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Lasič S, Chakwizira A, Lundell H, Westin CF, Nilsson M. Tuned exchange imaging: Can the filter exchange imaging pulse sequence be adapted for applications with thin slices and restricted diffusion? NMR IN BIOMEDICINE 2024; 37:e5208. [PMID: 38961745 DOI: 10.1002/nbm.5208] [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: 01/05/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
Filter exchange imaging (FEXI) is a double diffusion-encoding (DDE) sequence that is specifically sensitive to exchange between sites with different apparent diffusivities. FEXI uses a diffusion-encoding filtering block followed by a detection block at varying mixing times to map the exchange rate. Long mixing times enhance the sensitivity to exchange, but they pose challenges for imaging applications that require a stimulated echo sequence with crusher gradients. Thin imaging slices require strong crushers, which can introduce significant diffusion weighting and bias exchange rate estimates. Here, we treat the crushers as an additional encoding block and consider FEXI as a triple diffusion-encoding sequence. This allows the bias to be corrected in the case of multi-Gaussian diffusion, but not easily in the presence of restricted diffusion. Our approach addresses challenges in the presence of restricted diffusion and relies on the ability to independently gauge sensitivities to exchange and restricted diffusion for arbitrary gradient waveforms. It follows two principles: (i) the effects of crushers are included in the forward model using signal cumulant expansion; and (ii) timing parameters of diffusion gradients in filter and detection blocks are adjusted to maintain the same level of restriction encoding regardless of the mixing time. This results in the tuned exchange imaging (TEXI) protocol. The accuracy of exchange mapping with TEXI was assessed through Monte Carlo simulations in spheres of identical sizes and gamma-distributed sizes, and in parallel hexagonally packed cylinders. The simulations demonstrate that TEXI provides consistent exchange rates regardless of slice thickness and restriction size, even with strong crushers. However, the accuracy depends on b-values, mixing times, and restriction geometry. The constraints and limitations of TEXI are discussed, including suggestions for protocol adaptations. Further studies are needed to optimize the precision of TEXI and assess the approach experimentally in realistic, heterogeneous substrates.
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Affiliation(s)
- Samo Lasič
- Department of Diagnostic Radiology, Lund University, Lund, Sweden
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Arthur Chakwizira
- Department of Medical Radiation Physics, Lund, Lund University, Lund, Sweden
| | - Henrik Lundell
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- MR Section, DTU Health Tech, Technical University of Denmark, Lyngby, Denmark
| | - Carl-Fredrik Westin
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Markus Nilsson
- Department of Clinical Sciences Lund, Radiology, Lund University, Lund, Sweden
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Santini T, Shim A, Liou JJ, Rahman N, Varela-Mattatall G, Budde MD, Inoue W, Everling S, Baron CA. Investigating microstructural changes between in vivo and perfused ex vivo marmoset brains using oscillating gradient and b-tensor encoded diffusion MRI at 9.4 T. Magn Reson Med 2024. [PMID: 39323069 DOI: 10.1002/mrm.30298] [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: 03/26/2024] [Revised: 08/02/2024] [Accepted: 08/28/2024] [Indexed: 09/27/2024]
Abstract
PURPOSE To investigate microstructural alterations induced by perfusion fixation in brain tissues using advanced diffusion MRI techniques and estimate their potential impact on the application of ex vivo models to in vivo microstructure. METHODS We used oscillating gradient spin echo (OGSE) and b-tensor encoding diffusion MRI to examine in vivo and ex vivo microstructural differences in the marmoset brain. OGSE was used to shorten effective diffusion times, whereas b-tensor encoding allowed for the differentiation of isotropic and anisotropic kurtosis. Additionally, we performed Monte Carlo simulations to estimate the potential microstructural changes in the tissues. RESULTS We report large changes (˜50%-60%) in kurtosis frequency dispersion (OGSE) and in both anisotropic and isotropic kurtosis (b-tensor encoding) after perfusion fixation. Structural MRI showed an average volume reduction of about 10%. Monte Carlo simulations indicated that these alterations could likely be attributed to extracellular fluid loss possibly combined with axon beading and increased dot compartment signal fraction. Little evidence was observed for reductions in axonal caliber. CONCLUSION Our findings shed light on advanced MRI parameter changes that are induced by perfusion fixation and potential microstructural sources for these changes. This work also suggests that caution should be exercised when applying ex vivo models to infer in vivo tissue microstructure, as significant differences may arise.
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Affiliation(s)
- Tales Santini
- Western University, London, Ontario, Canada
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Jr-Jiun Liou
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Narvaez O, Yon M, Jiang H, Bernin D, Forssell-Aronsson E, Sierra A, Topgaard D. Nonparametric distributions of tensor-valued Lorentzian diffusion spectra for model-free data inversion in multidimensional diffusion MRI. J Chem Phys 2024; 161:084201. [PMID: 39171708 DOI: 10.1063/5.0213252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024] Open
Abstract
Magnetic resonance imaging (MRI) is the method of choice for noninvasive studies of micrometer-scale structures in biological tissues via their effects on the time- and frequency-dependent (restricted) and anisotropic self-diffusion of water. While new designs of time-dependent magnetic field gradient waveforms have enabled disambiguation between different aspects of translational motion that are convolved in traditional MRI methods relying on single pairs of field gradient pulses, data analysis for complex heterogeneous materials remains a challenge. Here, we propose and demonstrate nonparametric distributions of tensor-valued Lorentzian diffusion spectra, or "D(ω) distributions," as a general representation with sufficient flexibility to describe the MRI signal response from a wide range of model systems and biological tissues investigated with modulated gradient waveforms separating and correlating the effects of restricted and anisotropic diffusion.
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Affiliation(s)
- Omar Narvaez
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Maxime Yon
- Department of Chemistry, Lund University, Lund, Sweden
| | - Hong Jiang
- Department of Chemistry, Lund University, Lund, Sweden
| | - Diana Bernin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Eva Forssell-Aronsson
- Department of Medical Radiation Sciences, University of Gothenburg, Gothenburg, Sweden
- Medical Physics and Biomedical Engineering, Sahlgrenska University Hospital, Gothenburg, Sweden
- Sahlgrenska Center for Cancer Research, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Alejandra Sierra
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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Michael ES, Hennel F, Pruessmann KP. Motion-compensated diffusion encoding in multi-shot human brain acquisitions: Insights using high-performance gradients. Magn Reson Med 2024; 92:556-572. [PMID: 38441339 DOI: 10.1002/mrm.30069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/12/2023] [Accepted: 02/09/2024] [Indexed: 06/02/2024]
Abstract
PURPOSE To evaluate the utility of up to second-order motion-compensated diffusion encoding in multi-shot human brain acquisitions. METHODS Experiments were performed with high-performance gradients using three forms of diffusion encoding motion-compensated through different orders: conventional zeroth-order-compensated pulsed gradients (PG), first-order-compensated gradients (MC1), and second-order-compensated gradients (MC2). Single-shot acquisitions were conducted to correlate the order of motion compensation with resultant phase variability. Then, multi-shot acquisitions were performed at varying interleaving factors. Multi-shot images were reconstructed using three levels of shot-to-shot phase correction: no correction, channel-wise phase correction based on FID navigation, and correction based on explicit phase mapping (MUSE). RESULTS In single-shot acquisitions, MC2 diffusion encoding most effectively suppressed phase variability and sensitivity to brain pulsation, yielding residual variations of about 10° and of low spatial order. Consequently, multi-shot MC2 images were largely satisfactory without phase correction and consistently improved with the navigator correction, which yielded repeatable high-quality images; contrarily, PG and MC1 images were inadequately corrected using the navigator approach. With respect to MUSE reconstructions, the MC2 navigator-corrected images were in close agreement for a standard interleaving factor and considerably more reliable for higher interleaving factors, for which MUSE images were corrupted. Finally, owing to the advanced gradient hardware, the relative SNR penalty of motion-compensated diffusion sensitization was substantially more tolerable than that faced previously. CONCLUSION Second-order motion-compensated diffusion encoding mitigates and simplifies shot-to-shot phase variability in the human brain, rendering the multi-shot acquisition strategy an effective means to circumvent limitations of retrospective phase correction methods.
