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Shen X, Caverzasi E, Yang Y, Liu X, Green A, Henry RG, Emir U, Larson PEZ. 3D balanced SSFP UTE MRI for multiple contrasts whole brain imaging. Magn Reson Med 2024; 92:702-714. [PMID: 38525680 DOI: 10.1002/mrm.30093] [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: 08/18/2023] [Revised: 02/14/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE This study aimed to develop a new high-resolution MRI sequence for the imaging of the ultra-short transverse relaxation time (uT2) components in the brain, while simultaneously providing proton density (PD) contrast for reference and quantification. THEORY The sequence combines low flip angle balanced SSFP (bSSFP) and UTE techniques, together with a 3D dual-echo rosette k-space trajectory for readout. METHODS The expected image contrast was evaluated by simulations. A study cohort of six healthy volunteers and eight multiple sclerosis (MS) patients was recruited to test the proposed sequence. Subtraction between two TEs was performed to extract uT2 signals. In addition, conventional longitudinal relaxation time (T1) weighted, T2-weighted, and PD-weighted MRI sequences were also acquired for comparison. RESULTS Typical PD-contrast was found in the second TE images, while uT2 signals were selectively captured in the first TE images. The subtraction images presented signals primarily originating from uT2 components, but only if the first TE is short enough. Lesions in the MS subjects showed hyperintense signals in the second TE images but were hypointense signals in the subtraction images. The lesions had significantly lower signal intensity in subtraction images than normal white matter (WM), which indicated a reduction of uT2 components likely associated with myelin. CONCLUSION 3D isotropic sub-millimeter (0.94 mm) spatial resolution images were acquired with the novel bSSFP UTE sequence within 3 min. It provided easy extraction of uT2 signals and PD-contrast for reference within a single acquisition.
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Affiliation(s)
- Xin Shen
- Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Eduardo Caverzasi
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Department of Neuroradiology, IRCCS Mondino Foundation, Pavia, Italy
| | - Yang Yang
- Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Xiaoxi Liu
- Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Ari Green
- Neurology, University of California San Francisco, San Francisco, California, USA
| | - Roland G Henry
- Neurology, University of California San Francisco, San Francisco, California, USA
| | - Uzay Emir
- School of Health Science, Purdue University, West Lafayette, Indiana, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Peder E Z Larson
- Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
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Baadsvik EL, Weiger M, Froidevaux R, Schildknecht CM, Ineichen BV, Pruessmann KP. Myelin bilayer mapping in the human brain in vivo. Magn Reson Med 2024; 91:2332-2344. [PMID: 38171541 DOI: 10.1002/mrm.29998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/27/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
PURPOSE To quantitatively map the myelin lipid-protein bilayer in the live human brain. METHODS This goal was pursued by integrating a multi-TE acquisition approach targeting ultrashort T2 signals with voxel-wise fitting to a three-component signal model. Imaging was performed at 3 T in two healthy volunteers using high-performance RF and gradient hardware and the HYFI sequence. The design of a suitable imaging protocol faced substantial constraints concerning SNR, imaging volume, scan time, and RF power deposition. Model fitting to data acquired using the proposed protocol was made feasible through simulation-based optimization, and filtering was used to condition noise presentation and overall depiction fidelity. RESULTS A multi-TE protocol (11 TEs of 20-780 μs) for in vivo brain imaging was developed in adherence with applicable safety regulations and practical scan time limits. Data acquired using this protocol produced accurate model fitting results, validating the suitability of the protocol for this purpose. Structured, grainy texture of myelin bilayer maps was observed and determined to be a manifestation of correlated image noise resulting from the employed acquisition strategy. Map quality was significantly improved by filtering to uniformize the k-space noise distribution and simultaneously extending the k-space support. The final myelin bilayer maps provided selective depiction of myelin, reconciling competitive resolution (1.4 mm) with adequate SNR and benign noise texture. CONCLUSION Using the proposed technique, quantitative maps of the myelin bilayer can be obtained in vivo. These maps offer unique information content with potential applications in basic research, diagnosis, disease monitoring, and drug development.
