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Glutig K, Krüger PC, Oberreuther T, Nickel MD, Teichgräber U, Lorenz M, Mentzel HJ, Krämer M. Preliminary results of abdominal simultaneous multi-slice accelerated diffusion-weighted imaging with motion-correction in patients with cystic fibrosis and impaired compliance. Abdom Radiol (NY) 2022; 47:2783-2794. [PMID: 35596778 PMCID: PMC9300552 DOI: 10.1007/s00261-022-03549-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 01/18/2023]
Abstract
OBJECTIVES The aim of this prospective study was to compare scan time, image quality, signal-to-noise Ratio (SNR), and apparent diffusion coefficient (ADC) values of simultaneous multi-slice accelerated diffusion-weighted imaging with motion-correction (DWI SMS Moco) to standard diffusion-weighted imaging (sDWI) in free-breathing abdominal magnetic resonance imaging (MRI) in pediatric and young adult patients with cystic fibrosis (CF). MATERIAL AND METHODS 16 patients (7 male and 9 female, 12-41 years old) with CF were examined prospectively in a single-center from November 2020 to March 2021 on a 1.5 Tesla clinical MR scanner. The characteristics of overall image quality and delimitability of mesenteric lymph nodes were evaluated using a 5-point Likert scale by two experienced pediatric radiologists independently from each other. Quantitative parameters with SNR and ADC values were assessed in 8 different locations and compared using a Wilcoxon signed-rank test. RESULTS The acquisition time for DWI SMS Moco was 32% shorter than for sDWI. Regarding quality comparison, overall image quality and delimitability of mesenteric lymph nodes were significant higher in DWI SMS Moco (p ≤ 0.05 for both readers). The readers preferred DWI SMS Moco to sDWI in all cases (16/16). Mean SNR values from DWI SMS Moco and sDWI were similar in 7 from 8 locations. The ADC values showed no significant difference between DWI SMS Moco and sDWI in any of the evaluated locations (p > 0.05). CONCLUSIONS The DWI SMS Moco improves overall image quality and delimitability of mesenteric lymph nodes compared to sDWI with similar SNR and ADC values and a distinguished reduction of scan time in free-breathing by one third. We conclude that MRI with DWI SMS Moco could be helpful in monitoring the effect of the high-efficiency modulator (HEM) therapy in cystic fibrosis (CF) patients homozygous or heterozygous for F508del in the abdomen.
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Affiliation(s)
- Katja Glutig
- Department of Radiology, Section Pediatric Radiology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
| | - Paul-Christian Krüger
- Department of Radiology, Section Pediatric Radiology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Theresa Oberreuther
- Department of Radiology, Section Pediatric Radiology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | | | - Ulf Teichgräber
- Department of Radiology, Jena University Hospital, Jena, Germany
| | - Michael Lorenz
- Cystic Fibrosis Centre, Department of Paediatrics, Jena University Hospital, Jena, Germany
| | - Hans-Joachim Mentzel
- Department of Radiology, Section Pediatric Radiology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Martin Krämer
- Department of Radiology, Jena University Hospital, Jena, Germany
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What's New and What's Next in Diffusion MRI Preprocessing. Neuroimage 2021; 249:118830. [PMID: 34965454 PMCID: PMC9379864 DOI: 10.1016/j.neuroimage.2021.118830] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/26/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
Diffusion MRI (dMRI) provides invaluable information for the study of tissue microstructure and brain connectivity, but suffers from a range of imaging artifacts that greatly challenge the analysis of results and their interpretability if not appropriately accounted for. This review will cover dMRI artifacts and preprocessing steps, some of which have not typically been considered in existing pipelines or reviews, or have only gained attention in recent years: brain/skull extraction, B-matrix incompatibilities w.r.t the imaging data, signal drift, Gibbs ringing, noise distribution bias, denoising, between- and within-volumes motion, eddy currents, outliers, susceptibility distortions, EPI Nyquist ghosts, gradient deviations, B1 bias fields, and spatial normalization. The focus will be on “what’s new” since the notable advances prior to and brought by the Human Connectome Project (HCP), as presented in the predecessing issue on “Mapping the Connectome” in 2013. In addition to the development of novel strategies for dMRI preprocessing, exciting progress has been made in the availability of open source tools and reproducible pipelines, databases and simulation tools for the evaluation of preprocessing steps, and automated quality control frameworks, amongst others. Finally, this review will consider practical considerations and our view on “what’s next” in dMRI preprocessing.
