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Milovic C, Tejos C, Acosta-Cabronero J, Özbay PS, Schwesser F, Marques JP, Irarrazaval P, Bilgic B, Langkammer C. The 2016 QSM Challenge: Lessons learned and considerations for a future challenge design. Magn Reson Med 2020; 84:1624-1637. [PMID: 32086836 PMCID: PMC7526054 DOI: 10.1002/mrm.28185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/09/2019] [Accepted: 01/06/2020] [Indexed: 11/06/2022]
Abstract
PURPOSE The 4th International Workshop on MRI Phase Contrast and QSM (2016, Graz, Austria) hosted the first QSM Challenge. A single-orientation gradient recalled echo acquisition was provided, along with COSMOS and the χ33 STI component as ground truths. The submitted solutions differed more than expected depending on the error metric used for optimization and were generally over-regularized. This raised (unanswered) questions about the ground truths and the metrics utilized. METHODS We investigated the influence of background field remnants by applying additional filters. We also estimated the anisotropic contributions from the STI tensor to the apparent susceptibility to amend the χ33 ground truth and to investigate the impact on the reconstructions. Lastly, we used forward simulations from the COSMOS reconstruction to investigate the impact noise had on the metric scores. RESULTS Reconstructions compared against the amended STI ground truth returned lower errors. We show that the background field remnants had a minor impact in the errors. In the absence of inconsistencies, all metrics converged to the same regularization weights, whereas structural similarity index metric was more insensitive to such inconsistencies. CONCLUSION There was a mismatch between the provided data and the ground truths due to the presence of unaccounted anisotropic susceptibility contributions and noise. Given the lack of reliable ground truths when using in vivo acquisitions, simulations are suggested for future QSM Challenges.
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Affiliation(s)
- Carlos Milovic
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | - Cristian Tejos
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Biomedical Imaging Center, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | | | - Pinar Senay Özbay
- Laboratory of Functional and Molecular Imaging, National Institutes of Health, Bethesda, MD, USA
| | - Ferdinand Schwesser
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo, The State University of New York, NY, USA
- Center for Biomedical Imaging, Clinical and Translational Science Institute, University at Buffalo, The State University of New York, NY, USA
| | - Jose Pedro Marques
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Pablo Irarrazaval
- Department of Electrical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
- Institute for Biological and Medical Engineering, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Berkin Bilgic
- Martinos Center for Biomedical Imaging, Harvard Medical School, MA, USA
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Özbay PS, Chang C, Picchioni D, Mandelkow H, Chappel-Farley MG, van Gelderen P, de Zwart JA, Duyn J. Sympathetic activity contributes to the fMRI signal. Commun Biol 2019; 2:421. [PMID: 31754651 PMCID: PMC6861267 DOI: 10.1038/s42003-019-0659-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
The interpretation of functional magnetic resonance imaging (fMRI) studies of brain activity is often hampered by the presence of brain-wide signal variations that may arise from a variety of neuronal and non-neuronal sources. Recent work suggests a contribution from the sympathetic vascular innervation, which may affect the fMRI signal through its putative and poorly understood role in cerebral blood flow (CBF) regulation. By analyzing fMRI and (electro-) physiological signals concurrently acquired during sleep, we found that widespread fMRI signal changes often co-occur with electroencephalography (EEG) K-complexes, signatures of sub-cortical arousal, and episodic drops in finger skin vascular tone; phenomena that have been associated with intermittent sympathetic activity. These findings support the notion that the extrinsic sympathetic innervation of the cerebral vasculature contributes to CBF regulation and the fMRI signal. Accounting for this mechanism could help separate systemic from local signal contributions and improve interpretation of fMRI studies.
