1
|
Allen TJ, Henze Bancroft LC, Wang K, Wang PN, Unal O, Estkowski LD, Cashen TA, Bayram E, Strigel RM, Holmes JH. Automated Placement of Scan and Pre-Scan Volumes for Breast MRI Using a Convolutional Neural Network. Tomography 2023; 9:967-980. [PMID: 37218939 PMCID: PMC10204486 DOI: 10.3390/tomography9030079] [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: 04/07/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023] Open
Abstract
Graphically prescribed patient-specific imaging volumes and local pre-scan volumes are routinely placed by MRI technologists to optimize image quality. However, manual placement of these volumes by MR technologists is time-consuming, tedious, and subject to intra- and inter-operator variability. Resolving these bottlenecks is critical with the rise in abbreviated breast MRI exams for screening purposes. This work proposes an automated approach for the placement of scan and pre-scan volumes for breast MRI. Anatomic 3-plane scout image series and associated scan volumes were retrospectively collected from 333 clinical breast exams acquired on 10 individual MRI scanners. Bilateral pre-scan volumes were also generated and reviewed in consensus by three MR physicists. A deep convolutional neural network was trained to predict both the scan and pre-scan volumes from the 3-plane scout images. The agreement between the network-predicted volumes and the clinical scan volumes or physicist-placed pre-scan volumes was evaluated using the intersection over union, the absolute distance between volume centers, and the difference in volume sizes. The scan volume model achieved a median 3D intersection over union of 0.69. The median error in scan volume location was 2.7 cm and the median size error was 2%. The median 3D intersection over union for the pre-scan placement was 0.68 with no significant difference in mean value between the left and right pre-scan volumes. The median error in the pre-scan volume location was 1.3 cm and the median size error was -2%. The average estimated uncertainty in positioning or volume size for both models ranged from 0.2 to 3.4 cm. Overall, this work demonstrates the feasibility of an automated approach for the placement of scan and pre-scan volumes based on a neural network model.
Collapse
Affiliation(s)
- Timothy J. Allen
- Department of Medical Physics, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Leah C. Henze Bancroft
- Department of Radiology, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - Kang Wang
- GE Healthcare, 3000 N Grandview Blvd, Waukesha, WI 53188, USA
| | - Ping Ni Wang
- GE Healthcare, 3000 N Grandview Blvd, Waukesha, WI 53188, USA
| | - Orhan Unal
- Department of Medical Physics, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
- Department of Radiology, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | | | - Ty A. Cashen
- GE Healthcare, 3000 N Grandview Blvd, Waukesha, WI 53188, USA
| | - Ersin Bayram
- GE Healthcare, 3000 N Grandview Blvd, Waukesha, WI 53188, USA
| | - Roberta M. Strigel
- Department of Medical Physics, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
- Department of Radiology, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
- Carbone Cancer Center, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792, USA
| | - James H. Holmes
- Department of Radiology, University of Iowa, 169 Newton Road, Iowa City, IA 52242, USA
- Department of Biomedical Engineering, University of Iowa, 3100 Seamans Center, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| |
Collapse
|
2
|
Stamatelatou A, Scheenen TWJ, Heerschap A. Developments in proton MR spectroscopic imaging of prostate cancer. MAGMA (NEW YORK, N.Y.) 2022; 35:645-665. [PMID: 35445307 PMCID: PMC9363347 DOI: 10.1007/s10334-022-01011-9] [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] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/04/2022] [Accepted: 03/22/2022] [Indexed: 10/25/2022]
Abstract
In this paper, we review the developments of 1H-MR spectroscopic imaging (MRSI) methods designed to investigate prostate cancer, covering key aspects such as specific hardware, dedicated pulse sequences for data acquisition and data processing and quantification techniques. Emphasis is given to recent advancements in MRSI methodologies, as well as future developments, which can lead to overcome difficulties associated with commonly employed MRSI approaches applied in clinical routine. This includes the replacement of standard PRESS sequences for volume selection, which we identified as inadequate for clinical applications, by sLASER sequences and implementation of 1H MRSI without water signal suppression. These may enable a new evaluation of the complementary role and significance of MRSI in prostate cancer management.
