1
|
Adanyeguh IM, Park YW, Henry PG, Deelchand DK. B 0-insensitive image navigators for prospective motion-corrected MRS with localized second-order shimming. Magn Reson Med 2024; 92:1338-1347. [PMID: 38704666 PMCID: PMC11262980 DOI: 10.1002/mrm.30151] [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: 01/08/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024]
Abstract
PURPOSE Localized shimming in single-voxel MRS often results in large B0 inhomogeneity outside the volume-of-interest. This causes unacceptable degradation in motion navigator images. Switching back and forth between whole-brain shim and localized shim is possible for linear shims, but not for higher-order shims. Here we propose motion navigators largely insensitive to B0 inhomogeneity for prospective motion-corrected MRS with localized higher-order shimming. METHODS A recent fast high-resolution motion navigator based on spiral-in/out k-space trajectories and multislice-to-volume registration was modified by splitting the readout into multiple shot interleaves which shortened the echo time and reduced the effect of B0 inhomogeneity. The performance of motion correction was assessed in healthy subjects in the prefrontal cortex using a sLASER sequence at 3T (N = 5) and 7T (N = 5). RESULTS With multiple spatial interleaves, excellent quality navigator images were acquired in the whole brain in spite of large B0 inhomogeneity outside the MRS voxel. The total duration of the navigator in sLASER remained relatively short even with multiple shots (3T: 10 spatial interleaves 94 ms per slice; 7T: 15 spatial interleaves 103 ms per slice). Prospective motion correction using the multi-shot navigators yielded comparable spectral quality (water linewidth and metabolite SNR) with and without subject motion. CONCLUSION B0-insensitive motion navigators enable prospective motion correction for MRS with all first- and second-order shims adjusted in the MRS voxel, providing optimal spectral linewidth.
Collapse
Affiliation(s)
- Isaac M Adanyeguh
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Young Woo Park
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Pierre-Gilles Henry
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Dinesh K Deelchand
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| |
Collapse
|
2
|
Meng Y, Allen JW, Sharghi VK, Qiu D. Motion and temporal B 0-shift corrections for QSM and R 2 * mapping using dual-echo spiral navigators and conjugate-phase reconstruction. Magn Reson Med 2024. [PMID: 39233495 DOI: 10.1002/mrm.30266] [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: 02/29/2024] [Revised: 08/03/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024]
Abstract
PURPOSE To develop an efficient navigator-based motion and temporal B0-shift correction technique for 3D multi-echo gradient-echo (ME-GRE) MRI for quantitative susceptibility mapping (QSM) andR 2 * $$ {\mathrm{R}}_2^{\ast } $$ mapping. THEORY AND METHODS A dual-echo 3D stack-of-spiral navigator was designed to interleave with the Cartesian multi-echo gradient-echo acquisitions, allowing the acquisition of both low-echo and high-echo time signals. We additionally designed a novel conjugate phase-based reconstruction method for the joint correction of motion and temporal B0 shifts. We performed numerical simulation, phantom scans, and in vivo human scans to assess the performance of the methods. RESULTS Numerical simulation and human brain scans demonstrated that the proposed technique successfully corrected artifacts induced by both head motions and temporal B0 changes. Efficient B0-change correction with conjugate-phase reconstruction can be performed on fewer than 10 clustered k-space segments. In vivo scans showed that combining temporal B0 correction with motion correction further reduced artifacts and improved image quality in bothR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and QSM images. CONCLUSION Our proposed approach of using 3D spiral navigators and a novel conjugate-phase reconstruction method can improve susceptibility-related measurements using MR.