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Riedel Né Steinhoff M, Setsompop K, Mertins A, Börnert P. Segmented simultaneous multi-slice diffusion-weighted imaging with navigated 3D rigid motion correction. Magn Reson Med 2021; 86:1701-1717. [PMID: 33955588 DOI: 10.1002/mrm.28813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/09/2022]
Abstract
PURPOSE To improve the robustness of diffusion-weighted imaging (DWI) data acquired with segmented simultaneous multi-slice (SMS) echo-planar imaging (EPI) against in-plane and through-plane rigid motion. THEORY AND METHODS The proposed algorithm incorporates a 3D rigid motion correction and wavelet denoising into the image reconstruction of segmented SMS-EPI diffusion data. Low-resolution navigators are used to estimate shot-specific diffusion phase corruptions and 3D rigid motion parameters through SMS-to-volume registration. The shot-wise rigid motion and phase parameters are integrated into a SENSE-based full-volume reconstruction for each diffusion direction. The algorithm is compared to a navigated SMS reconstruction without gross motion correction in simulations and in vivo studies with four-fold interleaved 3-SMS diffusion tensor acquisitions. RESULTS Simulations demonstrate high fidelity was achieved in the SMS-to-volume registration, with submillimeter registration errors and improved image reconstruction quality. In vivo experiments validate successful artifact reduction in 3D motion-compromised in vivo scans with a temporal motion resolution of approximately 0.3 s. CONCLUSION This work demonstrates the feasibility of retrospective 3D rigid motion correction from shot navigators for segmented SMS DWI.
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Affiliation(s)
| | - Kawin Setsompop
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA.,Harvard-MIT Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
| | - Alfred Mertins
- Institute for Signal Processing, University of Luebeck, Luebeck, Germany
| | - Peter Börnert
- Philips Research, Hamburg, Germany.,Radiology, C.J. Gorter Center for High-Field MRI, Leiden University Medical Center, Leiden, The Netherlands
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Coll-Font J, Afacan O, Hoge S, Garg H, Shashi K, Marami B, Gholipour A, Chow J, Warfield S, Kurugol S. Retrospective Distortion and Motion Correction for Free-Breathing DW-MRI of the Kidneys Using Dual-Echo EPI and Slice-to-Volume Registration. J Magn Reson Imaging 2021; 53:1432-1443. [PMID: 33382173 DOI: 10.1002/jmri.27473] [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: 08/08/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Diffusion-weighted MRI (DW-MRI) of the kidneys is a technique that provides information about the microstructure of renal tissue without requiring exogenous contrasts such as gadolinium, and it can be used for diagnosis in cases of renal disease and assessing response-to-therapy. However, physiological motion and large geometric distortions due to main B0 field inhomogeneities degrade the image quality, reduce the accuracy of quantitative imaging markers, and impede their subsequent clinical applicability. PURPOSE To retrospectively correct for geometric distortion for free-breathing DW-MRI of the kidneys at 3T, in the presence of a nonstatic distortion field due to breathing and bulk motion. STUDY TYPE Prospective. SUBJECTS Ten healthy volunteers (ages 29-38, four females). FIELD STRENGTH/SEQUENCE 3T; DW-MR dual-echo echo-planar imaging (EPI) sequence (10 b-values and 17 directions) and a T2 volume. ASSESSMENT The distortion correction was evaluated subjectively (Likert scale 0-5) and numerically with cross-correlation between the DW images at b = 0 s/mm2 and a T2 volume. The intravoxel incoherent motion (IVIM) and diffusion tensor (DTI) model-fitting performance was evaluated using the root-mean-squared error (nRMSE) and the coefficient of variation (CV%) of their parameters. STATISTICAL TESTS Statistical comparisons were done using Wilcoxon tests. RESULTS The proposed method improved the Likert scores by 1.1 ± 0.8 (P < 0.05), the cross-correlation with the T2 reference image by 0.13 ± 0.05 (P < 0.05), and reduced the nRMSE by 0.13 ± 0.03 (P < 0.05) and 0.23 ± 0.06 (P < 0.05) for IVIM and DTI, respectively. The CV% of the IVIM parameters (slow and fast diffusion, and diffusion fraction for IVIM and mean diffusivity, and fractional anisotropy for DTI) was reduced by 2.26 ± 3.98% (P = 6.971 × 10-2 ), 11.24 ± 26.26% (P = 6.971 × 10-2 ), 4.12 ± 12.91% (P = 0.101), 3.22 ± 0.55% (P < 0.05), and 2.42 ± 1.15% (P < 0.05). DATA CONCLUSION The results indicate that the proposed Di + MoCo method can effectively correct for time-varying geometric distortions and for misalignments due to breathing motion. Consequently, the image quality and precision of the DW-MRI model parameters improved. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY STAGE: 1.