Collapse
Affiliation(s)
- Angeliki Stamatelatou
- Department of Medical Imaging (766), Radboud University Medical Center Nijmegen, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Tom W J Scheenen
- Department of Medical Imaging (766), Radboud University Medical Center Nijmegen, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Arend Heerschap
- Department of Medical Imaging (766), Radboud University Medical Center Nijmegen, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| |
Collapse
|
3
|
Maudsley AA, Andronesi OC, Barker PB, Bizzi A, Bogner W, Henning A, Nelson SJ, Posse S, Shungu DC, Soher BJ. Advanced magnetic resonance spectroscopic neuroimaging: Experts' consensus recommendations. NMR IN BIOMEDICINE 2021; 34:e4309. [PMID: 32350978 PMCID: PMC7606742 DOI: 10.1002/nbm.4309] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 02/01/2020] [Accepted: 03/10/2020] [Indexed: 05/04/2023]
Abstract
Magnetic resonance spectroscopic imaging (MRSI) offers considerable promise for monitoring metabolic alterations associated with disease or injury; however, to date, these methods have not had a significant impact on clinical care, and their use remains largely confined to the research community and a limited number of clinical sites. The MRSI methods currently implemented on clinical MRI instruments have remained essentially unchanged for two decades, with only incremental improvements in sequence implementation. During this time, a number of technological developments have taken place that have already greatly benefited the quality of MRSI measurements within the research community and which promise to bring advanced MRSI studies to the point where the technique becomes a true imaging modality, while making the traditional review of individual spectra a secondary requirement. Furthermore, the increasing use of biomedical MR spectroscopy studies has indicated clinical areas where advanced MRSI methods can provide valuable information for clinical care. In light of this rapidly changing technological environment and growing understanding of the value of MRSI studies for biomedical studies, this article presents a consensus from a group of experts in the field that reviews the state-of-the-art for clinical proton MRSI studies of the human brain, recommends minimal standards for further development of vendor-provided MRSI implementations, and identifies areas which need further technical development.
Collapse
Affiliation(s)
- Andrew A Maudsley
- Department of Radiology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Ovidiu C Andronesi
- Department of Radiology, Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, Massachusetts
| | - Peter B Barker
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, and the Kennedy Krieger Institute, F.M. Kirby Center for Functional Brain Imaging, Baltimore, Maryland
| | - Alberto Bizzi
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Wolfgang Bogner
- High Field MR Center, Department of Biomedical Imaging and Image-guided Therapy, Medical University Vienna, Vienna, Austria
| | - Anke Henning
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sarah J Nelson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Stefan Posse
- Department of Neurology, University of New Mexico, Albuquerque, New Mexico
| | - Dikoma C Shungu
- Department of Neuroradiology, Weill Cornell Medical College, New York, New York
| | - Brian J Soher
- Department of Radiology, Duke University Medical Center, Durham, North Carolina
| |
Collapse
|
4
|
Tkáč I, Deelchand D, Dreher W, Hetherington H, Kreis R, Kumaragamage C, Považan M, Spielman DM, Strasser B, de Graaf RA. Water and lipid suppression techniques for advanced 1 H MRS and MRSI of the human brain: Experts' consensus recommendations. NMR IN BIOMEDICINE 2021; 34:e4459. [PMID: 33327042 PMCID: PMC8569948 DOI: 10.1002/nbm.4459] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 11/23/2020] [Indexed: 05/09/2023]
Abstract
The neurochemical information provided by proton magnetic resonance spectroscopy (MRS) or MR spectroscopic imaging (MRSI) can be severely compromised if strong signals originating from brain water and extracranial lipids are not properly suppressed. The authors of this paper present an overview of advanced water/lipid-suppression techniques and describe their advantages and disadvantages. Moreover, they provide recommendations for choosing the most appropriate techniques for proper use. Methods of water signal handling are primarily focused on the VAPOR technique and on MRS without water suppression (metabolite cycling). The section on lipid-suppression methods in MRSI is divided into three parts. First, lipid-suppression techniques that can be implemented on most clinical MR scanners (volume preselection, outer-volume suppression, selective lipid suppression) are described. Second, lipid-suppression techniques utilizing the combination of k-space filtering, high spatial resolutions and lipid regularization are presented. Finally, three promising new lipid-suppression techniques, which require special hardware (a multi-channel transmit system for dynamic B1+ shimming, a dedicated second-order gradient system or an outer volume crusher coil) are introduced.