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Affiliation(s)
- Pinar Senay Özbay
- Advanced MRI Section, LFMI, NINDS, National Institutes of Health, Bethesda, MD USA
| | | | - Dante Picchioni
- Advanced MRI Section, LFMI, NINDS, National Institutes of Health, Bethesda, MD USA
| | - Hendrik Mandelkow
- Advanced MRI Section, LFMI, NINDS, National Institutes of Health, Bethesda, MD USA
| | | | - Peter van Gelderen
- Advanced MRI Section, LFMI, NINDS, National Institutes of Health, Bethesda, MD USA
| | | | - Jeff Duyn
- Advanced MRI Section, LFMI, NINDS, National Institutes of Health, Bethesda, MD USA
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Özbay PS, Stieb S, Rossi C, Riesterer O, Boss A, Weiss T, Kuhn FP, Pruessmann KP, Nanz D. Lesion magnetic susceptibility response to hyperoxic challenge: A biomarker for malignant brain tumor microenvironment? Magn Reson Imaging 2017; 47:147-153. [PMID: 29221966 DOI: 10.1016/j.mri.2017.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/30/2017] [Accepted: 12/03/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND AND PURPOSE Quantitative susceptibility mapping has been previously used to differentiate lesions in patients with brain tumors. The aim of this work was to characterize the response of magnetic susceptibility differences in malignant brain tumors and surrounding edema to hyperoxic and hypercapnic respiratory challenges. METHODS Images of malignant brain tumor patients (2 glioblastoma multiforme, 2 anaplastic astrocytoma, 1 brain metastasis) with clinical MRI exams (contrast-enhanced T1w) were acquired at 3T. 3D multi-gradient-echo data sets were acquired while the patients inhaled medical-air (21% O2), oxygen (100% O2), and carbogen (95% O2, 5% CO2). Susceptibility maps were generated from real and imaginary data. Regions of interest were analyzed with respect to respiration-gas-induced susceptibility changes. RESULTS Contrast-enhancing tumor regions with high baseline magnetic susceptibility exhibited a marked susceptibility reduction under hyperoxic challenges, with a stronger effect (-0.040 to -0.100ppm) under hypercapnia compared to hyperoxia (-0.010 to -0.067ppm). In contrast, regions attributed to necrotic tissue and to edema showed smaller changes of opposite sign, i.e. paramagnetic shift. There was a correlation between malignant tumor tissue magnetic susceptibility at baseline under normoxia and the corresponding susceptibility reduction under hypercapnia and - to a lesser degree - under hyperoxia. CONCLUSION In this small cohort of analysis, quantification of susceptibility changes in response to respiratory challenges allowed a complementary, functional differentiation of tumorous sub-regions. Those changes, together with the correlations observed between baseline susceptibility under normoxia and susceptibility reduction with challenges, could prove helpful for a non-invasive characterization of local tumor microenvironment.
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Affiliation(s)
- Pinar Senay Özbay
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich and University of Zurich, Switzerland; Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Switzerland; Advanced MRI Section, Laboratory of Functional and Molecular Imaging, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Sonja Stieb
- Department of Radiation Oncology, University Hospital Zurich and University of Zurich, Switzerland
| | - Cristina Rossi
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich and University of Zurich, Switzerland
| | - Oliver Riesterer
- Department of Radiation Oncology, University Hospital Zurich and University of Zurich, Switzerland
| | - Andreas Boss
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich and University of Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology, University Hospital Zurich and University of Zurich, Switzerland
| | - Felix Pierre Kuhn
- Department of Nuclear Medicine, University Hospital Zurich and University of Zurich, Switzerland
| | - Klaas Paul Pruessmann
- Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Switzerland
| | - Daniel Nanz
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich and University of Zurich, Switzerland; Swiss Center for Musculoskeletal Imaging, Balgrist Campus AG, Zurich
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Özbay PS, Duerst Y, Wilm BJ, Pruessmann KP, Nanz D. Enhanced quantitative susceptibility mapping (QSM) using real-time field control. Magn Reson Med 2017; 79:770-778. [DOI: 10.1002/mrm.26735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/31/2017] [Accepted: 04/02/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Pinar Senay Özbay
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology; Zurich Switzerland
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Yolanda Duerst
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Bertram Jakob Wilm
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Klaas Paul Pruessmann
- ETH Zurich and University of Zurich, Institute for Biomedical Engineering; Zurich Switzerland
| | - Daniel Nanz
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology; Zurich Switzerland