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Affiliation(s)
- Eric Seth Michael
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Franciszek Hennel
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Klaas Paul Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
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Johnson JTE, Irfanoglu MO, Manninen E, Ross TJ, Yang Y, Laun FB, Martin J, Topgaard D, Benjamini D. In vivo disentanglement of diffusion frequency-dependence, tensor shape, and relaxation using multidimensional MRI. Hum Brain Mapp 2024; 45:e26697. [PMID: 38726888 PMCID: PMC11082920 DOI: 10.1002/hbm.26697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Diffusion MRI with free gradient waveforms, combined with simultaneous relaxation encoding, referred to as multidimensional MRI (MD-MRI), offers microstructural specificity in complex biological tissue. This approach delivers intravoxel information about the microstructure, local chemical composition, and importantly, how these properties are coupled within heterogeneous tissue containing multiple microenvironments. Recent theoretical advances incorporated diffusion time dependency and integrated MD-MRI with concepts from oscillating gradients. This framework probes the diffusion frequency,ω $$ \omega $$ , in addition to the diffusion tensor,D $$ \mathbf{D} $$ , and relaxation,R 1 $$ {R}_1 $$ ,R 2 $$ {R}_2 $$ , correlations. AD ω - R 1 - R 2 $$ \mathbf{D}\left(\omega \right)-{R}_1-{R}_2 $$ clinical imaging protocol was then introduced, with limited brain coverage and 3 mm3 voxel size, which hinder brain segmentation and future cohort studies. In this study, we introduce an efficient, sparse in vivo MD-MRI acquisition protocol providing whole brain coverage at 2 mm3 voxel size. We demonstrate its feasibility and robustness using a well-defined phantom and repeated scans of five healthy individuals. Additionally, we test different denoising strategies to address the sparse nature of this protocol, and show that efficient MD-MRI encoding design demands a nuanced denoising approach. The MD-MRI framework provides rich information that allows resolving the diffusion frequency dependence into intravoxel components based on theirD ω - R 1 - R 2 $$ \mathbf{D}\left(\omega \right)-{R}_1-{R}_2 $$ distribution, enabling the creation of microstructure-specific maps in the human brain. Our results encourage the broader adoption and use of this new imaging approach for characterizing healthy and pathological tissues.
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Affiliation(s)
- Jessica T. E. Johnson
- Multiscale Imaging and Integrative Biophysics Unit, National Institute on Aging, NIHBaltimoreMarylandUSA
| | - M. Okan Irfanoglu
- Quantitative Medical Imaging Section, National Institute of Biomedical Imaging and Bioengineering, National Institutes of HealthBethesdaMarylandUSA
| | - Eppu Manninen
- Multiscale Imaging and Integrative Biophysics Unit, National Institute on Aging, NIHBaltimoreMarylandUSA
| | - Thomas J. Ross
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of HealthBaltimoreMarylandUSA
| | - Yihong Yang
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of HealthBaltimoreMarylandUSA
| | - Frederik B. Laun
- Institute of Radiology, University Hospital Erlangen, Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU)ErlangenGermany
| | - Jan Martin
- Department of ChemistryLund UniversityLundSweden
| | | | - Dan Benjamini
- Multiscale Imaging and Integrative Biophysics Unit, National Institute on Aging, NIHBaltimoreMarylandUSA
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Chakwizira A, Zhu A, Foo T, Westin CF, Szczepankiewicz F, Nilsson M. Diffusion MRI with free gradient waveforms on a high-performance gradient system: Probing restriction and exchange in the human brain. Neuroimage 2023; 283:120409. [PMID: 37839729 DOI: 10.1016/j.neuroimage.2023.120409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023] Open
Abstract
The dependence of the diffusion MRI signal on the diffusion time carries signatures of restricted diffusion and exchange. Here we seek to highlight these signatures in the human brain by performing experiments using free gradient waveforms designed to be selectively sensitive to the two effects. We examine six healthy volunteers using both strong and ultra-strong gradients (80, 200 and 300 mT/m). In an experiment featuring a large set of 150 gradient waveforms with different sensitivities to restricted diffusion and exchange, our results reveal unique and different time-dependence signatures in grey and white matter. Grey matter was characterised by both restricted diffusion and exchange and white matter predominantly by restricted diffusion. Exchange in grey matter was at least twice as fast as in white matter, across all subjects and all gradient strengths. The cerebellar cortex featured relatively short exchange times (115 ms). Furthermore, we show that gradient waveforms with tailored designs can be used to map exchange in the human brain. We also assessed the feasibility of clinical applications of the method used in this work and found that the exchange-related contrast obtained with a 25-minute protocol at 300 mT/m was preserved in a 4-minute protocol at 300 mT/m and a 10-minute protocol at 80 mT/m. Our work underlines the utility of free waveforms for detecting time dependence signatures due to restricted diffusion and exchange in vivo, which may potentially serve as a tool for studying diseased tissue.
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Affiliation(s)
- Arthur Chakwizira
- Department of Medical Radiation Physics, Clinical Sciences Lund, Lund University, Lund, Sweden.
| | - Ante Zhu
- GE Research, Niskayuna, New York, United States
| | - Thomas Foo
- GE Research, Niskayuna, New York, United States
| | - Carl-Fredrik Westin
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Filip Szczepankiewicz
- Department of Medical Radiation Physics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Markus Nilsson
- Department of Clinical Sciences Lund, Radiology, Lund University, Lund, Sweden; Department of Radiology, Skåne University Hospital, Lund, Sweden
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Zhu A, Shih R, Huang RY, DeMarco JK, Bhushan C, Morris HD, Kohls G, Yeo DTB, Marinelli L, Mitra J, Hood M, Ho VB, Foo TKF. Revealing tumor microstructure with oscillating diffusion encoding MRI in pre-surgical and post-treatment glioma patients. Magn Reson Med 2023; 90:1789-1801. [PMID: 37335831 DOI: 10.1002/mrm.29758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 06/21/2023]
Abstract
PURPOSE We hypothesized that the time-dependent diffusivity at short diffusion times, as measured by oscillating gradient spin echo (OGSE) diffusion MRI, can characterize tissue microstructures in glioma patients. THEORY AND METHODS Five adult patients with known diffuse glioma, including two pre-surgical and three with new enhancing lesions after treatment for high-grade glioma, were scanned in an ultra-high-performance gradient 3.0T MRI system. OGSE diffusion MRI at 30-100 Hz and pulsed gradient spin echo diffusion imaging (approximated as 0 Hz) were obtained. The ADC and trace-diffusion-weighted image at each acquired frequency were calculated, that is, ADC (f) and TraceDWI (f). RESULTS In pre-surgical patients, biopsy-confirmed solid enhancing tumor in a high-grade glioblastoma showed higherADC ( f ) ADC ( 0 Hz ) $$ \frac{\mathrm{ADC}\ (f)}{\mathrm{ADC}\ \left(0\ \mathrm{Hz}\right)} $$ and lowerTraceDWI ( f ) TraceDWI ( 0 Hz ) $$ \frac{\mathrm{TraceDWI}\ (f)}{\mathrm{TraceDWI}\ \left(0\ \mathrm{Hz}\right)} $$ , compared to that at same OGSE frequency in a low-grade astrocytoma. In post-treatment patients, the enhancing lesions of two patients who were diagnosed with tumor progression contained more voxels with highADC ( f ) ADC ( 0 Hz ) $$ \frac{\mathrm{ADC}\ (f)}{\mathrm{ADC}\ \left(0\ \mathrm{Hz}\right)} $$ and lowTraceDWI ( f ) TraceDWI ( 0 Hz ) $$ \frac{\mathrm{TraceDWI}\left(\mathrm{f}\right)}{\mathrm{TraceDWI}\left(0\ \mathrm{Hz}\right)} $$ , compared to the enhancing lesions of a patient who was diagnosed with treatment effect. Non-enhancing T2 signal abnormality lesions in both the pre-surgical high-grade glioblastoma and post-treatment tumor progressions showed regions with highADC ( f ) ADC ( 0 Hz ) $$ \frac{\mathrm{ADC}\ (f)}{\mathrm{ADC}\ \left(0\ \mathrm{Hz}\right)} $$ and lowTraceDWI ( f ) TraceDWI ( 0 Hz ) $$ \frac{\mathrm{TraceDWI}\ \left(\mathrm{f}\right)}{\mathrm{TraceDWI}\ \left(0\ \mathrm{Hz}\right)} $$ , consistent with infiltrative tumor. The solid tumor of the glioblastoma, the enhancing lesions of post-treatment tumor progressions, and the suspected infiltrative tumors showed high diffusion time-dependency from 30 to 100 Hz, consistent with high intra-tumoral volume fraction (cellular density). CONCLUSION Different characteristics of OGSE-based time-dependent diffusivity can reveal heterogenous tissue microstructures that indicate cellular density in glioma patients.