Collapse
Affiliation(s)
- Ivan Tkáč
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - Dinesh Deelchand
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - Wolfgang Dreher
- Department of Chemistry, In vivo-MR Group, University Bremen, Bremen, Germany
| | - Hoby Hetherington
- Department of Radiology Magnetic Resonance Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Roland Kreis
- Departments of Radiology and Biomedical Research, University Bern, Bern, Switzerland
| | - Chathura Kumaragamage
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Michal Považan
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel M. Spielman
- Department of Radiology, Stanford University, Stanford, California, CA, USA
| | - Bernhard Strasser
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Department of Radiology, Boston, MA, USA
| | - Robin A. de Graaf
- Department of Radiology and Biomedical Imaging, Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
5
|
Vidya Shankar R, Chang JC, Hu HH, Kodibagkar VD. Fast data acquisition techniques in magnetic resonance spectroscopic imaging. NMR IN BIOMEDICINE 2019; 32:e4046. [PMID: 30637822 DOI: 10.1002/nbm.4046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
Magnetic resonance spectroscopic imaging (MRSI) is an important technique for assessing the spatial variation of metabolites in vivo. The long scan times in MRSI limit clinical applicability due to patient discomfort, increased costs, motion artifacts, and limited protocol flexibility. Faster acquisition strategies can address these limitations and could potentially facilitate increased adoption of MRSI into routine clinical protocols with minimal addition to the current anatomical and functional acquisition protocols in terms of imaging time. Not surprisingly, a lot of effort has been devoted to the development of faster MRSI techniques that aim to capture the same underlying metabolic information (relative metabolite peak areas and spatial distribution) as obtained by conventional MRSI, in greatly reduced time. The gain in imaging time results, in some cases, in a loss of signal-to-noise ratio and/or in spatial and spectral blurring. This review examines the current techniques and advances in fast MRSI in two and three spatial dimensions and their applications. This review categorizes the acceleration techniques according to their strategy for acquisition of the k-space. Techniques such as fast/turbo-spin echo MRSI, echo-planar spectroscopic imaging, and non-Cartesian MRSI effectively cover the full k-space in a more efficient manner per TR . On the other hand, techniques such as parallel imaging and compressed sensing acquire fewer k-space points and employ advanced reconstruction algorithms to recreate the spatial-spectral information, which maintains statistical fidelity in test conditions (ie no statistically significant differences on voxel-wise comparisions) with the fully sampled data. The advantages and limitations of each state-of-the-art technique are reviewed in detail, concluding with a note on future directions and challenges in the field of fast spectroscopic imaging.
Collapse
Affiliation(s)
- Rohini Vidya Shankar
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - John C Chang
- Banner M D Anderson Cancer Center, Gilbert, AZ, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Houchun H Hu
- Department of Radiology and Medical Imaging, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Vikram D Kodibagkar
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
6
|
Vareth M, Lupo J, Larson P, Nelson S. A comparison of coil combination strategies in 3D multi-channel MRSI reconstruction for patients with brain tumors. NMR IN BIOMEDICINE 2018; 31:e3929. [PMID: 30168205 PMCID: PMC6290901 DOI: 10.1002/nbm.3929] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/01/2018] [Accepted: 03/07/2018] [Indexed: 05/12/2023]
Abstract
The goal of this study was to find the most robust algorithm for a phase-sensitive coil combination of 3D single-cycle and lactate-edited, multi-channel H-1 point-resolved spectroscopy (PRESS) localized echo planar spectroscopic imaging (EPSI) data for clinical applications in the brain. Data were acquired over 5-10 minutes at 3T using 8- or 32-channel array coils. Peak referencing with residual water and N-acetyl-aspartate, first-point phasing, generalized least squared (GLS) and whitened singular-value decomposition (WSVD) combination algorithms were evaluated relative to unsuppressed water with data from a phantom, six volunteers and 55 patients with brain tumors. Comparison metrics were signal-to-noise ratio, coefficient of variance and percent signal increase. Where residual water was present, using it as a reference peak for phasing and weighting factors from an imaging calibration scan gave the best overall performance. Greater improvement was seen for large selected volumes (>720 cm3 ) and for the 32-channel array (25%) compared with the 8-channel array (19%). Applying voxel-by-voxel phase corrections produced a larger increase in performance for the 32- versus 8-channel coil. We conclude that, for clinically relevant 3D H-1 PRESS localized EPSI studies, the most robust technique employed individual phase maps generated from high residual water and individual amplitude maps generated from calibration scans.
Collapse
Affiliation(s)
- Maryam Vareth
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Janine Lupo
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Peder Larson
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Sarah Nelson
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| |
Collapse
|
7
|
Vareth M, Lupo J, Larson P, Nelson S. A comparison of coil combination strategies in 3D multi-channel MRSI reconstruction for patients with brain tumors. NMR IN BIOMEDICINE 2018. [PMID: 30168205 DOI: 10.1002/nbm.3929e3929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The goal of this study was to find the most robust algorithm for a phase-sensitive coil combination of 3D single-cycle and lactate-edited, multi-channel H-1 point-resolved spectroscopy (PRESS) localized echo planar spectroscopic imaging (EPSI) data for clinical applications in the brain. Data were acquired over 5-10 minutes at 3T using 8- or 32-channel array coils. Peak referencing with residual water and N-acetyl-aspartate, first-point phasing, generalized least squared (GLS) and whitened singular-value decomposition (WSVD) combination algorithms were evaluated relative to unsuppressed water with data from a phantom, six volunteers and 55 patients with brain tumors. Comparison metrics were signal-to-noise ratio, coefficient of variance and percent signal increase. Where residual water was present, using it as a reference peak for phasing and weighting factors from an imaging calibration scan gave the best overall performance. Greater improvement was seen for large selected volumes (>720 cm3 ) and for the 32-channel array (25%) compared with the 8-channel array (19%). Applying voxel-by-voxel phase corrections produced a larger increase in performance for the 32- versus 8-channel coil. We conclude that, for clinically relevant 3D H-1 PRESS localized EPSI studies, the most robust technique employed individual phase maps generated from high residual water and individual amplitude maps generated from calibration scans.