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Özbay PS, Deistung A, Feng X, Nanz D, Reichenbach JR, Schweser F. A comprehensive numerical analysis of background phase correction with V-SHARP. NMR Biomed 2017; 30:10.1002/nbm.3550. [PMID: 27259117 PMCID: PMC5136354 DOI: 10.1002/nbm.3550] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 03/18/2016] [Accepted: 04/11/2016] [Indexed: 05/19/2023]
Abstract
Sophisticated harmonic artifact reduction for phase data (SHARP) is a method to remove background field contributions in MRI phase images, which is an essential processing step for quantitative susceptibility mapping (QSM). To perform SHARP, a spherical kernel radius and a regularization parameter need to be defined. In this study, we carried out an extensive analysis of the effect of these two parameters on the corrected phase images and on the reconstructed susceptibility maps. As a result of the dependence of the parameters on acquisition and processing characteristics, we propose a new SHARP scheme with generalized parameters. The new SHARP scheme uses a high-pass filtering approach to define the regularization parameter. We employed the variable-kernel SHARP (V-SHARP) approach, using different maximum radii (Rm ) between 1 and 15 mm and varying regularization parameters (f) in a numerical brain model. The local root-mean-square error (RMSE) between the ground-truth, background-corrected field map and the results from SHARP decreased towards the center of the brain. RMSE of susceptibility maps calculated with a spatial domain algorithm was smallest for Rm between 6 and 10 mm and f between 0 and 0.01 mm-1 , and for maps calculated with a Fourier domain algorithm for Rm between 10 and 15 mm and f between 0 and 0.0091 mm-1 . We demonstrated and confirmed the new parameter scheme in vivo. The novel regularization scheme allows the use of the same regularization parameter irrespective of other imaging parameters, such as image resolution. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Pinar Senay Özbay
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, University of Zurich and ETH Zürich, Zurich, Switzerland
| | - Andreas Deistung
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
| | - Xiang Feng
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Daniel Nanz
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Jürgen Rainer Reichenbach
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany
- Michael Stifel Center for Data-driven and Simulation Science Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Ferdinand Schweser
- MRI Clinical and Translational Research Center, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
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Özbay PS, Warnock G, Rossi C, Kuhn F, Akin B, Pruessmann KP, Nanz D. Probing neuronal activation by functional quantitative susceptibility mapping under a visual paradigm: A group level comparison with BOLD fMRI and PET. Neuroimage 2016; 137:52-60. [PMID: 27155125 DOI: 10.1016/j.neuroimage.2016.05.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 11/26/2022] Open
Abstract
Dynamic changes of brain-tissue magnetic susceptibility provide the basis for functional MR imaging (fMRI) via T2*-weighted signal-intensity modulations. Promising initial work on a detection of neuronal activity via quantitative susceptibility mapping (fQSM) has been published but consistently reported on ill-understood positive and negative activation patterns (Balla et al., 2014; Chen and Calhoun, 2015a). We set out to (i) demonstrate that fQSM can exploit established fMRI data acquisition and processing methods and to (ii) better describe aspects of the apparent activation patterns using fMRI and PET as standards of reference. Under a standardized visual-stimulation paradigm PET and 3-T gradient-echo EPI-based fQSM, fMRI data from 9 healthy volunteers were acquired and analyzed by means of Independent Component Analysis (ICA) at subject level and, for the first time, at group level. Numbers of activated (z-score>2.0) voxels were counted and their mean z-scores calculated in volumes of interest (occipital lobe (Nocc_lobe), segmented occipital gray-matter (NGM_occ_lobe), large veins (Nveins)), and in occipital-lobe voxels commonly activated in fQSM and fMRI component maps. Common but not entirely congruent regions of apparent activation were found in the occipital lobe in z-score maps from all modalities, fQSM, fMRI and PET, with distinct BOLD-negatively correlated regions in fQSM data. At subject-level, Nocc_lobe, NGM_occ_lobe and their mean z-scores were significantly smaller in fQSM than in fMRI, but their ratio, NGM_occ_lobe/Nocc_lobe, was comparable. Nveins did not statistically differ and the ratio Nveins/NGM_occ_lobe as well as the mean z-scores were higher for fQSM than for fMRI. In veins and immediate vicinity, z-score maps derived from both phase and fQSM-data showed positive and negative lobes resembling dipole shapes in simulated field and phase maps with no correlate in fMRI or PET data. Our results show that standard fMRI tools can directly be used for fQSM processing, and suggest that fQSM may have the potential to detect gray-matter activation distant from large veins, to improve detection of veins with stimulus-induced venous oxygen saturation (SvO2) variations, and to better localize areas of activation. However, our results seem to clearly expose issues that phenomenologically resemble an incomplete dipolar inversion and that need to be subject to further investigation.
