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Aigner CS, Sánchez Alarcon MF, D'Astous A, Alonso-Ortiz E, Cohen-Adad J, Schmitter S. Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T. Magn Reson Med 2024; 92:1496-1510. [PMID: 38733068 DOI: 10.1002/mrm.30137] [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: 02/16/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
PURPOSE To address the limitations of spinal cord imaging at ultra-high field (UHF) due to time-consuming parallel transmit (pTx) adjustments. This study introduces calibration-free offline computed universal shim modes that can be applied seamlessly for different pTx RF coils and spinal cord target regions, substantially enhancing spinal cord imaging efficiency at UHF. METHODS A library of channel-wise relativeB 1 + $$ {B}_1^{+} $$ maps for the cervical spinal cord (six datasets) and thoracic and lumbar spinal cord (nine datasets) was constructed to optimize transmit homogeneity and efficiency for these regions. A tailored B0 shim was optimized for the cervical spine to enhance spatial magnetic field homogeneity further. The performance of the universal shims was validated using absolute saturation basedB 1 + $$ {B}_1^{+} $$ mapping and high-resolution 2D and 3D multi-echo gradient-recalled echo (GRE) data to assess the image quality. RESULTS The proposed universal shims demonstrated a 50% improvement inB 1 + $$ {B}_1^{+} $$ efficiency compared to the default (zero phase) shim mode.B 1 + $$ {B}_1^{+} $$ homogeneity was also improved by 20%. The optimized universal shims achieved performance comparable to subject-specific pTx adjustments, while eliminating the need for lengthy pTx calibration times, saving about 10 min per experiment. CONCLUSION The development of universal shims represents a significant advance by eliminating time-consuming subject-specific pTx adjustments. This approach is expected to make UHF spinal cord imaging more accessible and user-friendly, particularly for non-pTx experts.
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Affiliation(s)
- Christoph S Aigner
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
| | - Manuel F Sánchez Alarcon
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
- Working Group on Cardiovascular Magnetic Resonance, Experimental and Clinical Research Center, A Joint Cooperation between the Charité Medical Faculty and the Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Alexandre D'Astous
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Quebec, Canada
| | - Eva Alonso-Ortiz
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montréal, Quebec, Canada
- Mila-Quebec AI Institute, Montréal, Quebec, Canada
| | - Julien Cohen-Adad
- Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montréal, Quebec, Canada
- Mila-Quebec AI Institute, Montréal, Quebec, Canada
- Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sebastian Schmitter
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
- Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota, USA
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Winter L, Periquito J, Kolbitsch C, Pellicer-Guridi R, Nunes RG, Häuer M, Broche L, O'Reilly T. Open-source magnetic resonance imaging: Improving access, science, and education through global collaboration. NMR IN BIOMEDICINE 2024; 37:e5052. [PMID: 37986655 DOI: 10.1002/nbm.5052] [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: 01/08/2023] [Revised: 08/01/2023] [Accepted: 09/09/2023] [Indexed: 11/22/2023]
Abstract
Open-source practices and resources in magnetic resonance imaging (MRI) have increased substantially in recent years. This trend started with software and data being published open-source and, more recently, open-source hardware designs have become increasingly available. These developments towards a culture of sharing and establishing nonexclusive global collaborations have already improved the reproducibility and reusability of code and designs, while providing a more inclusive approach, especially for low-income settings. Community-driven standardization and documentation efforts are further strengthening and expanding these milestones. The future of open-source MRI is bright and we have just started to discover its full collaborative potential. In this review we will give an overview of open-source software and open-source hardware projects in human MRI research.