Collapse
Affiliation(s)
- Maryam Vareth
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Janine Lupo
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Peder Larson
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Sarah Nelson
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| |
Collapse
|
8
|
Tsai SY, Lin YR, Lin HY, Lin FH. Reduction of lipid contamination in MR spectroscopy imaging using signal space projection. Magn Reson Med 2018; 81:1486-1498. [PMID: 30277271 DOI: 10.1002/mrm.27496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/22/2018] [Accepted: 07/25/2018] [Indexed: 12/27/2022]
Abstract
PURPOSE Lipid contamination can complicate the metabolite quantification in MR spectroscopic imaging (MRSI). In addition to various experimental methods demonstrated to be feasible for lipid suppression, the postprocessing method is beneficial in the flexibility of applications. In this study, the signal space projection (SSP) algorithm is proposed to suppress the lipid signal in the MRSI. METHODS The performance of lipid suppression using SSP and SSP combined with the Papoulis-Gerchberg (PG) algorithm (PG+SSP) is examined in 2D MRSI data and the results were compared with outer volume saturation (OVS) methods. Up to 10 lipid spatial components were extracted by SSP from lipid signals in the range of 0.8~1.5 ppm. RESULTS Our results show that most lipid signals were found in the first 4 to 5 components and that lipid signals on the spectra can be suppressed using 4 to 5 components. Metabolites concentrations were quantified using LCModel. Two regions of interest (ROIs) were manually selected on the peripheral and inner brain regions. The quantification of metabolites in terms of fitting reliability (CRLB) and spatial variations within ROIs (SpaVar) is improved using SSP. When 5 to 6 components were used in SSP and PG+SSP, the metabolite concentrations and the associated SpaVar and CRLB are at the same level as those from the OVS. CONCLUSION We have demonstrated that the SSP method can be used to suppress the lipid signals of MRSI and SSP with 5 to 6 components is suggested to have a similar suppression performance as the OVS method.
Collapse
Affiliation(s)
- Shang-Yueh Tsai
- Graduate Institute of Applied Physics, National Chengchi University, Taipei, Taiwan.,Research Center for Mind, Brain and Learning, National Chengchi University, Taipei, Taiwan
| | - Yi-Ru Lin
- Department of Electronic and Computer Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Hsin-Yu Lin
- Department of Electronic and Computer Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Fa-Hsuan Lin
- Institute of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
9
|
Park YW, Deelchand DK, Joers JM, Hanna B, Berrington A, Gillen JS, Kantarci K, Soher BJ, Barker PB, Park H, Öz G, Lenglet C. AutoVOI: real-time automatic prescription of volume-of-interest for single voxel spectroscopy. Magn Reson Med 2018; 80:1787-1798. [PMID: 29624727 DOI: 10.1002/mrm.27203] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 01/18/2023]
Abstract
PURPOSE To develop a fast and automated volume-of-interest (VOI) prescription pipeline (AutoVOI) for single-voxel MRS that removes the need for manual VOI placement, allows flexible VOI planning in any brain region, and enables high inter- and intra-subject consistency of VOI prescription. METHODS AutoVOI was designed to transfer pre-defined VOIs from an atlas to the 3D anatomical data of the subject during the scan. The AutoVOI pipeline was optimized for consistency in VOI placement (precision), enhanced coverage of the targeted tissue (accuracy), and fast computation speed. The tool was evaluated against manual VOI placement using existing T1 -weighted data sets and corresponding VOI prescriptions. Finally, it was implemented on 2 scanner platforms to acquire MRS data from clinically relevant VOIs that span the cerebrum, cerebellum, and the brainstem. RESULTS The AutoVOI pipeline includes skull stripping, non-linear registration of the atlas to the subject's brain, and computation of the VOI coordinates and angulations using a minimum oriented bounding box algorithm. When compared against manual prescription, AutoVOI showed higher intra- and inter-subject spatial consistency, as quantified by generalized Dice coefficients (GDC), lower intra- and inter-subject variability in tissue composition (gray matter, white matter, and cerebrospinal fluid) and higher or equal accuracy, as quantified by GDC of prescribed VOI with targeted tissues. High quality spectra were obtained on Siemens and Philips 3T systems from 6 automatically prescribed VOIs by the tool. CONCLUSION Robust automatic VOI prescription is feasible and can help facilitate clinical adoption of MRS by avoiding operator dependence of manual selection.