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Affiliation(s)
- Jaume Coll-Font
- Cardiovascular Research Center, Cardiology, Massachusetts General Hospital, 149 13th St, Charlestown, United States, 02129, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Onur Afacan
- Harvard Medical School, Boston, Massachusetts, USA
- Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Scott Hoge
- Harvard Medical School, Boston, Massachusetts, USA
- Radiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Harsha Garg
- Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kumar Shashi
- Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Bahram Marami
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ali Gholipour
- Harvard Medical School, Boston, Massachusetts, USA
- Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jeanne Chow
- Harvard Medical School, Boston, Massachusetts, USA
- Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Simon Warfield
- Harvard Medical School, Boston, Massachusetts, USA
- Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Sila Kurugol
- Harvard Medical School, Boston, Massachusetts, USA
- Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
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Singh A, Salehi SSM, Gholipour A. Deep Predictive Motion Tracking in Magnetic Resonance Imaging: Application to Fetal Imaging. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:3523-3534. [PMID: 32746102 PMCID: PMC7787194 DOI: 10.1109/tmi.2020.2998600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Fetal magnetic resonance imaging (MRI) is challenged by uncontrollable, large, and irregular fetal movements. It is, therefore, performed through visual monitoring of fetal motion and repeated acquisitions to ensure diagnostic-quality images are acquired. Nevertheless, visual monitoring of fetal motion based on displayed slices, and navigation at the level of stacks-of-slices is inefficient. The current process is highly operator-dependent, increases scanner usage and cost, and significantly increases the length of fetal MRI scans which makes them hard to tolerate for pregnant women. To help build automatic MRI motion tracking and navigation systems to overcome the limitations of the current process and improve fetal imaging, we have developed a new real-time image-based motion tracking method based on deep learning that learns to predict fetal motion directly from acquired images. Our method is based on a recurrent neural network, composed of spatial and temporal encoder-decoders, that infers motion parameters from anatomical features extracted from sequences of acquired slices. We compared our trained network on held-out test sets (including data with different characteristics, e.g. different fetuses scanned at different ages, and motion trajectories recorded from volunteer subjects) with networks designed for estimation as well as methods adopted to make predictions. The results show that our method outperformed alternative techniques, and achieved real-time performance with average errors of 3.5 and 8 degrees for the estimation and prediction tasks, respectively. Our real-time deep predictive motion tracking technique can be used to assess fetal movements, to guide slice acquisitions, and to build navigation systems for fetal MRI.
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Christiaens D, Cordero-Grande L, Pietsch M, Hutter J, Price AN, Hughes EJ, Vecchiato K, Deprez M, Edwards AD, Hajnal JV, Tournier JD. Scattered slice SHARD reconstruction for motion correction in multi-shell diffusion MRI. Neuroimage 2020; 225:117437. [PMID: 33068713 PMCID: PMC7779423 DOI: 10.1016/j.neuroimage.2020.117437] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 10/01/2020] [Indexed: 11/18/2022] Open
Abstract
Subject motion in dMRI leads to a set of scattered slices with unique contrast. We introduce a slice-to-volume reconstruction framework for multi-shell HARDI data Based on a data-driven representation as spherical harmonics and radial decomposition (SHARD). The method is evaluated in test-retest scans and in the neonatal dHCP cohort. Results show robust reconstruction in severely motion-corrupted scans.