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Affiliation(s)
- Lukas Winter
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
| | - João Periquito
- Department of Infection, Immunity & Cardiovascular Disease, The University of Sheffield, Sheffield, UK
| | - Christoph Kolbitsch
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
| | | | - Rita G Nunes
- Institute for Systems and Robotics and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Martin Häuer
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
- Open Source Ecology Germany e.V. (nonprofit), Berlin, Germany
| | - Lionel Broche
- Biomedical Physics, University of Aberdeen, Aberdeen, UK
| | - Tom O'Reilly
- Leiden University Medical Center (LUMC), Leiden, The Netherlands
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Guillemin PC, Ferreira Branco D, M’Rad Y, Mattera L, Lorton O, Piredda GF, Klauser A, Martuzzi R, Poletti PA, Salomir R, Boudabbous S. High-Resolution Magnetic Resonance Neurography at 7T: A Pilot Study of Hand Innervation. Diagnostics (Basel) 2024; 14:1230. [PMID: 38928648 PMCID: PMC11202541 DOI: 10.3390/diagnostics14121230] [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: 04/30/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
The emergence of 7T clinical MRI technology has sparked our interest in its ability to discern the complex structures of the hand. Our primary objective was to assess the sensory and motor nerve structures of the hand, specifically nerves and Pacinian corpuscles, with the dual purpose of aiding diagnostic endeavors and supporting reconstructive surgical procedures. Ethical approval was obtained to carry out 7T MRI scans on a cohort of volunteers. Four volunteers assumed a prone position, with their hands (N = 8) positioned in a "superman" posture. To immobilize and maintain the hand in a strictly horizontal position, it was affixed to a plastic plate. Passive B0 shimming was implemented. Once high-resolution 3D images had been acquired using a multi-transmit head coil, advanced post-processing techniques were used to meticulously delineate the nerve fiber networks and mechanoreceptors. Across all participants, digital nerves were consistently located on the phalanges area, on average, between 2.5 and 3.5 mm beneath the skin, except within flexion folds where the nerve was approximately 1.8 mm from the surface. On the phalanges area, the mean distance from digital nerves to joints was approximately 1.5 mm. The nerves of the fingers were closer to the bone than to the surface of the skin. Furthermore, Pacinian corpuscles exhibited a notable clustering primarily within the metacarpal zone, situated on the palmar aspect. Our study yielded promising results, successfully reconstructing and meticulously describing the anatomy of nerve fibers spanning from the carpus to the digital nerve division, alongside the identification of Pacinian corpuscles, in four healthy volunteers (eight hands).
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Affiliation(s)
- Pauline C. Guillemin
- Image Guided Interventions Laboratory (GR-949), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (Y.M.); (O.L.); (R.S.); (S.B.)
| | - David Ferreira Branco
- Radiology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland; (D.F.B.); (P.-A.P.)
| | - Yacine M’Rad
- Image Guided Interventions Laboratory (GR-949), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (Y.M.); (O.L.); (R.S.); (S.B.)
| | - Loan Mattera
- Human Neuroscience Platform, Fondation Campus Biotech Geneva, 1202 Geneva, Switzerland; (L.M.); (R.M.)
| | - Orane Lorton
- Image Guided Interventions Laboratory (GR-949), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (Y.M.); (O.L.); (R.S.); (S.B.)
| | - Gian Franco Piredda
- Advanced Clinical Imaging Technology, Siemens Healthineers International AG, 1015 Lausanne, Switzerland; (G.F.P.); (A.K.)
- CIBM Center for Biomedical Imaging, 1202 Geneva, Switzerland
| | - Antoine Klauser
- Advanced Clinical Imaging Technology, Siemens Healthineers International AG, 1015 Lausanne, Switzerland; (G.F.P.); (A.K.)
- CIBM Center for Biomedical Imaging, 1202 Geneva, Switzerland
| | - Roberto Martuzzi
- Human Neuroscience Platform, Fondation Campus Biotech Geneva, 1202 Geneva, Switzerland; (L.M.); (R.M.)
| | - Pierre-Alexandre Poletti
- Radiology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland; (D.F.B.); (P.-A.P.)
| | - Rares Salomir
- Image Guided Interventions Laboratory (GR-949), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (Y.M.); (O.L.); (R.S.); (S.B.)
- Radiology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland; (D.F.B.); (P.-A.P.)
| | - Sana Boudabbous
- Image Guided Interventions Laboratory (GR-949), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (Y.M.); (O.L.); (R.S.); (S.B.)
- Radiology Department, University Hospitals of Geneva, 1205 Geneva, Switzerland; (D.F.B.); (P.-A.P.)