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Affiliation(s)
- Ante Zhu
- GE Research, Niskayuna, New York, USA
| | - Robert Shih
- Uniformed Services University, Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Raymond Y Huang
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - J Kevin DeMarco
- Uniformed Services University, Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | | | - H Douglas Morris
- Uniformed Services University, Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Gail Kohls
- Uniformed Services University, Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | | | | | | | - Maureen Hood
- Uniformed Services University, Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Vincent B Ho
- Uniformed Services University, Bethesda, Maryland, USA
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Thomas K F Foo
- GE Research, Niskayuna, New York, USA
- Uniformed Services University, Bethesda, Maryland, USA
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Johnson JT, Irfanoglu MO, Manninen E, Ross TJ, Yang Y, Laun FB, Martin J, Topgaard D, Benjamini D. In vivo disentanglement of diffusion frequency-dependence, tensor shape, and relaxation using multidimensional MRI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561702. [PMID: 37987005 PMCID: PMC10659440 DOI: 10.1101/2023.10.10.561702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Diffusion MRI with free gradient waveforms, combined with simultaneous relaxation encoding, referred to as multidimensional MRI (MD-MRI), offers microstructural specificity in complex biological tissue. This approach delivers intravoxel information about the microstructure, local chemical composition, and importantly, how these properties are coupled within heterogeneous tissue containing multiple microenvironments. Recent theoretical advances incorporated diffusion time dependency and integrated MD-MRI with concepts from oscillating gradients. This framework probes the diffusion frequency, ω , in addition to the diffusion tensor, D , and relaxation, R 1 , R 2 , correlations. A D ( ω ) - R 1 - R 2 clinical imaging protocol was then introduced, with limited brain coverage and 3 mm3 voxel size, which hinder brain segmentation and future cohort studies. In this study, we introduce an efficient, sparse in vivo MD-MRI acquisition protocol providing whole brain coverage at 2 mm3 voxel size. We demonstrate its feasibility and robustness using a well-defined phantom and repeated scans of five healthy individuals. Additionally, we test different denoising strategies to address the sparse nature of this protocol, and show that efficient MD-MRI encoding design demands a nuanced denoising approach. The MD-MRI framework provides rich information that allows resolving the diffusion frequency dependence into intravoxel components based on their D ( ω ) - R 1 - R 2 distribution, enabling the creation of microstructure-specific maps in the human brain. Our results encourage the broader adoption and use of this new imaging approach for characterizing healthy and pathological tissues.
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Affiliation(s)
- Jessica T.E. Johnson
- Multiscale Imaging and Integrative Biophysics Unit, National Institute on Aging, NIH, Baltimore, MD, USA
| | - M. Okan Irfanoglu
- Quantitative Medical Imaging Section, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Eppu Manninen
- Multiscale Imaging and Integrative Biophysics Unit, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Thomas J. Ross
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Yihong Yang
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Frederik B. Laun
- Institute of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jan Martin
- Department of Chemistry, Lund University, Lund, Sweden
| | | | - Dan Benjamini
- Multiscale Imaging and Integrative Biophysics Unit, National Institute on Aging, NIH, Baltimore, MD, USA
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Dai E, Zhu A, Yang GK, Quah K, Tan ET, Fiveland E, Foo TKF, McNab JA. Frequency-dependent diffusion kurtosis imaging in the human brain using an oscillating gradient spin echo sequence and a high-performance head-only gradient. Neuroimage 2023; 279:120328. [PMID: 37586445 PMCID: PMC10529993 DOI: 10.1016/j.neuroimage.2023.120328] [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: 03/15/2023] [Revised: 07/17/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023] Open
Abstract
Measuring the time/frequency dependence of diffusion MRI is a promising approach to distinguish between the effects of different tissue microenvironments, such as membrane restriction, tissue heterogeneity, and compartmental water exchange. In this study, we measure the frequency dependence of diffusivity (D) and kurtosis (K) with oscillating gradient diffusion encoding waveforms and a diffusion kurtosis imaging (DKI) model in human brains using a high-performance, head-only MAGNUS gradient system, with a combination of b-values, oscillating frequencies (f), and echo time that has not been achieved in human studies before. Frequency dependence of diffusivity and kurtosis are observed in both global and local white matter (WM) and gray matter (GM) regions and characterized with a power-law model ∼Λ*fθ. The frequency dependences of diffusivity and kurtosis (including changes between fmin and fmax, Λ, and θ) vary over different WM and GM regions, indicating potential microstructural differences between regions. A trend of decreasing kurtosis over frequency in the short-time limit is successfully captured for in vivo human brains. The effects of gradient nonlinearity (GNL) on frequency-dependent diffusivity and kurtosis measurements are investigated and corrected. Our results show that the GNL has prominent scaling effects on the measured diffusivity values (3.5∼5.5% difference in the global WM and 6∼8% difference in the global cortex) and subsequently affects the corresponding power-law parameters (Λ, θ) while having a marginal influence on the measured kurtosis values (<0.05% difference) and power-law parameters (Λ, θ). This study expands previous OGSE studies and further demonstrates the translatability of frequency-dependent diffusivity and kurtosis measurements to human brains, which may provide new opportunities to probe human brain microstructure in health and disease.
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Affiliation(s)
- Erpeng Dai
- Department of Radiology, Stanford University, Stanford, CA, USA.
| | | | - Grant K Yang
- Department of Radiology, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Kristin Quah
- Department of Radiology, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Ek T Tan
- Department of Radiology and Imaging, Hospital for Special Surgery, New York, NY, USA
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10
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Xu J, Xie J, Semmineh NB, Devan SP, Jiang X, Gore JC. Diffusion time dependency of extracellular diffusion. Magn Reson Med 2023; 89:2432-2440. [PMID: 36740894 PMCID: PMC10392121 DOI: 10.1002/mrm.29594] [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: 04/24/2022] [Revised: 12/10/2022] [Accepted: 01/09/2023] [Indexed: 02/07/2023]
Abstract
PURPOSE To quantify the variations of the power-law dependences on diffusion time t or gradient frequencyf $$ f $$ of extracellular water diffusion measured by diffusion MRI (dMRI). METHODS Model cellular systems containing only extracellular water were used to investigate thet / f $$ t/f $$ dependence ofD ex $$ {D}_{ex} $$ , the extracellular diffusion coefficient. Computer simulations used a randomly packed tissue model with realistic intracellular volume fractions and cell sizes. DMRI measurements were performed on samples consisting of liposomes containing heavy water(D2 O, deuterium oxide) dispersed in regular water (H2 O).D ex $$ {D}_{ex} $$ was obtained over a broadt $$ t $$ range (∼1-1000 ms) and then fit power-law equationsD ex ( t ) = D const + const · t - ϑ t $$ {D}_{ex}(t)={D}_{\mathrm{const}}+\mathrm{const}\cdotp {t}^{-{\vartheta}_t} $$ andD ex ( f ) = D const + const · f ϑ f $$ {D}_{ex}(f)={D}_{\mathrm{const}}+\mathrm{const}\cdotp {f}^{\vartheta_f} $$ . RESULTS Both simulated and experimental results suggest that no single power-law adequately describes the behavior ofD ex $$ {D}_{ex} $$ over the range of diffusion times of most interest in practical dMRI. Previous theoretical predictions are accurate over only limitedt $$ t $$ ranges; for example,θ t = θ f = - 1 2 $$ {\theta}_t={\theta}_f=-\frac{1}{2} $$ is valid only for short times, whereasθ t = 1 $$ {\theta}_t=1 $$ orθ f = 3 2 $$ {\theta}_f=\frac{3}{2} $$ is valid only for long times but cannot describe other ranges simultaneously. For the specifict $$ t $$ range of 5-70 ms used in typical human dMRI measurements,θ t = θ f = 1 $$ {\theta}_t={\theta}_f=1 $$ matches the data well empirically. CONCLUSION The optimal power-law fit of extracellular diffusion varies with diffusion time. The dependency obtained at short or longt $$ t $$ limits cannot be applied to typical dMRI measurements in human cancer or liver. It is essential to determine the appropriate diffusion time range when modeling extracellular diffusion in dMRI-based quantitative microstructural imaging.
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Affiliation(s)
- Junzhong Xu
- Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee
| | - Jingping Xie
- Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Sean P. Devan
- Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiaoyu Jiang
- Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John C. Gore
- Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee
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11
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Jiang H, Svenningsson L, Topgaard D. Multidimensional encoding of restricted and anisotropic diffusion by double rotation of the q vector. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:73-85. [PMID: 37904800 PMCID: PMC10583292 DOI: 10.5194/mr-4-73-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/11/2023] [Indexed: 11/01/2023]
Abstract
Diffusion NMR and MRI methods building on the classic pulsed gradient spin-echo sequence are sensitive to many aspects of translational motion, including time and frequency dependence ("restriction"), anisotropy, and flow, leading to ambiguities when interpreting experimental data from complex heterogeneous materials such as living biological tissues. While the oscillating gradient technique specifically targets frequency dependence and permits control of the sensitivity to flow, tensor-valued encoding enables investigations of anisotropy in orientationally disordered materials. Here, we propose a simple scheme derived from the "double-rotation" technique in solid-state NMR to generate a family of modulated gradient waveforms allowing for comprehensive exploration of the 2D frequency-anisotropy space and convenient investigation of both restricted and anisotropic diffusion with a single multidimensional acquisition protocol, thereby combining the desirable characteristics of the oscillating gradient and tensor-valued encoding techniques. The method is demonstrated by measuring multicomponent isotropic Gaussian diffusion in simple liquids, anisotropic Gaussian diffusion in a polydomain lyotropic liquid crystal, and restricted diffusion in a yeast cell sediment.