Collapse
Affiliation(s)
- Yuguang Meng
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, Georgia, USA
| | - Jason W Allen
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, Georgia, USA
- Department of Radiology and Imaging Sciences, Indiana University, Indianapolis, Indiana, USA
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Deqiang Qiu
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, Georgia, USA
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
3
|
De Moura HL, Monga A, Zhang X, Zibetti MVW, Keerthivasan MB, Regatte RR. Feasibility of 3D MRI fingerprinting for rapid knee cartilage T 1, T 2, and T 1ρ mapping at 0.55T: Comparison with 3T. NMR IN BIOMEDICINE 2024:e5250. [PMID: 39169559 DOI: 10.1002/nbm.5250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
Low-field strength scanners present an opportunity for more inclusive imaging exams and bring several challenges including lower signal-to-noise ratio (SNR) and longer scan times. Magnetic resonance fingerprinting (MRF) is a rapid quantitative multiparametric method that can enable multiple quantitative maps simultaneously. To demonstrate the feasibility of an MRF sequence for knee cartilage evaluation in a 0.55T system we performed repeatability and accuracy experiments with agar-gel phantoms. Additionally, five healthy volunteers (age 32 ± 4 years old, 2 females) were scanned at 3T and 0.55T. The MRI acquisition protocols include a stack-of-stars T1ρ-enabled MRF sequence, a VIBE sequence with variable flip angles (VFA) for T1 mapping, and fat-suppressed turbo flash (TFL) sequences for T2 and T1ρ mappings. Double-Echo steady-state (DESS) sequence was also used for cartilage segmentation. Acquisitions were performed at two different field strengths, 0.55T and 3T, with the same sequences but protocols were slightly different to accommodate differences in signal-to-noise ratio and relaxation times. Cartilage segmentation was done using five compartments. T1, T2, and T1ρ values were measured in the knee cartilage using both MRF and conventional relaxometry sequences. The MRF sequence demonstrated excellent repeatability in a test-retest experiment with model agar-gel phantoms, as demonstrated with correlation and Bland-Altman plots. Underestimation of T1 values was observed on both field strengths, with the average global difference between reference values and the MRF being 151 ms at 0.55T and 337 ms at 3T. At 0.55T, MRF measurements presented significant biases but strong correlations with the reference measurements. Although a larger error was present in T1 measurements, MRF measurements trended similarly to the conventional measurements for human subjects and model agar-gel phantoms.
Collapse
Affiliation(s)
- Hector L De Moura
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Anmol Monga
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Xiaoxia Zhang
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Marcelo V W Zibetti
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | | | - Ravinder R Regatte
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| |
Collapse
|
4
|
Yang H, Wang G, Li Z, Li H, Zheng J, Hu Y, Cao X, Liao C, Ye H, Tian Q. Artificial intelligence for neuro MRI acquisition: a review. MAGMA (NEW YORK, N.Y.) 2024; 37:383-396. [PMID: 38922525 DOI: 10.1007/s10334-024-01182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024]
Abstract
OBJECT To review recent advances of artificial intelligence (AI) in enhancing the efficiency and throughput of the MRI acquisition workflow in neuroimaging, including planning, sequence design, and correction of acquisition artifacts. MATERIALS AND METHODS A comprehensive analysis was conducted on recent AI-based methods in neuro MRI acquisition. The study focused on key technological advances, their impact on clinical practice, and potential risks associated with these methods. RESULTS The findings indicate that AI-based algorithms have a substantial positive impact on the MRI acquisition process, improving both efficiency and throughput. Specific algorithms were identified as particularly effective in optimizing acquisition steps, with reported improvements in workflow efficiency. DISCUSSION The review highlights the transformative potential of AI in neuro MRI acquisition, emphasizing the technological advances and clinical benefits. However, it also discusses potential risks and challenges, suggesting areas for future research to mitigate these concerns and further enhance AI integration in MRI acquisition.
Collapse
Affiliation(s)
- Hongjia Yang
- School of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Guanhua Wang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ziyu Li
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Haoxiang Li
- School of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Jialan Zheng
- School of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Yuxin Hu
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Xiaozhi Cao
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Congyu Liao
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Huihui Ye
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Qiyuan Tian
- School of Biomedical Engineering, Tsinghua University, Beijing, China.
- Tsinghua Laboratory of Brain and Intelligence, Tsinghua University, Beijing, China.
| |
Collapse
|
5
|
Rivera-Rivera LA, Vikner T, Eisenmenger L, Johnson SC, Johnson KM. Four-dimensional flow MRI for quantitative assessment of cerebrospinal fluid dynamics: Status and opportunities. NMR IN BIOMEDICINE 2024; 37:e5082. [PMID: 38124351 PMCID: PMC11162953 DOI: 10.1002/nbm.5082] [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: 05/16/2023] [Revised: 10/03/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
Neurological disorders can manifest with altered neurofluid dynamics in different compartments of the central nervous system. These include alterations in cerebral blood flow, cerebrospinal fluid (CSF) flow, and tissue biomechanics. Noninvasive quantitative assessment of neurofluid flow and tissue motion is feasible with phase contrast magnetic resonance imaging (PC MRI). While two-dimensional (2D) PC MRI is routinely utilized in research and clinical settings to assess flow dynamics through a single imaging slice, comprehensive neurofluid dynamic assessment can be limited or impractical. Recently, four-dimensional (4D) flow MRI (or time-resolved three-dimensional PC with three-directional velocity encoding) has emerged as a powerful extension of 2D PC, allowing for large volumetric coverage of fluid velocities at high spatiotemporal resolution within clinically reasonable scan times. Yet, most 4D flow studies have focused on blood flow imaging. Characterizing CSF flow dynamics with 4D flow (i.e., 4D CSF flow) is of high interest to understand normal brain and spine physiology, but also to study neurological disorders such as dysfunctional brain metabolite waste clearance, where CSF dynamics appear to play an important role. However, 4D CSF flow imaging is challenged by the long T1 time of CSF and slower velocities compared with blood flow, which can result in longer scan times from low flip angles and extended motion-sensitive gradients, hindering clinical adoption. In this work, we review the state of 4D CSF flow MRI including challenges, novel solutions from current research and ongoing needs, examples of clinical and research applications, and discuss an outlook on the future of 4D CSF flow.