Collapse
Affiliation(s)
- Young Woo Park
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dinesh K Deelchand
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - James M Joers
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Brian Hanna
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Adam Berrington
- Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph S Gillen
- Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kejal Kantarci
- Department of Radiology, Mayo Clinic, Rochester, Minnesota
| | - Brian J Soher
- Department of Radiology, Duke University Medical Center, Durham, North Carolina
| | - Peter B Barker
- Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - HyunWook Park
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Gülin Öz
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Christophe Lenglet
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota
| |
Collapse
|
10
|
Li Y, Lafontaine M, Chang S, Nelson SJ. Comparison between Short and Long Echo Time Magnetic Resonance Spectroscopic Imaging at 3T and 7T for Evaluating Brain Metabolites in Patients with Glioma. ACS Chem Neurosci 2018; 9:130-137. [PMID: 29035503 DOI: 10.1021/acschemneuro.7b00286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Three-dimensional proton magnetic resonance spectroscopic imaging (MRSI) is a powerful non-invasive tool for characterizing spatial variations in metabolic profiles for patients with glioma. Metabolic parameters obtained using this technique have been shown to predict treatment response, disease progression, and transformation to a more malignant phenotype. The availability of ultra-high-field MR systems has the potential to improve the characterization of metabolites. The purpose of this study was to compare the metabolite profiles acquired with conventional long echo time (TE) MRSI at 3T with those obtained with short TE MRSI at 3T and 7T in patients with glioma. The data acquisition parameters were optimized separately for each echo time and field strength to obtain volumetric coverage within clinically feasible data acquisition times of 5-10 min. While a higher field strength did provide better detection of metabolites with overlapping peaks, spatial coverage was reduced and the use of inversion recovery to reduce lipid precluded the detection of lipid in regions of necrosis. For serial evaluation of large, heterogeneous lesions, the use of 3T short TE MRSI may thus be preferred. Despite the limited number of metabolites that it is able to detect, the use of 3T long TE MRSI gives the best contrast in choline/N-acetyl aspartate between normal appearing brain and tumor and also allows the separate detection of lactate and lipid. It may therefore be preferred for serial evaluation of patients with high-grade glioma and for detection of malignant transformation in patients with low-grade glioma.
Collapse
Affiliation(s)
- Yan Li
- Department of Radiology
and Biomedical Imaging, University of California, San Francisco, California 94143, United States
| | - Marisa Lafontaine
- Department of Radiology
and Biomedical Imaging, University of California, San Francisco, California 94143, United States
| | - Susan Chang
- Department of Neurological Surgery, University of California, San Francisco, California 94122, United States
| | - Sarah J. Nelson
- Department of Radiology
and Biomedical Imaging, University of California, San Francisco, California 94143, United States
- Department of Bioengineering and Therapeutic
Sciences, University of California, San Francisco, California 94158, United States
| |
Collapse
|
11
|
Nelson SJ, Kadambi AK, Park I, Li Y, Crane J, Olson M, Molinaro A, Roy R, Butowski N, Cha S, Chang S. Association of early changes in 1H MRSI parameters with survival for patients with newly diagnosed glioblastoma receiving a multimodality treatment regimen. Neuro Oncol 2017; 19:430-439. [PMID: 27576874 DOI: 10.1093/neuonc/now159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/16/2016] [Indexed: 12/27/2022] Open
Abstract
Background The heterogeneous biology of glioblastoma (GBM) emphasizes the need for imaging methods to assess tumor burden and assist in evaluating individual patients. The purpose of this study was to investigate early changes in metrics from 3D 1H magnetic resonance spectroscopic imaging (MRSI) data, compare them with anatomic lesion volumes, and determine whether they were associated with survival for patients with newly diagnosed GBM receiving a multimodality treatment regimen. Methods Serial MRI and MRSI scans provided estimates of anatomic lesion volumes and levels of choline, creatine, N-acetylaspartate, lactate, and lipid. The association of metrics derived from these data with survival was assessed using Cox proportional hazards models with adjustments for age, Karnofsky performance score, and extent of resection. Temporal changes in parameters were evaluated using a Wilcoxon signed rank test. Results Anatomic lesion volumes at the post-radiotherapy (RT) scan, metabolic lesion volume at mid-RT and post-RT scans, as well as metrics describing levels of choline, lactate, and lipid were associated with overall survival. There was a significant reduction in the enhancing lesion volume, increase in T2 lesion volume from mid-RT to post-RT, and decrease in parameters describing metabolite levels during these early time points. Conclusion The MRSI data provided metrics that described the effects of treatment on the metabolic lesion burden and were associated with overall survival. This suggests that adding these parameters to standard assessments of changes in anatomic lesion volumes could contribute to making early decisions about the efficacy of such combination therapies.