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Affiliation(s)
- Hong Jiang
- Physical Chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Leo Svenningsson
- Physical Chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Daniel Topgaard
- Physical Chemistry, Lund University, P.O. Box 124, 22100 Lund, Sweden
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Rahman N, Xu K, Budde MD, Brown A, Baron CA. A longitudinal microstructural MRI dataset in healthy C57Bl/6 mice at 9.4 Tesla. Sci Data 2023; 10:94. [PMID: 36788251 PMCID: PMC9929084 DOI: 10.1038/s41597-023-01942-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/06/2023] [Indexed: 02/16/2023] Open
Abstract
Multimodal microstructural MRI has shown increased sensitivity and specificity to changes in various brain disease and injury models in the preclinical setting. Here, we present an in vivo longitudinal dataset, including a subset of ex vivo data, acquired as control data and to investigate microstructural changes in the healthy mouse brain. The dataset consists of structural T2-weighted imaging, magnetization transfer ratio and saturation imaging, and advanced quantitative diffusion MRI (dMRI) methods. The dMRI methods include oscillating gradient spin echo (OGSE) dMRI and microscopic anisotropy (μA) dMRI, which provide additional insight by increasing sensitivity to smaller spatial scales and disentangling fiber orientation dispersion from true microstructural changes, respectively. The technical skills required to analyze microstructural MRI data are complex and include MRI sequence development, acquisition, and computational neuroimaging expertise. Here, we share unprocessed and preprocessed data, and scalar maps of quantitative MRI metrics. We envision utility of this dataset in the microstructural MRI field to develop and test biophysical models, methods that model temporal brain dynamics, and registration and preprocessing pipelines.
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Affiliation(s)
- Naila Rahman
- Centre for Functional and Metabolic Mapping (CFMM), Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.
| | - Kathy Xu
- Translational Neuroscience Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Matthew D Budde
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Arthur Brown
- Translational Neuroscience Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Corey A Baron
- Centre for Functional and Metabolic Mapping (CFMM), Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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13
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Li H, Zu T, Hsu YC, Zhao Z, Liu R, Zheng T, Li Q, Sun Y, Liu D, Zhang J, Zhang Y, Wu D. Inversion-Recovery-Prepared Oscillating Gradient Sequence Improves Diffusion-Time Dependency Measurements in the Human Brain. J Magn Reson Imaging 2023; 57:446-453. [PMID: 35723048 DOI: 10.1002/jmri.28311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Oscillating gradient diffusion MRI (dMRI) enables measurements at a short diffusion-time (td ), but it is challenging for clinical systems. Particularly, the low b-value and low resolution may give rise to cerebrospinal fluid (CSF) contamination. PURPOSE To assess the effect of CSF partial volume on td -dMRI measurements and efficacy of inversion-recovery (IR) prepared oscillating and pulsed gradient dMRI sequence to improve td -dMRI measurements in the human brain. STUDY TYPE Prospective. SUBJECTS Ten normal volunteers and six glioma patients. FIELD STRENGTH/SEQUENCE A 3 T; three-dimensional (3D) IR-prepared oscillating gradient-prepared gradient spin-echo (GRASE) and two-dimensional (2D) IR-prepared oscillating gradient echo-planar imaging (EPI) sequences. ASSESSMENT We assessed the td -dependent patterns of apparent diffusion coefficient (ADC) in several gray and white matter structures, including the hippocampal subfields (head, body, and tail), cortical gray matter, thalamus, and posterior white matter in normal volunteers. Pulsed gradient (0 Hz) and oscillating gradients at frequencies of 20 Hz, 40 Hz, and 60 Hz dMRI were acquired with GRASE and EPI sequences with or without the IR module. We also tested the td -dependency patterns in glioma patients using the EPI sequence with or without the IR module. STATISTICAL TESTS The differences in ADC across the different td s were compared by one-way ANOVA followed by post hoc pairwise t-tests with Bonferroni correction. RESULTS In the healthy subjects, brain regions that were possibly contaminated by CSF signals, such as the hippocampus (head, body, and tail) and cortical gray matter, td -dependent ADC changes were only significant with the IR-prepared 2D and 3D sequences but not with the non-IR sequences. In brain glioblastomas patients, significantly higher td -dependence was observed in the tumor region with the IR module than that without IR (slope = 0.0196 μm2 /msec2 vs. 0.0034 μm2 /msec2 ). CONCLUSION The IR-prepared sequence effectively suppressed the CSF partial volume effect and significantly improved the td -dependent measurements in the human brain. EVIDENCE LEVEL 1 TECHNICAL EFFICACY: Stage 1.
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Affiliation(s)
- Haotian Li
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Zu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi-Cheng Hsu
- MR Collaboration, Siemens Healthcare China, Shanghai, China
| | - Zhiyong Zhao
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ruibin Liu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tianshu Zheng
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qing Li
- MR Collaboration, Siemens Healthcare China, Shanghai, China
| | - Yi Sun
- MR Collaboration, Siemens Healthcare China, Shanghai, China
| | - Daihong Liu
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jiuquan Zhang
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yi Zhang
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
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14
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Borsos KB, Tse DHY, Dubovan PI, Baron CA. Tuned bipolar oscillating gradients for mapping frequency dispersion of diffusion kurtosis in the human brain. Magn Reson Med 2023; 89:756-766. [PMID: 36198030 DOI: 10.1002/mrm.29473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE Oscillating gradient spin-echo (OGSE) sequences have demonstrated an ability to probe time-dependent microstructural features, although they often suffer from low SNR due to increased TEs. In this work we introduce frequency-tuned bipolar (FTB) gradients as a variation of oscillating gradients with reduced TE and demonstrate their utility by mapping the frequency dispersion of kurtosis in human subjects. METHODS An FTB oscillating gradient waveform is presented that provides encoding of 1.5 net oscillation periods, thereby reducing the TE of the acquisition. Simulations were performed to determine an optimal protocol based on the SNR of kurtosis frequency dispersion-defined as the difference in kurtosis between pulsed and oscillating gradient acquisitions. Healthy human subjects were scanned at 7T using pulsed gradient and an optimized 23 Hz FTB protocol, which featured a maximum b-value of 2500 s/mm2 . In addition, to directly compare existing methods, measurements using traditional cosine OGSE were also acquired. RESULTS FTB oscillating gradients demonstrated equivalent frequency-dependent diffusion measurements compared with cosine-modulated OGSE while enabling a significant reduction in TE. Optimization and in vivo results suggest that FTB gradients provide increased SNR of kurtosis dispersion maps compared with traditional cosine OGSE. The optimized FTB gradient protocol demonstrated consistent reductions in apparent kurtosis values and increased diffusivity in generated frequency dispersion maps. CONCLUSIONS This work presents an alternative to traditional cosine OGSE sequences, enabling more time-efficient acquisitions of frequency-dependent diffusion quantities as demonstrated through in vivo kurtosis frequency dispersion maps.
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Affiliation(s)
- Kevin B Borsos
- Department of Medical Biophysics, Western University, London, Ontario, Canada.,Center for Functional and Metabolic Mapping, Western University, London, Ontario, Canada
| | - Desmond H Y Tse
- Center for Functional and Metabolic Mapping, Western University, London, Ontario, Canada
| | - Paul I Dubovan
- Department of Medical Biophysics, Western University, London, Ontario, Canada.,Center for Functional and Metabolic Mapping, Western University, London, Ontario, Canada
| | - Corey A Baron
- Department of Medical Biophysics, Western University, London, Ontario, Canada.,Center for Functional and Metabolic Mapping, Western University, London, Ontario, Canada.,Imaging Laboratories, Robarts Research Institute, London, Ontario, Canada
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15
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Jelescu IO, de Skowronski A, Geffroy F, Palombo M, Novikov DS. Neurite Exchange Imaging (NEXI): A minimal model of diffusion in gray matter with inter-compartment water exchange. Neuroimage 2022; 256:119277. [PMID: 35523369 PMCID: PMC10363376 DOI: 10.1016/j.neuroimage.2022.119277] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/26/2022] [Accepted: 05/01/2022] [Indexed: 01/18/2023] Open
Abstract
Biophysical models of diffusion in white matter have been center-stage over the past two decades and are essentially based on what is now commonly referred to as the "Standard Model" (SM) of non-exchanging anisotropic compartments with Gaussian diffusion. In this work, we focus on diffusion MRI in gray matter, which requires rethinking basic microstructure modeling blocks. In particular, at least three contributions beyond the SM need to be considered for gray matter: water exchange across the cell membrane - between neurites and the extracellular space; non-Gaussian diffusion along neuronal and glial processes - resulting from structural disorder; and signal contribution from soma. For the first contribution, we propose Neurite Exchange Imaging (NEXI) as an extension of the SM of diffusion, which builds on the anisotropic Kärger model of two exchanging compartments. Using datasets acquired at multiple diffusion weightings (b) and diffusion times (t) in the rat brain in vivo, we investigate the suitability of NEXI to describe the diffusion signal in the gray matter, compared to the other two possible contributions. Our results for the diffusion time window 20-45 ms show minimal diffusivity time-dependence and more pronounced kurtosis decay with time, which is well fit by the exchange model. Moreover, we observe lower signal for longer diffusion times at high b. In light of these observations, we identify exchange as the mechanism that best explains these signal signatures in both low-b and high-b regime, and thereby propose NEXI as the minimal model for gray matter microstructure mapping. We finally highlight multi-b multi-t acquisition protocols as being best suited to estimate NEXI model parameters reliably. Using this approach, we estimate the inter-compartment water exchange time to be 15 - 60 ms in the rat cortex and hippocampus in vivo, which is of the same order or shorter than the diffusion time in typical diffusion MRI acquisitions. This suggests water exchange as an essential component for interpreting diffusion MRI measurements in gray matter.