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Dong Z, Wald LL, Polimeni JR, Wang F. Single-shot Echo Planar Time-resolved Imaging for multi-echo functional MRI and distortion-free diffusion imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577002. [PMID: 38328081 PMCID: PMC10849706 DOI: 10.1101/2024.01.24.577002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Purpose To develop EPTI, a multi-shot distortion-free multi-echo imaging technique, into a single-shot acquisition to achieve improved robustness to motion and physiological noise, increased temporal resolution, and high SNR efficiency for dynamic imaging applications. Methods A new spatiotemporal encoding was developed to achieve single-shot EPTI by enhancing spatiotemporal correlation in k-t space. The proposed single-shot encoding improves reconstruction conditioning and sampling efficiency, with additional optimization under various accelerations to achieve optimized performance. To achieve high SNR efficiency, continuous readout with minimized deadtime was employed that begins immediately after excitation and extends for an SNR-optimized length. Moreover, k-t partial Fourier and simultaneous multi-slice acquisition were integrated to further accelerate the acquisition and achieve high spatial and temporal resolution. Results We demonstrated that ss-EPTI achieves higher tSNR efficiency than multi-shot EPTI, and provides distortion-free imaging with densely-sampled multi-echo images at resolutions ~1.25-3 mm at 3T and 7T-with high SNR efficiency and with comparable temporal resolutions to ss-EPI. The ability of ss-EPTI to eliminate dynamic distortions common in EPI also further improves temporal stability. For fMRI, ss-EPTI also provides early-TE images (e.g., 2.9ms) to recover signal-intensity and functional-sensitivity dropout in challenging regions. The multi-echo images provide TE-dependent information about functional fluctuations, successfully distinguishing noise-components from BOLD signals and further improving tSNR. For diffusion MRI, ss-EPTI provides high-quality distortion-free diffusion images and multi-echo diffusion metrics. Conclusion ss-EPTI provides distortion-free imaging with high image quality, rich multi-echo information, and enhanced efficiency within comparable temporal resolution to ss-EPI, offering a robust and efficient acquisition for dynamic imaging.
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Affiliation(s)
- Zijing Dong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lawrence L. Wald
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
| | - Jonathan R. Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
| | - Fuyixue Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
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Tsivaka D, Williams SCR, Medina S, Kowalczyk OS, Brooks JCW, Howard MA, Lythgoe DJ, Tsougos I. A second-order and slice-specific linear shimming technique to improve spinal cord fMRI. Magn Reson Imaging 2023:S0730-725X(23)00108-X. [PMID: 37353180 DOI: 10.1016/j.mri.2023.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/20/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
PURPOSE To develop a second-order and slice-specific linear shimming technique and investigate its efficiency in the mitigation of signal loss and distortions, and the increase of temporal signal-to-noise ratio (tSNR) within the spinal cord during functional Magnetic Resonance Imaging (fMRI) of the human cervical spinal cord. METHODS All scans were performed on a General Electric Discovery MR750 3 T scanner, using a head, neck and spine coil and a neurovascular array. To improve B0 homogeneity, a field map was acquired, and second-order shims (SOS) were optimized over manually defined regions of interest (ROIs). Signal loss from dephasing by susceptibility-induced gradients was reduced by optimizing slice-specific x-, y- and z-shims to maximize signal within the spinal cord. Spectral-spatial excitation pulses were used in both the slice-specific linear shimming calibration scan and fMRI acquisitions. The shimming technique's efficiency was initially tested on eight healthy volunteers by comparing tSNR between images acquired with the manufacturer's standard linear shimming and with our SOS and xyz-shimming technique. Subsequently, using an increased spatial resolution as needed for fMRI of the spinal cord, tSNR measurements were performed on resting-state fMRI images from 14 healthy participants. RESULTS Spinal fMRI images acquired with only the standard linear shimming suffered from severe signal loss below the C5 vertebral level. The developed shimming technique compensated for this loss especially at levels C6 and C7, while tSNR was significantly higher at all vertebral levels with SOS and xyz-shimming than without it. CONCLUSION A comprehensive shimming approach which includes the use of spectral-spatial excitation pulses along with both second-order and slice-specific linear shim optimization reduces regional signal loss and increases tSNR along the c-spine (C3-C7), improving the ability to record functional signals from the human spinal cord.
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Affiliation(s)
- D Tsivaka
- Medical Physics Department, Medical School, University of Thessaly, Larisa, Greece; Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - S C R Williams
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - S Medina
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - O S Kowalczyk
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - J C W Brooks
- School of Psychology, University of East Anglia, Norwich, UK
| | - M A Howard
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D J Lythgoe
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - I Tsougos
- Medical Physics Department, Medical School, University of Thessaly, Larisa, Greece; Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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