Collapse
Affiliation(s)
- Sarah J Nelson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Achuta K Kadambi
- Surbeck Laboratory of Advanced Imaging, University of California, San Francisco, California
| | - Ilwoo Park
- Surbeck Laboratory of Advanced Imaging, University of California, San Francisco, California
| | - Yan Li
- Surbeck Laboratory of Advanced Imaging, University of California, San Francisco, California
| | - Jason Crane
- Surbeck Laboratory of Advanced Imaging, University of California, San Francisco, California
| | - Marram Olson
- Surbeck Laboratory of Advanced Imaging, University of California, San Francisco, California
| | - Annette Molinaro
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Neurological Surgery, University of California, San Francisco, California
| | - Ritu Roy
- Surbeck Laboratory of Advanced Imaging, University of California, San Francisco, California
| | - Nicholas Butowski
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Neurological Surgery, University of California, San Francisco, California
| | - Soonmee Cha
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Neurological Surgery, University of California, San Francisco, California
| | - Susan Chang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| |
Collapse
|
12
|
Bian W, Li Y, Crane JC, Nelson SJ. Fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging: Toward robust and reproducible metabolite measurements in human brain. Magn Reson Med 2017; 79:636-642. [PMID: 28470861 DOI: 10.1002/mrm.26718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/07/2017] [Accepted: 03/27/2017] [Indexed: 11/10/2022]
Abstract
PURPOSE To implement a fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging (MRSI). METHODS The PRESS selected volume and outer-volume suppression bands were predefined on the MNI152 standard template image. The template image was aligned to the subject T1 -weighted image during a scan, and the resulting transformation was then applied to the predefined prescription. To evaluate the method, H-1 MRSI data were obtained in repeat scan sessions from 20 healthy volunteers. In each session, datasets were acquired twice without repositioning. The overlap ratio of the prescribed volume in the two sessions was calculated and the reproducibility of inter- and intrasession metabolite peak height and area ratios was measured by the coefficient of variation (CoV). The CoVs from intra- and intersession were compared by a paired t-test. RESULTS The average overlap ratio of the automatically prescribed selection volumes between two sessions was 97.8%. The average voxel-based intersession CoVs were less than 0.124 and 0.163 for peak height and area ratios, respectively. Paired t-test showed no significant difference between the intra- and intersession CoVs. CONCLUSION The proposed method provides a time efficient method to prescribe 3D PRESS MRSI with reproducible imaging positioning and metabolite measurements. Magn Reson Med 79:636-642, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Collapse
Affiliation(s)
- Wei Bian
- Department of Radiology, Stanford University, Palo Alto, California, USA
| | - Yan Li
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Jason C Crane
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Sarah J Nelson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| |
Collapse
|
13
|
Al-Iedani O, Lechner-Scott J, Ribbons K, Ramadan S. Fast magnetic resonance spectroscopic imaging techniques in human brain- applications in multiple sclerosis. J Biomed Sci 2017; 24:17. [PMID: 28245815 PMCID: PMC5331701 DOI: 10.1186/s12929-017-0323-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 02/08/2017] [Indexed: 01/04/2023] Open
Abstract
Multi voxel magnetic resonance spectroscopic imaging (MRSI) is an important imaging tool that combines imaging and spectroscopic techniques. MRSI of the human brain has been beneficially applied to different clinical applications in neurology, particularly in neurooncology but also in multiple sclerosis, stroke and epilepsy. However, a major challenge in conventional MRSI is the longer acquisition time required for adequate signal to be collected. Fast MRSI of the brain in vivo is an alternative approach to reduce scanning time and make MRSI more clinically suitable.Fast MRSI can be categorised into spiral, echo-planar, parallel and turbo imaging techniques, each with its own strengths. After a brief introduction on the basics of non-invasive examination (1H-MRS) and localization techniques principles, different fast MRSI techniques will be discussed from their initial development to the recent innovations with particular emphasis on their capacity to record neurochemical changes in the brain in a variety of pathologies.The clinical applications of whole brain fast spectroscopic techniques, can assist in the assessment of neurochemical changes in the human brain and help in understanding the roles they play in disease. To give a good example of the utilities of these techniques in clinical context, MRSI application in multiple sclerosis was chosen. The available up to date and relevant literature is discussed and an outline of future research is presented.