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Affiliation(s)
- Emily Louise Baadsvik
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Markus Weiger
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Romain Froidevaux
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - Benjamin Victor Ineichen
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Reproducible Science, University of Zurich, Zurich, Switzerland
| | - Klaas Paul Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
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Deveshwar N, Yao J, Han M, Dwork N, Shen X, Ljungberg E, Caverzasi E, Cao P, Henry R, Green A, Larson PEZ. Quantification of the in vivo brain ultrashort-T 2* component in healthy volunteers. Magn Reson Med 2024; 91:2417-2430. [PMID: 38291598 DOI: 10.1002/mrm.30013] [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: 04/28/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024]
Abstract
PURPOSE Recent work has shown MRI is able to measure and quantify signals of phospholipid membrane-bound protons associated with myelin in the human brain. This work seeks to develop an improved technique for characterizing this brain ultrashort-T 2 ∗ $$ {\mathrm{T}}_2\ast $$ component in vivo accounting forT 1 $$ {\mathrm{T}}_1 $$ weighting. METHODS Data from ultrashort echo time scans from 16 healthy volunteers with variable flip angles (VFA) were collected and fitted into an advanced regression model to quantify signal fraction, relaxation time, and frequency shift of the ultrashort-T 2 ∗ $$ {\mathrm{T}}_2\ast $$ component. RESULTS The fitted components show intra-subject differences of different white matter structures and significantly elevated ultrashort-T 2 ∗ $$ {\mathrm{T}}_2\ast $$ signal fraction in the corticospinal tracts measured at 0.09 versus 0.06 in other white matter structures and significantly elevated ultrashort-T 2 ∗ $$ {\mathrm{T}}_2\ast $$ frequency shift in the body of the corpus callosum at- $$ - $$ 1.5 versus- $$ - $$ 2.0 ppm in other white matter structures. CONCLUSION The significantly different measured components and measuredT 1 $$ {\mathrm{T}}_1 $$ relaxation time of the ultrashort-T 2 ∗ $$ {\mathrm{T}}_2\ast $$ component suggest that this method is picking up novel signals from phospholipid membrane-bound protons.
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Affiliation(s)
- Nikhil Deveshwar
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
- UC Berkeley - UCSF Graduate Program in Bioengineering, San Francisco, California, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California, USA
| | - Jingwen Yao
- UC Berkeley - UCSF Graduate Program in Bioengineering, San Francisco, California, USA
| | - Misung Han
- UC Berkeley - UCSF Graduate Program in Bioengineering, San Francisco, California, USA
| | - Nicholas Dwork
- Departments of Biomedical Informatics and Radiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Xin Shen
- UC Berkeley - UCSF Graduate Program in Bioengineering, San Francisco, California, USA
| | - Emil Ljungberg
- Department of Medical Radiation Physics, Lund University, Lund, Sweden
| | - Eduardo Caverzasi
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Peng Cao
- Department of Diagnostic Radiology, Hong Kong University, Hong Kong, China
| | - Roland Henry
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Ari Green
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Peder E Z Larson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
- UC Berkeley - UCSF Graduate Program in Bioengineering, San Francisco, California, USA
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Villarreal CX, Shen X, Alhulail AA, Buffo NM, Zhou X, Ozen AC, Chiew M, Sawiak S, Emir U, Chan DD. An Accelerated PETALUTE MRI Sequence for In Vivo Quantification of Sodium Content in Human Articular Cartilage at 3T. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24305807. [PMID: 38746343 PMCID: PMC11092686 DOI: 10.1101/2024.05.02.24305807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
In this work, we demonstrate the sodium magnetic resonance imaging (MRI) capabilities of a three-dimensional (3D) dual-echo ultrashort echo time (UTE) sequence with a novel rosette petal trajectory (PETALUTE), in comparison to the 3D density-adapted (DA) radial spokes UTE sequence. We scanned five healthy subjects using a 3D dual-echo PETALUTE acquisition and two comparable implementations of 3D DA-radial spokes acquisitions, one matching the number of k-space projections (Radial-Matched Trajectories) and the other matching the total number of samples (Radial-Matched Samples) acquired in k-space. The PETALUTE acquisition enabled equivalent sodium quantification in articular cartilage volumes of interest (168.8 ± 29.9 mM) to those derived from the 3D radial acquisitions (171.62 ± 28.7 mM and 149.8 ± 22.2 mM, respectively). We achieved a shorter scan time of 2:06 for 3D PETALUTE, compared to 3:36 for 3D radial acquisitions. We also evaluated the feasibility of further acceleration of the PETALUTE sequence through retrospective compressed sensing with 2× and 4× acceleration of the first echo and showed structural similarity of 0.89 ± 0.03 and 0.87 ± 0.03 when compared to non-retrospectively accelerated reconstruction. Together, these results demonstrate improved scan time with equivalent performance of the PETALUTE sequence compared to the 3D DA-radial sequence for sodium MRI of articular cartilage.