Collapse
Affiliation(s)
- Leonardo A Rivera-Rivera
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Physics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Tomas Vikner
- Department of Medical Physics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Radiation Sciences, Radiation Physics and Biomedical Engineering, Umeå University, Umeå, Sweden
| | - Laura Eisenmenger
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sterling C Johnson
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kevin M Johnson
- Department of Medical Physics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| |
Collapse
|
6
|
Amor Z, Ciuciu P, G R C, Daval-Frérot G, Mauconduit F, Thirion B, Vignaud A. Non-Cartesian 3D-SPARKLING vs Cartesian 3D-EPI encoding schemes for functional Magnetic Resonance Imaging at 7 Tesla. PLoS One 2024; 19:e0299925. [PMID: 38739571 PMCID: PMC11090341 DOI: 10.1371/journal.pone.0299925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/16/2024] [Indexed: 05/16/2024] Open
Abstract
The quest for higher spatial and/or temporal resolution in functional MRI (fMRI) while preserving a sufficient temporal signal-to-noise ratio (tSNR) has generated a tremendous amount of methodological contributions in the last decade ranging from Cartesian vs. non-Cartesian readouts, 2D vs. 3D acquisition strategies, parallel imaging and/or compressed sensing (CS) accelerations and simultaneous multi-slice acquisitions to cite a few. In this paper, we investigate the use of a finely tuned version of 3D-SPARKLING. This is a non-Cartesian CS-based acquisition technique for high spatial resolution whole-brain fMRI. We compare it to state-of-the-art Cartesian 3D-EPI during both a retinotopic mapping paradigm and resting-state acquisitions at 1mm3 (isotropic spatial resolution). This study involves six healthy volunteers and both acquisition sequences were run on each individual in a randomly-balanced order across subjects. The performances of both acquisition techniques are compared to each other in regards to tSNR, sensitivity to the BOLD effect and spatial specificity. Our findings reveal that 3D-SPARKLING has a higher tSNR than 3D-EPI, an improved sensitivity to detect the BOLD contrast in the gray matter, and an improved spatial specificity. Compared to 3D-EPI, 3D-SPARKLING yields, on average, 7% more activated voxels in the gray matter relative to the total number of activated voxels.
Collapse
Affiliation(s)
- Zaineb Amor
- CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Ciuciu
- CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND team, Université Paris-Saclay, Palaiseau, France
| | - Chaithya G R
- CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND team, Université Paris-Saclay, Palaiseau, France
| | - Guillaume Daval-Frérot
- CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND team, Université Paris-Saclay, Palaiseau, France
- Siemens Heathineers, Courbevoie, France
| | - Franck Mauconduit
- CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Bertrand Thirion
- CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
- Inria, MIND team, Université Paris-Saclay, Palaiseau, France
| | - Alexandre Vignaud
- CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
| |
Collapse
|
7
|
Adanyeguh IM, Bikkamane Jayadev N, Henry PG, Deelchand DK. Fast high-resolution prospective motion correction for single-voxel spectroscopy. Magn Reson Med 2024; 91:1301-1313. [PMID: 38084392 PMCID: PMC10872424 DOI: 10.1002/mrm.29950] [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: 09/19/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 01/04/2024]
Abstract
PURPOSE To develop a fast high-resolution image-based motion correction method using spiral navigators with multislice-to-volume registration. METHODS A semi-LASER sequence was modified to include a multislice spiral navigator for prospective motion correction (∼305 ms including acquisition, processing, and feedback) as well as shim and frequency navigators for prospective shim and frequency correction (∼100 ms for each). MR spectra were obtained in the prefrontal cortex in five healthy subjects at 3 T with and without prospective motion and shim correction. The effect of key navigator parameters (number of slices, image resolution, and excitation flip angle) on registration accuracy was assessed using simulations. RESULTS Without prospective motion and shim correction, spectral quality degraded significantly in the presence of voluntary motion. In contrast, with prospective motion and shim correction, spectral quality was improved (metabolite linewidth = 6.7 ± 0.6 Hz, SNR= 67 ± 9) and in good agreement with baseline data without motion (metabolite linewidth = 6.9 ± 0.9 Hz, SNR = 73 ± 9). In addition, there was no significant difference in metabolites concentrations measured without motion and with prospective motion and shim correction in the presence of motion. Simulations showed that the registration precision was comparable when using three navigator slices with 3 mm resolution and when using the entire volume (all slices) with 8 mm resolution. CONCLUSION The proposed motion correction scheme allows fast and precise prospective motion and shim correction for single-voxel spectroscopy at 3 T. With 3 mm resolution, only a few navigator slices are necessary to achieve excellent motion correction performance.