Collapse
Affiliation(s)
- Oun Al-Iedani
- School of Health Sciences, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jeannette Lechner-Scott
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.,Department of Neurology, John Hunter Hospital, Lookout Road, New Lambton, NSW 2305, Australia.,Hunter Medical Research Institute, Kookaburra Circuit, New Lambton, NSW 2305, Australia
| | - Karen Ribbons
- Department of Neurology, John Hunter Hospital, Lookout Road, New Lambton, NSW 2305, Australia
| | - Saadallah Ramadan
- School of Health Sciences, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia.
| |
Collapse
|
14
|
Li Y, Larson P, Chen AP, Lupo JM, Ozhinsky E, Kelley D, Chang SM, Nelson SJ. Short-echo three-dimensional H-1 MR spectroscopic imaging of patients with glioma at 7 Tesla for characterization of differences in metabolite levels. J Magn Reson Imaging 2014; 41:1332-41. [PMID: 24935758 DOI: 10.1002/jmri.24672] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND The purpose of this study was to evaluate the feasibility of using a short echo time, three-dimensional H-1 magnetic resonance spectroscopic imaging (MRSI) sequence at 7 Tesla (T) to assess the metabolic signature of lesions for patients with glioma. METHODS Twenty-nine patients with glioma were studied. MRSI data were obtained using CHESS water suppression, spectrally selective adiabatic inversion-recovery pulses and automatically prescribed outer-volume-suppression for lipid suppression, and spin echo slice selection (echo time = 30 ms). An interleaved flyback echo-planar trajectory was applied to shorten the total acquisition time (∼10 min). Relative metabolite ratios were estimated in tumor and in normal-appearing white and gray matter (NAWM, GM). RESULTS Levels of glutamine, myo-inositol, glycine, and glutathione relative to total creatine (tCr) were significantly increased in the T2 lesions for all tumor grades compared with those in the NAWM (P < 0.05), while N-acetyl aspartate to tCr were significantly decreased (P < 0.05). In grade 2 gliomas, level of total choline-containing-compounds to tCr was significantly increased (P = 0.0137), while glutamate to tCr was significantly reduced (P = 0.0012). CONCLUSION The improved sensitivity of MRSI and the increased number of metabolites that can be evaluated using 7T MR scanners is of interest for evaluating patients with glioma. This study has successfully demonstrated the application of a short-echo spin-echo MRSI sequence to detect characteristic differences in regions of tumor versus normal appearing brain.
Collapse
Affiliation(s)
- Yan Li
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | | | | | | | | | | | | | | |
Collapse
|
15
|
A historical overview of magnetic resonance imaging, focusing on technological innovations. Invest Radiol 2013; 47:725-41. [PMID: 23070095 DOI: 10.1097/rli.0b013e318272d29f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Magnetic resonance imaging (MRI) has now been used clinically for more than 30 years. Today, MRI serves as the primary diagnostic modality for many clinical problems. In this article, historical developments in the field of MRI will be discussed with a focus on technological innovations. Topics include the initial discoveries in nuclear magnetic resonance that allowed for the advent of MRI as well as the development of whole-body, high field strength, and open MRI systems. Dedicated imaging coils, basic pulse sequences, contrast-enhanced, and functional imaging techniques will also be discussed in a historical context. This article describes important technological innovations in the field of MRI, together with their clinical applicability today, providing critical insights into future developments.
Collapse
|
16
|
Nelson SJ, Ozhinsky E, Li Y, Park IW, Crane J. Strategies for rapid in vivo 1H and hyperpolarized 13C MR spectroscopic imaging. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 229:187-97. [PMID: 23453759 PMCID: PMC3808990 DOI: 10.1016/j.jmr.2013.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/01/2013] [Accepted: 02/01/2013] [Indexed: 05/13/2023]
Abstract
In vivo MRSI is an important imaging modality that has been shown in numerous research studies to give biologically relevant information for assessing the underlying mechanisms of disease and for monitoring response to therapy. The increasing availability of high field scanners and multichannel radiofrequency coils has provided the opportunity to acquire in vivo data with significant improvements in sensitivity and signal to noise ratio. These capabilities may be used to shorten acquisition time and provide increased coverage. The ability to acquire rapid, volumetric MRSI data is critical for examining heterogeneity in metabolic profiles and for relating serial changes in metabolism within the same individual during the course of the disease. In this review we discuss the implementation of strategies that use alternative k-space sampling trajectories and parallel imaging methods in order to speed up data acquisition. The impact of such methods is demonstrated using three recent examples of how these methods have been applied. These are to the acquisition of robust 3D (1)H MRSI data within 5-10 min at a field strength of 3 T, to obtaining higher sensitivity for (1)H MRSI at 7 T and to using ultrafast volumetric and dynamic (13)C MRSI for monitoring the changes in signals that occur following the injection of hyperpolarized (13)C agents.