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Affiliation(s)
- Ileana O Jelescu
- CIBM Center for Biomedical Imaging, Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Radiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland; School of Biology and Medicine, University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Alexandre de Skowronski
- CIBM Center for Biomedical Imaging, Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Marco Palombo
- School of Psychology, Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, UK; School of Computer Science and Informatics, Cardiff University, Cardiff, UK; Department of Computer Science, Centre for Medical Image Computing, University College London, London, UK
| | - Dmitry S Novikov
- Department of Radiology, Center for Biomedical Imaging, New York University School of Medicine, New York, NY, USA
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16
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Rosenberg JT, Grant SC, Topgaard D. Nonparametric 5D D-R 2 distribution imaging with single-shot EPI at 21.1 T: Initial results for in vivo rat brain. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 341:107256. [PMID: 35753184 PMCID: PMC9339475 DOI: 10.1016/j.jmr.2022.107256] [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: 03/04/2022] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
In vivo human diffusion MRI is by default performed using single-shot EPI with greater than 50-ms echo times and associated signal loss from transverse relaxation. The individual benefits of the current trends of increasing B0 to boost SNR and employing more advanced signal preparation schemes to improve the specificity for selected microstructural properties eventually may be cancelled by increased relaxation rates at high B0 and echo times with advanced encoding. Here, initial attempts to translate state-of-the-art diffusion-relaxation correlation methods from 3 T to 21.1 T are made to identify hurdles that need to be overcome to fulfill the promises of both high SNR and readily interpretable microstructural information.
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Affiliation(s)
- Jens T Rosenberg
- National High Magnetic Field Laboratory, Florida State University, Tallahassee FL, United States.
| | - Samuel C Grant
- National High Magnetic Field Laboratory, Florida State University, Tallahassee FL, United States; Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL, United States.
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17
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Novello L, Henriques RN, Ianuş A, Feiweier T, Shemesh N, Jovicich J. In vivo Correlation Tensor MRI reveals microscopic kurtosis in the human brain on a clinical 3T scanner. Neuroimage 2022; 254:119137. [PMID: 35339682 DOI: 10.1016/j.neuroimage.2022.119137] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/17/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022] Open
Abstract
Diffusion MRI (dMRI) has become one of the most important imaging modalities for noninvasively probing tissue microstructure. Diffusional Kurtosis MRI (DKI) quantifies the degree of non-gaussian diffusion, which in turn has been shown to increase sensitivity towards, e.g., disease and orientation mapping in neural tissue. However, the specificity of DKI is limited as different sources can contribute to the total intravoxel diffusional kurtosis, including: variance in diffusion tensor magnitudes (Kiso), variance due to diffusion anisotropy (Kaniso), and microscopic kurtosis (μK) related to restricted diffusion, microstructural disorder, and/or exchange. Interestingly, μK is typically ignored in diffusion MRI signal modeling as it is assumed to be negligible in neural tissues. However, recently, Correlation Tensor MRI (CTI) based on Double-Diffusion-Encoding (DDE) was introduced for kurtosis source separation, revealing non negligible μK in preclinical imaging. Here, we implemented CTI for the first time on a clinical 3T scanner and investigated the sources of total kurtosis in healthy subjects. A robust framework for kurtosis source separation in humans is introduced, followed by estimation of μK (and the other kurtosis sources) in the healthy brain. Using this clinical CTI approach, we find that μK significantly contributes to total diffusional kurtosis both in gray and white matter tissue but, as expected, not in the ventricles. The first μK maps of the human brain are presented, revealing that the spatial distribution of μK provides a unique source of contrast, appearing different from isotropic and anisotropic kurtosis counterparts. Moreover, group average templates of these kurtosis sources have been generated for the first time, which corroborated our findings at the underlying individual-level maps. We further show that the common practice of ignoring μK and assuming the multiple gaussian component approximation for kurtosis source estimation introduces significant bias in the estimation of other kurtosis sources and, perhaps even worse, compromises their interpretation. Finally, a twofold acceleration of CTI is discussed in the context of potential future clinical applications. We conclude that CTI has much potential for future in vivo microstructural characterizations in healthy and pathological tissue.
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Affiliation(s)
- Lisa Novello
- Center for Mind/Brain Sciences - CIMeC, University of Trento, Rovereto, Italy.
| | | | - Andrada Ianuş
- Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal
| | | | - Noam Shemesh
- Champalimaud Research, Champalimaud Foundation, Lisbon, Portugal
| | - Jorge Jovicich
- Center for Mind/Brain Sciences - CIMeC, University of Trento, Rovereto, Italy
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18
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Michael ES, Hennel F, Pruessmann KP. Evaluating diffusion dispersion across an extended range of b-values and frequencies: Exploiting gap-filled OGSE shapes, strong gradients, and spiral readouts. Magn Reson Med 2022; 87:2710-2723. [PMID: 35049104 PMCID: PMC9306807 DOI: 10.1002/mrm.29161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 12/15/2022]
Abstract
Purpose To address the long echo times and relatively weak diffusion sensitization that typically limit oscillating gradient spin‐echo (OGSE) experiments, an OGSE implementation combining spiral readouts, gap‐filled oscillating gradient shapes providing stronger diffusion encoding, and a high‐performance gradient system is developed here and utilized to investigate the tradeoff between b‐value and maximum OGSE frequency in measurements of diffusion dispersion (i.e., the frequency dependence of diffusivity) in the in vivo human brain. In addition, to assess the effects of the marginal flow sensitivity introduced by these OGSE waveforms, flow‐compensated variants are devised for experimental comparison. Methods Using DTI sequences, OGSE acquisitions were performed on three volunteers at b‐values of 300, 500, and 1000 s/mm2 and frequencies up to 125, 100, and 75 Hz, respectively; scans were performed for gap‐filled oscillating gradient shapes with and without flow sensitivity. Pulsed gradient spin‐echo DTI acquisitions were also performed at each b‐value. Upon reconstruction, mean diffusivity (MD) maps and maps of the diffusion dispersion rate were computed. Results The power law diffusion dispersion model was found to fit best to MD measurements acquired at b = 1000 s/mm2 despite the associated reduction of the spectral range; this observation was consistent with Monte Carlo simulations. Furthermore, diffusion dispersion rates without flow sensitivity were slightly higher than flow‐sensitive measurements. Conclusion The presented OGSE implementation provided an improved depiction of diffusion dispersion and demonstrated the advantages of measuring dispersion at higher b‐values rather than higher frequencies within the regimes employed in this study.
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Affiliation(s)
- Eric Seth Michael
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Franciszek Hennel
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Klaas Paul Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
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19
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Nonparametric D-R 1-R 2 distribution MRI of the living human brain. Neuroimage 2021; 245:118753. [PMID: 34852278 DOI: 10.1016/j.neuroimage.2021.118753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022] Open
Abstract
Diffusion-relaxation correlation NMR can simultaneously characterize both the microstructure and the local chemical composition of complex samples that contain multiple populations of water. Recent developments on tensor-valued diffusion encoding and Monte Carlo inversion algorithms have made it possible to transfer diffusion-relaxation correlation NMR from small-bore scanners to clinical MRI systems. Initial studies on clinical MRI systems employed 5D D-R1 and D-R2 correlation to characterize healthy brain in vivo. However, these methods are subject to an inherent bias that originates from not including R2 or R1 in the analysis, respectively. This drawback can be remedied by extending the concept to 6D D-R1-R2 correlation. In this work, we present a sparse acquisition protocol that records all data necessary for in vivo 6D D-R1-R2 correlation MRI across 633 individual measurements within 25 min-a time frame comparable to previous lower-dimensional acquisition protocols. The data were processed with a Monte Carlo inversion algorithm to obtain nonparametric 6D D-R1-R2 distributions. We validated the reproducibility of the method in repeated measurements of healthy volunteers. For a post-therapy glioblastoma case featuring cysts, edema, and partially necrotic remains of tumor, we present representative single-voxel 6D distributions, parameter maps, and artificial contrasts over a wide range of diffusion-, R1-, and R2-weightings based on the rich information contained in the D-R1-R2 distributions.