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Pan Z, Qi N, Meng Q, Pan B, Feng T, Zhao J, Gong NJ. Fast SPECT/CT planar bone imaging enabled by deep learning enhancement. Med Phys 2024. [PMID: 38652084 DOI: 10.1002/mp.17094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/21/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The application of deep learning methods in rapid bone scintigraphy is increasingly promising for minimizing the duration of SPECT examinations. Recent works showed several deep learning models based on simulated data for the synthesis of high-count bone scintigraphy images from low-count counterparts. Few studies have been conducted and validated on real clinical pairs due to the misalignment inherent in multiple scan procedures. PURPOSE To generate high quality whole-body bone images from 2× and 3× fast scans using deep learning based enhancement method. MATERIALS AND METHODS Seventy-six cases who underwent whole-body bone scans were enrolled in this prospective study. All patients went through a standard scan at a speed of 20 cm/min, which followed by fast scans consisting of 2× and 3× accelerations at speeds of 40 and 60 cm/min. A content-attention image restoration approach based on Residual-in-Residual Dense Block (RRDB) is introduced to effectively recover high-quality images from fast scans with fine-details and less noise. Our approach is robust with misalignment introduced from patient's metabolism, and shows valid count-level consistency. Learned Perceptual Image Patch Similarity (LPIPS) and Fréchet Inception Distance (FID) are employed in evaluating the similarity to the standard bone images. To further prove our method practical in clinical settings, image quality of the anonymous images was evaluated by two experienced nuclear physicians on a 5-point Likert scale (5 = excellent) . RESULTS The proposed method reaches the state-of-the-art performance on FID and LPIPS with 0.583 and 0.176 for 2× fast scans and 0.583 and 0.185 for 3× fast scans. Clinic evaluation further demonstrated the restored images had a significant improvement compared to fast scan in image quality, technetium 99m-methyl diphosphonate (Tc-99 m MDP) distribution, artifacts, and diagnostic confidence. CONCLUSIONS Our method was validated for accelerating whole-body bone scans by introducing real clinical data. Confirmed by nuclear medicine physicians, the proposed method can effectively enhance image diagnostic value, demonstrating potential for efficient high-quality fast bone imaging in practical settings.
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Affiliation(s)
| | - Na Qi
- Department of Nuclear Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qingyuan Meng
- Department of Nuclear Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Boyang Pan
- RadioDynamic Healthcare, Shanghai, China
| | - Tao Feng
- Laboratory for Intelligent Medical Imaging, Tsinghua Cross-Strait Research Institute, Beijing, China
| | - Jun Zhao
- Department of Nuclear Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Nan-Jie Gong
- Laboratory for Intelligent Medical Imaging, Tsinghua Cross-Strait Research Institute, Beijing, China
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Bozymski B, Emir U, Dydak U, Shen X, Thomas MA, Özen A, Chiew M, Clarke W, Sawiak S. 3D ultra-short echo time 31P-MRSI with rosette k-space pattern: Feasibility and comparison with conventional weighted CSI. RESEARCH SQUARE 2024:rs.3.rs-4223790. [PMID: 38659806 PMCID: PMC11042414 DOI: 10.21203/rs.3.rs-4223790/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Phosphorus-31 magnetic resonance spectroscopic imaging (31P-MRSI) provides valuable non-invasive in vivo information on tissue metabolism but is burdened by poor sensitivity and prolonged scan duration. Ultra-short echo time (UTE) acquisitions minimize signal loss when probing signals with relatively short spin-spin relaxation time (T2), while also preventing first-order dephasing. Here, a three-dimensional (3D) UTE sequence with a rosette k-space trajectory is applied to 31P-MRSI at 3T. Conventional chemical shift imaging (CSI) employs highly regular Cartesian k-space sampling, susceptible to substantial artifacts when accelerated via undersampling. In contrast, this novel sequence's "petal-like" pattern offers incoherent sampling more suitable for compressed sensing (CS). These results showcase the competitive performance of UTE rosette 31P-MRSI against conventional weighted CSI with simulation, phantom, and in vivo leg muscle comparisons.
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Affiliation(s)
| | - Uzay Emir
- School of Health Sciences, Purdue University
| | | | - Xin Shen
- Radiology and Biomedical Imaging, University of California San Francisco
| | | | - Ali Özen
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg
| | - Mark Chiew
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences
| | - William Clarke
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences
| | - Stephen Sawiak
- Department of Clinical Neuroscience, University of Cambridge
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Blömer S, Hingerl L, Marjańska M, Bogner W, Motyka S, Hangel G, Klauser A, Andronesi OC, Strasser B. Proton Free Induction Decay MRSI at 7T in the Human Brain Using an Egg-Shaped Modified Rosette K-Space Trajectory. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.26.24304840. [PMID: 38645249 PMCID: PMC11027556 DOI: 10.1101/2024.03.26.24304840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Purpose 1.1 Proton ( 1 H)-MRSI via spatial-spectral encoding poses high demands on gradient hardware at ultra-high fields and high-resolutions. Rosette trajectories help alleviate these problems, but at reduced SNR-efficiency due to their k-space densities not matching any desired k-space filter. We propose modified rosette trajectories, which more closely match a Hamming filter, and thereby improve SNR performance while still staying within gradient hardware limitations and without prolonging scan time. Methods 1.2Analytical and synthetic simulations were validated with phantom and in vivo measurements at 7 T. The rosette and modified rosette trajectories were measured in five healthy volunteers in six minutes in a 2D slice in the brain. A 3D sequence was measured in one volunteer within 19 minutes. The SNR, linewidth, CRLBs, lipid contamination and data quality of the proposed modified rosette trajectory were compared to the rosette trajectory. Results 1.3Using the modified rosette trajectories, an improved k-space weighting function was achieved resulting in an increase of up to 12% in SNR compared to rosette's dependent on the two additional trajectory parameters. Similar results were achieved for the theoretical SNR calculation based on k-space densities, as well as when using the pseudo-replica method for simulated, in-vivo and phantom data. The CRLBs improved slightly, but non-significantly for the modified rosette trajectories, while the linewidths and lipid contamination remained similar. Conclusion 1.4By improving the rosette trajectory's shape, modified rosette trajectories achieved higher SNR at the same scan time and data quality.