Collapse
Affiliation(s)
- Sarah J Nelson
- Surbeck Laboratory for Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158-2330, USA.
| | | | | | | | | |
Collapse
|
17
|
Posse S, Otazo R, Dager SR, Alger J. MR spectroscopic imaging: Principles and recent advances. J Magn Reson Imaging 2012. [DOI: 10.1002/jmri.23945] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
18
|
Ozhinsky E, Vigneron DB, Chang SM, Nelson SJ. Automated prescription of oblique brain 3D magnetic resonance spectroscopic imaging. Magn Reson Med 2012; 69:920-30. [PMID: 22692829 DOI: 10.1002/mrm.24339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Revised: 04/24/2012] [Accepted: 04/25/2012] [Indexed: 11/07/2022]
Abstract
Two major difficulties encountered in implementing Magnetic Resonance Spectroscopic Imaging (MRSI) in a clinical setting are limited coverage and difficulty in prescription. The goal of this project was to automate completely the process of 3D PRESS MRSI prescription, including placement of the selection box, saturation bands and shim volume, while maximizing the coverage of the brain. The automated prescription technique included acquisition of an anatomical MRI image, optimization of the oblique selection box parameters, optimization of the placement of outer-volume suppression saturation bands, and loading of the calculated parameters into a customized 3D MRSI pulse sequence. To validate the technique and compare its performance with existing protocols, 3D MRSI data were acquired from six exams from three healthy volunteers. To assess the performance of the automated 3D MRSI prescription for patients with brain tumors, the data were collected from 16 exams from 8 subjects with gliomas. This technique demonstrated robust coverage of the tumor, high consistency of prescription and very good data quality within the T2 lesion.
Collapse
Affiliation(s)
- Eugene Ozhinsky
- Surbeck Laboratory of Advanced Imaging, Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA 94158-2330, USA.
| | | | | | | |
Collapse
|
19
|
Venugopal N, McCurdy B, Hovdebo J, Al Mehairi S, Alamri A, Sandhu GS, Sivalingam S, Drachenberg D, Ryner L. Automatic conformal prescription of very selective saturation bands for in vivo 1H-MRSI of the prostate. NMR IN BIOMEDICINE 2012; 25:643-653. [PMID: 22162346 DOI: 10.1002/nbm.1780] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 07/11/2011] [Accepted: 07/13/2011] [Indexed: 05/31/2023]
Abstract
An important step in the implementation of three-dimensional in vivo proton magnetic resonance spectroscopic imaging ((1)H-MRSI) of the prostate is the placement of spatial saturation pulses around the region of interest (ROI) for the removal of unwanted contaminating signals from peripheral tissue. The present study demonstrates the use of a technique called conformal voxel magnetic resonance spectroscopy (CV-MRS). This method automates the placement, orientation, timing and flip angle of very selective saturation (VSS) pulses around an irregularly-shaped, user-defined ROI. The method employs a user adjustable number of automatically positioned VSS pulses (20 used in the present study) which null the signal from periprostatic lipids while closely conforming the shape of the excitation voxel to the shape of the prostate. A standard endorectal coil in combination with a torso-phased array coil was used for all in vivo prostate studies. Three-dimensional in vivo prostate (1)H-MRSI data were obtained using the proposed semi-automated CV-MRS technique, and compared with a standard point resolved spectroscopy (PRESS) technique at TE = 130 ms using manual placement of saturation pulses. The in vivo prostate (1)H-MRSI data collected from 12 healthy subjects using the CV-MRS method showed significantly reduced lipid contamination throughout the prostate, and reduced baseline distortions. On average there was a 50 ± 17% (range 12% - 68%) reduction in lipids throughout the prostate. A voxel-by-voxel benchmark test of over 850 voxels showed that there were 63% more peaks fitted using the LCModel when using a Cramer-Rao Lower Bound (CRLB) cut-off of 40% when using the optimized conformal voxel technique in comparison to the manual placement approach. The evaluation of this CV-MRS technique has demonstrated the potential for easy automation of the graphical prescription of saturation bands for use in (1)H-MRSI.
Collapse
Affiliation(s)
- N Venugopal
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada.
| | | | | | | | | | | | | | | | | |
Collapse
|