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20
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Valsamis JJ, Dubovan PI, Baron CA. Characterization and correction of time-varying eddy currents for diffusion MRI. Magn Reson Med 2021; 87:2209-2223. [PMID: 34894640 DOI: 10.1002/mrm.29124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/16/2022]
Abstract
PURPOSE To develop and test a method for reducing artifacts due to time-varying eddy currents in oscillating gradient spin-echo (OGSE) diffusion images. METHODS An in-house algorithm (TVEDDY), that for the first time retrospectively models eddy current decay, was tested on pulsed gradient spin echo and OGSE brain images acquired at 7 T. Image pairs were acquired using opposite polarity diffusion gradients. A three-parameter exponential decay model (two amplitudes and a time constant) was used to characterize and correct eddy current distortions by minimizing the intensity difference between image pairs. Correction performance was compared with conventional correction methods by evaluating the mean squared error (MSE) between diffusion-weighted images acquired with opposite polarity diffusion gradients. As a ground-truth comparison, images were corrected using field dynamics up to third order in space, measured using a field monitoring system. RESULTS Time-varying eddy currents were observed for OGSE, which introduced blurring that was not reduced using the traditional approach but was diminished considerably with TVEDDY and field monitoring-informed model-based reconstruction. No MSE difference was observed between the conventional approach and TVEDDY for pulsed gradient spin echo, but for OGSE TVEDDY resulted in significantly lower MSE than the conventional approach. The field-monitoring reconstruction had the lowest MSE for both pulsed gradient spin echo and OGSE. CONCLUSION This work establishes that it is possible to estimate time-varying eddy currents from the actual diffusion data, which provides substantial image-quality improvements for gradient-intensive diffusion MRI acquisitions like OGSE.
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Affiliation(s)
- Jake J Valsamis
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.,Center for Functional and Metabolic Mapping, Robarts Research Institute, London, Ontario, Canada
| | - Paul I Dubovan
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.,Center for Functional and Metabolic Mapping, Robarts Research Institute, London, Ontario, Canada
| | - Corey A Baron
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.,Center for Functional and Metabolic Mapping, Robarts Research Institute, London, Ontario, Canada
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21
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Rahman N, Xu K, Omer M, Budde MD, Brown A, Baron CA. Test-retest reproducibility of in vivo oscillating gradient and microscopic anisotropy diffusion MRI in mice at 9.4 Tesla. PLoS One 2021; 16:e0255711. [PMID: 34739479 PMCID: PMC8570471 DOI: 10.1371/journal.pone.0255711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND PURPOSE Microstructure imaging with advanced diffusion MRI (dMRI) techniques have shown increased sensitivity and specificity to microstructural changes in various disease and injury models. Oscillating gradient spin echo (OGSE) dMRI, implemented by varying the oscillating gradient frequency, and microscopic anisotropy (μA) dMRI, implemented via tensor valued diffusion encoding, may provide additional insight by increasing sensitivity to smaller spatial scales and disentangling fiber orientation dispersion from true microstructural changes, respectively. The aims of this study were to characterize the test-retest reproducibility of in vivo OGSE and μA dMRI metrics in the mouse brain at 9.4 Tesla and provide estimates of required sample sizes for future investigations. METHODS Twelve adult C57Bl/6 mice were scanned twice (5 days apart). Each imaging session consisted of multifrequency OGSE and μA dMRI protocols. Metrics investigated included μA, linear diffusion kurtosis, isotropic diffusion kurtosis, and the diffusion dispersion rate (Λ), which explores the power-law frequency dependence of mean diffusivity. The dMRI metric maps were analyzed with mean region-of-interest (ROI) and whole brain voxel-wise analysis. Bland-Altman plots and coefficients of variation (CV) were used to assess the reproducibility of OGSE and μA metrics. Furthermore, we estimated sample sizes required to detect a variety of effect sizes. RESULTS Bland-Altman plots showed negligible biases between test and retest sessions. ROI-based CVs revealed high reproducibility for most metrics (CVs < 15%). Voxel-wise CV maps revealed high reproducibility for μA (CVs ~ 10%), but low reproducibility for OGSE metrics (CVs ~ 50%). CONCLUSION Most of the μA dMRI metrics are reproducible in both ROI-based and voxel-wise analysis, while the OGSE dMRI metrics are only reproducible in ROI-based analysis. Given feasible sample sizes (10-15), μA metrics and OGSE metrics may provide sensitivity to subtle microstructural changes (4-8%) and moderate changes (> 6%), respectively.
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Affiliation(s)
- Naila Rahman
- Centre for Functional and Metabolic Mapping (CFMM), Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Kathy Xu
- Translational Neuroscience Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Mohammad Omer
- Centre for Functional and Metabolic Mapping (CFMM), Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Matthew D. Budde
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Arthur Brown
- Translational Neuroscience Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Corey A. Baron
- Centre for Functional and Metabolic Mapping (CFMM), Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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22
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Gao F, Shen X, Zhang H, Ba R, Ma X, Lai C, Zhang J, Zhang Y, Wu D. Feasibility of oscillating and pulsed gradient diffusion MRI to assess neonatal hypoxia-ischemia on clinical systems. J Cereb Blood Flow Metab 2021; 41:1240-1250. [PMID: 32811261 PMCID: PMC8142137 DOI: 10.1177/0271678x20944353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Diffusion-time- (td) dependent diffusion MRI (dMRI) extends our ability to characterize brain microstructure by measuring dMRI signals at varying td. The use of oscillating gradient (OG) is essential for accessing short td but is technically challenging on clinical MRI systems. This study aims to investigate the clinical feasibility and value of td-dependent dMRI in neonatal hypoxic-ischemic encephalopathy (HIE). Eighteen HIE neonates and six normal term-born neonates were scanned on a 3 T scanner, with OG-dMRI at an oscillating frequency of 33 Hz (equivalent td ≈ 7.5 ms) and pulsed gradient (PG)-dMRI at a td of 82.8 ms and b-value of 700 s/mm2. The td-dependence, as quantified by the difference in apparent diffusivity coefficients between OG- and PG-dMRI (ΔADC), was observed in the normal neonatal brains, and the ΔADC was higher in the subcortical white matter than the deep grey matter. In HIE neonates with severe and moderate injury, ΔADC significantly increased in the basal ganglia (BG) compared to the controls (23.7% and 10.6%, respectively). In contrast, the conventional PG-ADC showed a 12.6% reduction only in the severe HIE group. White matter edema regions also demonstrated increased ΔADC, where PG-ADC did not show apparent changes. Our result demonstrated that td-dependent dMRI provided high sensitivity in detecting moderate-to-severe HIE.
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Affiliation(s)
- Fusheng Gao
- Department of Radiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiaoxia Shen
- Department of Neonatal Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Hongxi Zhang
- Department of Radiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Ruicheng Ba
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Xiaolu Ma
- Department of Neonatal Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Can Lai
- Department of Radiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jiangyang Zhang
- Department of Radiology, New York University School of Medicine, New York, NY, USA
| | - Yi Zhang
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
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23
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Wu D, Zhang Y, Cheng B, Mori S, Reeves RH, Gao FJ. Time-dependent diffusion MRI probes cerebellar microstructural alterations in a mouse model of Down syndrome. Brain Commun 2021; 3:fcab062. [PMID: 33937769 PMCID: PMC8063586 DOI: 10.1093/braincomms/fcab062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/09/2021] [Accepted: 02/22/2021] [Indexed: 01/27/2023] Open
Abstract
The cerebellum is a complex system with distinct cortical laminar organization. Alterations in cerebellar microstructure are common and associated with many factors such as genetics, cancer and ageing. Diffusion MRI (dMRI) provides a non-invasive tool to map the brain structural organization, and the recently proposed diffusion-time (td )-dependent dMRI further improves its capability to probe the cellular and axonal/dendritic microstructures by measuring water diffusion at multiple spatial scales. The td -dependent diffusion profile in the cerebellum and its utility in detecting cerebellar disorders, however, are not yet elucidated. Here, we first deciphered the spatial correspondence between dMRI contrast and cerebellar layers, based on which the cerebellar layer-specific td -dependent dMRI patterns were characterized in both euploid and Ts65Dn mice, a mouse model of Down syndrome. Using oscillating gradient dMRI, which accesses diffusion at short td 's by modulating the oscillating frequency, we detected subtle changes in the apparent diffusivity coefficient of the cerebellar internal granular layer and Purkinje cell layer of Ts65Dn mice that were not detectable by conventional pulsed gradient dMRI. The detection sensitivity of oscillating gradient dMRI increased with the oscillating frequency at both the neonatal and adult stages. The td -dependence, quantified by ΔADC map, was reduced in Ts65Dn mice, likely associated with the reduced granule cell density and abnormal dendritic arborization of Purkinje cells as revealed from histological evidence. Our study demonstrates superior sensitivity of short-td diffusion using oscillating gradient dMRI to detect cerebellar microstructural changes in Down syndrome, suggesting the potential application of this technique in cerebellar disorders.