Diffusion MRI offers a unique probe into neural microstructure and connectivity in the developing brain. However, analysis of neonatal brain imaging data is complicated by inevitable subject motion, leading to a series of scattered slices that need to be aligned within and across diffusion-weighted contrasts. Here, we develop a reconstruction method for scattered slice multi-shell high angular resolution diffusion imaging (HARDI) data, jointly estimating an uncorrupted data representation and motion parameters at the slice or multiband excitation level. The reconstruction relies on data-driven representation of multi-shell HARDI data using a bespoke spherical harmonics and radial decomposition (SHARD), which avoids imposing model assumptions, thus facilitating to compare various microstructure imaging methods in the reconstructed output. Furthermore, the proposed framework integrates slice-level outlier rejection, distortion correction, and slice profile correction. We evaluate the method in the neonatal cohort of the developing Human Connectome Project (650 scans). Validation experiments demonstrate accurate slice-level motion correction across the age range and across the range of motion in the population. Results in the neonatal data show successful reconstruction even in severely motion-corrupted subjects. In addition, we illustrate how local tissue modelling can extract advanced microstructure features such as orientation distribution functions from the motion-corrected reconstructions.
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Affiliation(s)
- Daan Christiaens
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
| | - Lucilio Cordero-Grande
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid & CIBER-BBN, Madrid, Spain
| | - Maximilian Pietsch
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Jana Hutter
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Anthony N Price
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Emer J Hughes
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Katy Vecchiato
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Maria Deprez
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - A David Edwards
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Joseph V Hajnal
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - J-Donald Tournier
- Centre for the Developing Brain, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
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Sui Y, Afacan O, Gholipour A, Warfield SK. SLIMM: Slice localization integrated MRI monitoring. Neuroimage 2020; 223:117280. [PMID: 32853815 PMCID: PMC7735257 DOI: 10.1016/j.neuroimage.2020.117280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/17/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Functional MRI (fMRI) is extremely challenging to perform in subjects who move because subject motion disrupts blood oxygenation level dependent (BOLD) signal measurement. It has become common to use retrospective framewise motion detection and censoring in fMRI studies to eliminate artifacts arising from motion. Data censoring results in significant loss of data and statistical power unless the data acquisition is extended to acquire more data not corrupted by motion. Acquiring more data than is necessary leads to longer than necessary scan duration, which is more expensive and may lead to additional subject non-compliance. Therefore, it is well established that real-time prospective motion monitoring is crucial to ensure data quality and reduce imaging costs. In addition, real-time monitoring of motion allows for feedback to the operator and the subject during the acquisition, to enable intervention to reduce the subject motion. The most widely used form of motion monitoring for fMRI is based on volume-to-volume registration (VVR), which quantifies motion as the misalignment between subsequent volumes. However, motion is not constrained to occur only at the boundaries of volume acquisition, but instead may occur at any time. Consequently, each slice of an fMRI acquisition may be displaced by motion, and assessment of whole volume to volume motion may be insensitive to both intra-volume and inter-volume motion that is revealed by displacement of the slices. We developed the first slice-by-slice self-navigated motion monitoring system for fMRI by developing a real-time slice-to-volume registration (SVR) algorithm. Our real-time SVR algorithm, which is the core of the system, uses a local image patch-based matching criterion along with a Levenberg-Marquardt optimizer, all accelerated via symmetric multi-processing, with interleaved and simultaneous multi-slice acquisition schemes. Extensive experimental results on real motion data demonstrated that our fast motion monitoring system, named Slice Localization Integrated MRI Monitoring (SLIMM), provides more accurate motion measurements than a VVR based approach. Therefore, SLIMM offers improved online motion monitoring which is particularly important in fMRI for challenging patient populations. Real-time motion monitoring is crucial for online data quality control and assurance, for enabling feedback to the subject and the operator to act to mitigate motion, and in adaptive acquisition strategies that aim to ensure enough data of sufficient quality is acquired without acquiring excess data.
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Affiliation(s)
- Yao Sui
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Onur Afacan
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ali Gholipour
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Simon K Warfield
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
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