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Baadsvik EL, Weiger M, Froidevaux R, Faigle W, Ineichen BV, Pruessmann KP. Quantitative magnetic resonance mapping of the myelin bilayer reflects pathology in multiple sclerosis brain tissue. SCIENCE ADVANCES 2023; 9:eadi0611. [PMID: 37566661 PMCID: PMC10421026 DOI: 10.1126/sciadv.adi0611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/07/2023] [Indexed: 08/13/2023]
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disease characterized by loss of myelin (demyelination) and, to a certain extent, subsequent myelin repair (remyelination). To better understand the pathomechanisms underlying de- and remyelination and to monitor the efficacy of treatments aimed at regenerating myelin, techniques offering noninvasive visualizations of myelin are warranted. Magnetic resonance (MR) imaging has long been at the forefront of efforts to visualize myelin, but it has only recently become feasible to access the rapidly decaying resonance signals stemming from the myelin lipid-protein bilayer itself. Here, we show that direct MR mapping of the bilayer yields highly specific myelin maps in brain tissue from patients with MS. Furthermore, examination of the bilayer signal behavior is found to reveal pathological alterations in normal-appearing white and gray matter. These results indicate promise for in vivo implementations of the myelin bilayer mapping technique, with prospective applications in basic research, diagnostics, disease monitoring, and drug development.
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Affiliation(s)
- Emily Louise Baadsvik
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Markus Weiger
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Romain Froidevaux
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research Section, Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- Institut Curie, Immunity and Cancer Unit 932, Paris, France
| | - Benjamin V. Ineichen
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Reproducible Science, University of Zurich, Zurich, Switzerland
| | - Klaas P. Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
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Shen X, Özen AC, Monsivais H, Susnjar A, Ilbey S, Zheng W, Du Y, Chiew M, Emir U. High-resolution 3D ultra-short echo time MRI with Rosette k-space pattern for brain iron content mapping. J Trace Elem Med Biol 2023; 77:127146. [PMID: 36871432 PMCID: PMC10107748 DOI: 10.1016/j.jtemb.2023.127146] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/10/2023] [Accepted: 01/31/2023] [Indexed: 03/05/2023]
Abstract
BACKGROUND The iron concentration increases during normal brain development and is identified as a risk factor for many neurodegenerative diseases, it is vital to monitor iron content in the brain non-invasively. PURPOSE This study aimed to quantify in vivo brain iron concentration with a 3D rosette-based ultra-short echo time (UTE) magnetic resonance imaging (MRI) sequence. METHODS A cylindrical phantom containing nine vials of different iron concentrations (iron (II) chloride) from 0.5 millimoles to 50 millimoles and six healthy subjects were scanned using 3D high-resolution (0.94 ×0.94 ×0.94 mm3) rosette UTE sequence at an echo time (TE) of 20 μs. RESULTS Iron-related hyperintense signals (i.e., positive contrast) were detected based on the phantom scan, and were used to establish an association between iron concentration and signal intensity. The signal intensities from in vivo scans were then converted to iron concentrations based on the association. The deep brain structures, such as the substantia nigra, putamen, and globus pallidus, were highlighted after the conversion, which indicated potential iron accumulations. CONCLUSION This study suggested that T1-weighted signal intensity could be used for brain iron mapping.
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Affiliation(s)
- Xin Shen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Ali Caglar Özen
- Department of Radiology, Medical Physics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Antonia Susnjar
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Serhat Ilbey
- Department of Radiology, Medical Physics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wei Zheng
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Yansheng Du
- Department of Neurology, School of Medicine, Indiana University, Bloomington, IN, USA
| | - Mark Chiew
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
| | - Uzay Emir
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA; School of Health Sciences, Purdue University, West Lafayette, IN, USA.
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