton density from one single short scan. A typical two-dimensional (2D) MR-STAT acquisition uses a gradient-spoiled, gradient-echo sequence with a slowly varying RF flip-angle train and Cartesian readouts, and the quantitative tissue maps are reconstructed by an iterative, model-based optimization algorithm. In this work, we design a three-dimensional (3D) MR-STAT framework based on previous 2D work, in order to achieve better image signal-to-noise ratio, higher though-plane resolution, and better tissue characterization. Specifically, we design a 7-min, high-resolution 3D MR-STAT sequence, and the corresponding two-step reconstruction algorithm for the large-scale dataset. To reduce the long acquisition time, Cartesian undersampling strategies such as SENSE are adopted in our transient-state quantitative framework. To reduce the computational burden, a data-splitting scheme is designed for decoupling the 3D reconstruction problem into independent 2D reconstructions. The proposed 3D framework is validated by numerical simulations, phantom experiments, and in vivo experiments. High-quality knee quantitative maps with 0.8 × 0.8 × 1.5 mm3 resolution and bilateral lower leg maps with 1.6 mm isotropic resolution can be acquired using the proposed 7-min acquisition sequence and the 3-min-per-slice decoupled reconstruction algorithm. The proposed 3D MR-STAT framework could have wide clinical applications in the future.
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Affiliation(s)
- Hongyan Liu
- Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Oscar van der Heide
- Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Versteeg
- Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martijn Froeling
- Department of Radiology, Imaging Division, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Miha Fuderer
- Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Fei Xu
- Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis A T van den Berg
- Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alessandro Sbrizzi
- Computational Imaging Group for MRI Therapy & Diagnostics, Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
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Kleinloog JPD, Mandija S, D'Agata F, Liu H, van der Heide O, Koktas B, Jacobs SM, van den Berg CAT, Hendrikse J, van der Kolk AG, Sbrizzi A. Synthetic MRI with Magnetic Resonance Spin TomogrAphy in Time-Domain (MR-STAT): Results from a Prospective Cross-Sectional Clinical Trial. J Magn Reson Imaging 2022; 57:1451-1461. [PMID: 36098348 DOI: 10.1002/jmri.28425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Magnetic Resonance Spin TomogrAphy in Time-domain (MR-STAT) can reconstruct whole-brain multi-parametric quantitative maps (eg, T1 , T2 ) from a 5-minute MR acquisition. These quantitative maps can be leveraged for synthetization of clinical image contrasts. PURPOSE The objective was to assess image quality and overall diagnostic accuracy of synthetic MR-STAT contrasts compared to conventional contrast-weighted images. STUDY TYPE Prospective cross-sectional clinical trial. POPULATION Fifty participants with a median age of 45 years (range: 21-79 years) consisting of 10 healthy participants and 40 patients with neurological diseases (brain tumor, epilepsy, multiple sclerosis or stroke). FIELD STRENGTH/SEQUENCE 3T/Conventional contrast-weighted imaging (T1 /T2 weighted, proton density [PD] weighted, and fluid-attenuated inversion recovery [FLAIR]) and a MR-STAT acquisition (2D Cartesian spoiled gradient echo with varying flip angle preceded by a non-selective inversion pulse). ASSESSMENT Quantitative T1 , T2 , and PD maps were computed from the MR-STAT acquisition, from which synthetic contrasts were generated. Three neuroradiologists blinded for image type and disease randomly and independently evaluated synthetic and conventional datasets for image quality and diagnostic accuracy, which was assessed by comparison with the clinically confirmed diagnosis. STATISTICAL TESTS Image quality and consequent acceptability for diagnostic use was assessed with a McNemar's test (one-sided α = 0.025). Wilcoxon signed rank test with a one-sided α = 0.025 and a margin of Δ = 0.5 on the 5-level Likert scale was used to assess non-inferiority. RESULTS All data sets were similar in acceptability for diagnostic use (≥3 Likert-scale) between techniques (T1 w:P = 0.105, PDw:P = 1.000, FLAIR:P = 0.564). However, only the synthetic MR-STAT T2 weighted images were significantly non-inferior to their conventional counterpart; all other synthetic datasets were inferior (T1 w:P = 0.260, PDw:P = 1.000, FLAIR:P = 1.000). Moreover, true positive/negative rates were similar between techniques (conventional: 88%, MR-STAT: 84%). DATA CONCLUSION MR-STAT is a quantitative technique that may provide radiologists with clinically useful synthetic contrast images within substantially reduced scan time. EVIDENCE LEVEL 1 Technical Efficacy: Stage 2.
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Affiliation(s)
- Jordi P D Kleinloog
- Computational Imaging Group for MR Therapy and Diagnostics, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefano Mandija
- Computational Imaging Group for MR Therapy and Diagnostics, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Hongyan Liu
- Computational Imaging Group for MR Therapy and Diagnostics, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Oscar van der Heide
- Computational Imaging Group for MR Therapy and Diagnostics, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Beyza Koktas
- Computational Imaging Group for MR Therapy and Diagnostics, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sarah M Jacobs
- Department of Radiology and Nuclear Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis A T van den Berg
- Computational Imaging Group for MR Therapy and Diagnostics, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen Hendrikse
- Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anja G van der Kolk
- Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alessandro Sbrizzi
- Computational Imaging Group for MR Therapy and Diagnostics, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiotherapy, University Medical Center Utrecht, Utrecht, The Netherlands
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