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Affiliation(s)
- Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Yi Zhang
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Bei Cheng
- Department of Radiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Susumu Mori
- Department of Radiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Roger H Reeves
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Feng J Gao
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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24
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MR cell size imaging with temporal diffusion spectroscopy. Magn Reson Imaging 2021; 77:109-123. [PMID: 33338562 PMCID: PMC7878439 DOI: 10.1016/j.mri.2020.12.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023]
Abstract
Cytological features such as cell size and intracellular morphology provide fundamental information on cell status and hence may provide specific information on changes that arise within biological tissues. Such information is usually obtained by invasive biopsy in current clinical practice, which suffers several well-known disadvantages. Recently, novel MRI methods such as IMPULSED (imaging microstructural parameters using limited spectrally edited diffusion) have been developed for direct measurements of mean cell size non-invasively. The IMPULSED protocol is based on using temporal diffusion spectroscopy (TDS) to combine measurements of water diffusion over a wide range of diffusion times to probe cellular microstructure over varying length scales. IMPULSED has been shown to provide rapid, robust, and reliable mapping of mean cell size and is suitable for clinical imaging. More recently, cell size distributions have also been derived by appropriate analyses of data acquired with IMPULSED or similar sequences, which thus provides MRI-cytometry. This review summarizes the basic principles, practical implementations, validations, and example applications of MR cell size imaging based on TDS and demonstrates how cytometric information can be used in various applications. In addition, the limitations and potential future directions of MR cytometry are identified including the diagnosis of nonalcoholic steatohepatitis of the liver and the assessment of treatment response of cancers.
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25
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Hennel F, Michael ES, Pruessmann KP. Improved gradient waveforms for oscillating gradient spin-echo (OGSE) diffusion tensor imaging. NMR IN BIOMEDICINE 2021; 34:e4434. [PMID: 33124071 DOI: 10.1002/nbm.4434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/11/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
The dependence of the diffusion tensor on frequency is of great interest in studies of tissue microstructure because it reveals restrictions to the Brownian motion of water molecules caused by cell membranes. Oscillating gradient spin-echo (OGSE) sequences can sample this dependence with gradient shapes for which the power spectrum of the zeroth moment is focused at a target frequency. In order to maintain the total spectral power (ie the b-value), oscillating gradient amplitudes must grow with the frequency squared. For this reason, OGSE applications on clinical MRI scanners are limited to low frequencies, for which it is difficult to obtain a narrow frequency bandwidth of the gradient moment in a useful echo time. In particular, the commonly used pair of single-period trapezoidal-cosine pulses separated by a half-period produces significant side lobes away from the target frequency. To mitigate this effect, improved OGSE waveforms are proposed, which reduce the gap between the two gradient pulses to the minimum duration required for the refocusing RF pulse. Additionally, a slight deviation from the periodicity of the waveforms is proposed in order to permit using the maximum slew rate of the gradient system for all lobes of trapezoidal waveforms while maintaining advantageous spectral properties, which is not the case for the currently used OGSE sequences. Numerical calculations validate these changes, showing that both modifications significantly narrow the gradient moment power spectrum and increase the contribution of its main lobe to the b-value, thus improving the specificity of the measurement. The utility of the new shapes is demonstrated by diffusion tensor measurements of human white matter in vivo over the range of 30-75 Hz with a b-value of nearly 1000 s/mm2 , using a high-performance gradient insert. However, the improvement should increase the sampling precision of OGSE experiments for all gradient systems.
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Affiliation(s)
- Franciszek Hennel
- Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Eric Seth Michael
- Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Klaas P Pruessmann
- Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
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26
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Xu J. Probing neural tissues at small scales: Recent progress of oscillating gradient spin echo (OGSE) neuroimaging in humans. J Neurosci Methods 2020; 349:109024. [PMID: 33333089 PMCID: PMC10124150 DOI: 10.1016/j.jneumeth.2020.109024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022]
Abstract
The detection sensitivity of diffusion MRI (dMRI) is dependent on diffusion times. A shorter diffusion time can increase the sensitivity to smaller length scales. However, the conventional dMRI uses the pulse gradient spin echo (PGSE) sequence that probes relatively long diffusion times only. To overcome this, the oscillating gradient spin echo (OGSE) sequence has been developed to probe much shorter diffusion times with hardware limitations on preclinical and clinical MRI systems. The OGSE sequence has been previously used on preclinical animal MRI systems. Recently, several studies have translated the OGSE sequence to humans on clinical MRI systems and achieved new information that is invisible using conventional PGSE sequence. This paper provides an overview of the recent progress of the OGSE neuroimaging in humans, including the technical improvements in the translation of the OGSE sequence to human imaging and various applications in different neurological disorders and stroke. Some possible future directions of the OGSE sequence are also discussed.
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Affiliation(s)
- Junzhong Xu
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, 37232, USA; Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37232, USA; Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, 37232, USA.
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27
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Harkins KD, Beaulieu C, Xu J, Gore JC, Does MD. A simple estimate of axon size with diffusion MRI. Neuroimage 2020; 227:117619. [PMID: 33301942 PMCID: PMC7949481 DOI: 10.1016/j.neuroimage.2020.117619] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/06/2020] [Accepted: 11/29/2020] [Indexed: 12/18/2022] Open
Abstract
Noninvasive estimation of mean axon diameter presents a new opportunity to explore white matter plasticity, development, and pathology. Several diffusion-weighted MRI (DW-MRI) methods have been proposed to measure the average axon diameter in white matter, but they typically require many diffusion encoding measurements and complicated mathematical models to fit the signal to multiple tissue compartments, including intra- and extra-axonal spaces. Here, Monte Carlo simulations uncovered a straightforward DW-MRI metric of axon diameter: the change in radial apparent diffusion coefficient estimated at different effective diffusion times, ΔD⊥. Simulations indicated that this metric increases monotonically within a relevant range of effective mean axon diameter while being insensitive to changes in extra-axonal volume fraction, axon diameter distribution, g-ratio, and influence of myelin water. Also, a monotonic relationship was found to exist for signals coming from both intra- and extra-axonal compartments. The slope in ΔD⊥ with effective axon diameter increased with the difference in diffusion time of both oscillating and pulsed gradient diffusion sequences.
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Affiliation(s)
- Kevin D Harkins
- Biomedical Engineering, Vanderbilt University, United States; Institute of Imaging Science, Vanderbilt University, United States.
| | | | - Junzhong Xu
- Institute of Imaging Science, Vanderbilt University, United States; Radiology and Radiological Sciences, Vanderbilt University Medical Center, United States
| | - John C Gore
- Biomedical Engineering, Vanderbilt University, United States; Institute of Imaging Science, Vanderbilt University, United States; Radiology and Radiological Sciences, Vanderbilt University Medical Center, United States
| | - Mark D Does
- Biomedical Engineering, Vanderbilt University, United States; Institute of Imaging Science, Vanderbilt University, United States
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28
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Lee HH, Papaioannou A, Novikov DS, Fieremans E. In vivo observation and biophysical interpretation of time-dependent diffusion in human cortical gray matter. Neuroimage 2020; 222:117054. [PMID: 32585341 PMCID: PMC7736473 DOI: 10.1016/j.neuroimage.2020.117054] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/25/2022] Open
Abstract
The dependence of the diffusion MRI signal on the diffusion time t is a hallmark of tissue microstructure at the scale of the diffusion length. Here we measure the time-dependence of the mean diffusivity D(t) and mean kurtosis K(t) in cortical gray matter and in 25 gray matter sub-regions, in 10 healthy subjects. Significant diffusivity and kurtosis time-dependence is observed for t=21.2-100 ms, and is characterized by a power-law tail ∼t-ϑ with dynamical exponent ϑ. To interpret our measurements, we systematize the relevant scenarios and mechanisms for diffusion time-dependence in the brain. Using the effective medium theory formalism, we derive an exact relation between the power-law tails in D(t) and K(t). The estimated dynamical exponent ϑ≃1/2 in both D(t) and K(t) is consistent with one-dimensional diffusion in the presence of randomly positioned restrictions along neurites. We analyze the short-range disordered statistics of synapses on axon collaterals in the cortex, and perform one-dimensional Monte Carlo simulations of diffusion restricted by permeable barriers with a similar randomness in their placement, to confirm the ϑ=1/2 exponent. In contrast, the Kärger model of exchange is less consistent with the data since it does not capture the diffusivity time-dependence, and the estimated exchange time from K(t) falls below our measured t-range. Although we cannot exclude exchange as a contributing factor, we argue that structural disorder along neurites is mainly responsible for the observed time-dependence of diffusivity and kurtosis. Our observation and theoretical interpretation of the t-1/2 tail in D(t) and K(t) altogether establish the sensitivity of a macroscopic MRI signal to micrometer-scale structural heterogeneities along neurites in human gray matter in vivo.