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Affiliation(s)
- Pinar Senay Özbay
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Institute for Biomedical Engineering, University of Zurich, ETH Zurich, Switzerland.
| | - Geoffrey Warnock
- PMOD Technologies Ltd., Zurich, Switzerland; Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Cristina Rossi
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Felix Kuhn
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Burak Akin
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | | | - Daniel Nanz
- Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Özbay PS, Rossi C, Kocian R, Redle M, Boss A, Pruessmann KP, Nanz D. Effect of respiratory hyperoxic challenge on magnetic susceptibility in human brain assessed by quantitative susceptibility mapping (QSM). NMR Biomed 2015; 28:1688-1696. [PMID: 26484968 DOI: 10.1002/nbm.3433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 09/04/2015] [Accepted: 09/17/2015] [Indexed: 06/05/2023]
Abstract
The purpose of this study was to measure the regional change of magnetic susceptibility in human brain upon inhalation of 100% oxygen by MRI quantitative susceptibility mapping (QSM). Fourteen healthy volunteers were scanned in a 3 T MR scanner with a 3D multi-gradient-echo sequence while breathing medical air (normoxia) and pure oxygen (hyperoxia). QSM images and R2* maps were calculated. Mean susceptibility differences versus white matter were measured in regions of interest covering veins, gray matter (GM), and cerebrospinal fluid (CSF) under both conditions. Hyperoxia resulted in a strong susceptibility decrease in large veins (-154.4 ± 65.9 ppb, p < 10(-6)), in a smaller reduction in GM (-1.3 ± 1 ppb, p < 0.001), and in a susceptibility increase in ventricular CSF (3.8 ± 1.8 ppb, p < 10(-5)). The susceptibility decrease in veins implied an increase of venous oxygen saturation (SvO2) by 10.1 ± 4.0%. Compared with QSM, R2* was more seriously affected by long-distance effects not related to local tissue oxygenation and increased in cerebral frontal regions (3 ± 2 s(-1), p < 0.0004) due to paramagnetic molecular oxygen in cavities. The results highlight the potential of QSM to yield region-specific quantitative oxygenation information, and, thus, for applications such as oxygen-therapy monitoring or identification of hypoxic tumor tissue during radiotherapy planning.
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Affiliation(s)
- Pinar Senay Özbay
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology, Zurich, Switzerland
- University of Zurich and ETH Zürich, Institute for Biomedical Engineering, Zurich, Switzerland
| | - Cristina Rossi
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology, Zurich, Switzerland
| | - Roman Kocian
- University Hospital Zurich, Institute of Anesthesiology, Zurich, Switzerland
| | - Manuel Redle
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology, Zurich, Switzerland
| | - Andreas Boss
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology, Zurich, Switzerland
| | - Klaas Paul Pruessmann
- University of Zurich and ETH Zürich, Institute for Biomedical Engineering, Zurich, Switzerland
| | - Daniel Nanz
- University Hospital Zurich and University of Zurich, Institute of Diagnostic and Interventional Radiology, Zurich, Switzerland
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