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Affiliation(s)
- Hong-Hsi Lee
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA.
| | - Antonios Papaioannou
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA
| | - Dmitry S Novikov
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA
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29
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Novikov DS. The present and the future of microstructure MRI: From a paradigm shift to normal science. J Neurosci Methods 2020; 351:108947. [PMID: 33096152 DOI: 10.1016/j.jneumeth.2020.108947] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/29/2020] [Accepted: 09/10/2020] [Indexed: 12/29/2022]
Abstract
The aspiration of imaging tissue microstructure with MRI is to uncover micrometer-scale tissue features within millimeter-scale imaging voxels, in vivo. This kind of super-resolution has fueled a paradigm shift within the biomedical imaging community. However, what feels like an ongoing revolution in MRI, has been conceptually experienced in physics decades ago; from this point of view, our current developments can be seen as Thomas Kuhn's "normal science" stage of progress. While the concept of model-based quantification below the nominal imaging resolution is not new, its possibilities in neuroscience and neuroradiology are only beginning to be widely appreciated. This disconnect calls for communicating the progress of tissue microstructure MR imaging to its potential users. Here, a number of recent research developments are outlined in terms of the overarching concept of coarse-graining the tissue structure over an increasing diffusion length. A variety of diffusion models and phenomena are summarized on the phase diagram of diffusion MRI, with the unresolved problems and future directions corresponding to its unexplored domains.
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Affiliation(s)
- Dmitry S Novikov
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA.
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30
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Wu D, Liu D, Hsu YC, Li H, Sun Y, Qin Q, Zhang Y. Diffusion-prepared 3D gradient spin-echo sequence for improved oscillating gradient diffusion MRI. Magn Reson Med 2020; 85:78-88. [PMID: 32643240 DOI: 10.1002/mrm.28401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE Oscillating gradient (OG) enables the access of short diffusion times for time-dependent diffusion MRI (dMRI); however, it poses several technical challenges for clinical use. This study proposes a 3D oscillating gradient-prepared gradient spin-echo (OGprep-GRASE) sequence to improve SNR and shorten acquisition time for OG dMRI on clinical scanners. METHODS The 3D OGprep-GRASE sequence consisted of global saturation, diffusion encoding, fat saturation, and GRASE readout modules. Multiplexed sensitivity-encoding reconstruction was used to correct the phase errors between multiple shots. We compared the scan time and SNR of the proposed sequence and the conventional 2D-EPI sequence for OG dMRI at 30-90-mm slice coverage. We also examined the time-dependent diffusivity changes with OG dMRI acquired at frequencies of 50 Hz and 25 Hz and pulsed-gradient dMRI at diffusion times of 30 ms and 60 ms. RESULTS The OGprep-GRASE sequence reduced the scan time by a factor of 1.38, and increased the SNR by 1.74-2.27 times compared with 2D EPI for relatively thick slice coverage (60-90 mm). The SNR gain led to improved diffusion-tensor reconstruction in the multishot protocols. Image distortion in 2D-EPI images was also reduced in GRASE images. Diffusivity measurements from the pulsed-gradient dMRI and OG dMRI showed clear diffusion-time dependency in the white matter and gray matter of the human brain, using both the GRASE and EPI sequences. CONCLUSION The 3D OGprep-GRASE sequence improved scan time and SNR and reduced image distortion compared with the 2D multislice acquisition for OG dMRI on a 3T clinical system, which may facilitate the clinical translation of time-dependent dMRI.
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Affiliation(s)
- Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dapeng Liu
- The Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Csenter for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Yi-Cheng Hsu
- MR Collaboration, Siemens Healthcare China, Shanghai, China
| | - Haotian Li
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi Sun
- MR Collaboration, Siemens Healthcare China, Shanghai, China
| | - Qin Qin
- The Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,F.M. Kirby Research Csenter for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Yi Zhang
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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31
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Wilm BJ, Hennel F, Roesler MB, Weiger M, Pruessmann KP. Minimizing the echo time in diffusion imaging using spiral readouts and a head gradient system. Magn Reson Med 2020; 84:3117-3127. [PMID: 32573807 DOI: 10.1002/mrm.28346] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/26/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Diffusion weighted imaging (DWI) is commonly limited by low signal-to-noise ratio (SNR) as well as motion artifacts. To address this limitation, a method that allows to maximize the achievable signal yield and increase the resolution in motion robust single-shot DWI is presented. METHODS DWI was performed on a 3T scanner equipped with a recently developed gradient insert (gradient strength: 200 mT/m, slew rate: 600 T/m/s). To further shorten the echo time, Stejskal-Tanner diffusion encoding with a single-shot spiral readout was implemented. To allow non-Cartesian image reconstruction using such strong and fast gradients, the characterization of eddy current and concomitant field effects was performed based on field-camera measurements. RESULTS An echo time of only 19 ms was achieved for a b-factor of 1000 s/mm2 . An in-plane resolution of 0.68 mm was encoded by a single-shot spiral readout of 40.5 ms using 3-fold undersampling. The resulting images did not suffer from off-resonance artifacts and T 2 ∗ blurring that are common to single-shot images acquired with regular gradient systems. CONCLUSION Spiral diffusion imaging using a head gradient system, together with an accurate characterization of the encoding process allows for a substantial reduction of the echo time, and improves the achievable resolution in motion-insensitive single-shot DWI.
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Affiliation(s)
- Bertram Jakob Wilm
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Franciszek Hennel
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Manuela Barbara Roesler
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Markus Weiger
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Klaas Paul Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
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32
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Tan ET, Shih RY, Mitra J, Sprenger T, Hua Y, Bhushan C, Bernstein MA, McNab JA, DeMarco JK, Ho VB, Foo TKF. Oscillating diffusion-encoding with a high gradient-amplitude and high slew-rate head-only gradient for human brain imaging. Magn Reson Med 2020; 84:950-965. [PMID: 32011027 DOI: 10.1002/mrm.28180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/09/2019] [Accepted: 01/02/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE We investigate the importance of high gradient-amplitude and high slew-rate on oscillating gradient spin echo (OGSE) diffusion imaging for human brain imaging and evaluate human brain imaging with OGSE on the MAGNUS head-gradient insert (200 mT/m amplitude and 500 T/m/s slew rate). METHODS Simulations with cosine-modulated and trapezoidal-cosine OGSE at various gradient amplitudes and slew rates were performed. Six healthy subjects were imaged with the MAGNUS gradient at 3T with OGSE at frequencies up to 100 Hz and b = 450 s/mm2 . Comparisons were made against standard pulsed gradient spin echo (PGSE) diffusion in vivo and in an isotropic diffusion phantom. RESULTS Simulations show that to achieve high frequency and b-value simultaneously for OGSE, high gradient amplitude, high slew rates, and high peripheral nerve stimulation limits are required. A strong linear trend for increased diffusivity (mean: 8-19%, radial: 9-27%, parallel: 8-15%) was observed in normal white matter with OGSE (20 Hz to 100 Hz) as compared to PGSE. Linear fitting to frequency provided excellent correlation, and using a short-range disorder model provided radial long-term diffusivities of D∞,MD = 911 ± 72 µm2 /s, D∞,PD = 1519 ± 164 µm2 /s, and D∞,RD = 640 ± 111 µm2 /s and correlation lengths of lc ,MD = 0.802 ± 0.156 µm, lc ,PD = 0.837 ± 0.172 µm, and lc ,RD = 0.780 ± 0.174 µm. Diffusivity changes with OGSE frequency were negligible in the phantom, as expected. CONCLUSION The high gradient amplitude, high slew rate, and high peripheral nerve stimulation thresholds of the MAGNUS head-gradient enables OGSE acquisition for in vivo human brain imaging.
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Affiliation(s)
- Ek T Tan
- GE Research, Niskayuna, New York.,Department of Radiology and Imaging, Hospital for Special Surgery, New York, New York
| | - Robert Y Shih
- Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Walter Reed National Military Medical Center, Bethesda, Maryland
| | | | | | - Yihe Hua
- GE Research, Niskayuna, New York
| | | | | | - Jennifer A McNab
- Department of Radiology, Stanford University, Stanford, California
| | - J Kevin DeMarco
- Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Vincent B Ho
- Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Thomas K F Foo
- GE Research, Niskayuna, New York.,Uniformed Services University of the Health Sciences, Bethesda, Maryland
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