Collapse
Affiliation(s)
- Isaac M Adanyeguh
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Nutandev Bikkamane Jayadev
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Pierre-Gilles Henry
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Dinesh K Deelchand
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| |
Collapse
|
8
|
Engel M, Mueller L, Döring A, Afzali M, Jones DK. Maximizing SNR per unit time in diffusion MRI with multiband T-Hex spirals. Magn Reson Med 2024; 91:1323-1336. [PMID: 38156527 PMCID: PMC10953427 DOI: 10.1002/mrm.29953] [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: 05/18/2023] [Revised: 10/03/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023]
Abstract
PURPOSE The characterization of tissue microstructure using diffusion MRI (dMRI) signals is rapidly evolving, with increasing sophistication of signal representations and microstructure models. However, this progress often requires signals to be acquired with very high b-values (e.g., b > 30 ms/μm2 ), along many directions, and using multiple b-values, leading to long scan times and extremely low SNR in dMRI images. The purpose of this work is to boost the SNR efficiency of dMRI by combining three particularly efficient spatial encoding techniques and utilizing a high-performance gradient system (Gmax ≤ 300 mT/m) for efficient diffusion encoding. METHODS Spiral readouts, multiband imaging, and sampling on tilted hexagonal grids (T-Hex) are combined and implemented on a 3T MRI system with ultra-strong gradients. Image reconstruction is performed through an iterative cg-SENSE algorithm incorporating static off-resonance distributions and field dynamics as measured with an NMR field camera. Additionally, T-Hex multiband is combined with a more conventional EPI-readout and compared with state-of-the-art blipped-CAIPIRINHA sampling. The advantage of the proposed approach is furthermore investigated for clinically available gradient performance and diffusion kurtosis imaging. RESULTS High fidelity in vivo images with b-values up to 40 ms/μm2 are obtained. The approach provides superior SNR efficiency over other state-of-the-art multiband diffusion readout schemes. CONCLUSION The demonstrated gains hold promise for the widespread dissemination of advanced microstructural scans, especially in clinical populations.
Collapse
Affiliation(s)
- Maria Engel
- Cardiff University Brain Research Imaging Centre (CUBRIC)Cardiff UniversityCardiffUK
| | - Lars Mueller
- Cardiff University Brain Research Imaging Centre (CUBRIC)Cardiff UniversityCardiffUK
- Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - André Döring
- Cardiff University Brain Research Imaging Centre (CUBRIC)Cardiff UniversityCardiffUK
| | - Maryam Afzali
- Cardiff University Brain Research Imaging Centre (CUBRIC)Cardiff UniversityCardiffUK
- Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Derek K. Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC)Cardiff UniversityCardiffUK
| |
Collapse
|
9
|
Zibetti MVW, De Moura HL, Keerthivasan MB, Regatte RR. Optimizing variable flip angles in magnetization-prepared gradient-echo sequences for efficient 3D-T1ρ mapping. Magn Reson Med 2023; 90:1465-1483. [PMID: 37288538 PMCID: PMC10524308 DOI: 10.1002/mrm.29740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/24/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
PURPOSE To optimize the choice of the flip angles of magnetization-prepared gradient-echo sequences for improved accuracy, precision, and speed of 3D-T1ρ mapping. METHODS We propose a new optimization approach for finding variable flip-angle values that improve magnetization-prepared gradient-echo sequences used for 3D-T1ρ mapping. This new approach can improve the accuracy and SNR, while reducing filtering effects. We demonstrate the concept in the three different versions of the magnetization-prepared gradient-echo sequences that are typically used for 3D-T1ρ mapping and evaluate their performance in model agarose phantoms (n = 4) and healthy volunteers (n = 5) for knee joint imaging. We also tested the optimization with sequence parameters targeting faster acquisitions. RESULTS Our results show that optimized variable flip angle can improve the accuracy and the precision of the sequences, seen as a reduction of the mean of normalized absolute difference from about 5%-6% to 3%-4% in model phantoms and from 15%-16% to 11%-13% in the knee joint, and improving SNR from about 12-28 to 22-32 in agarose phantoms and about 7-14 to 13-17 in healthy volunteers. The optimization can also compensate for the loss in quality caused by making the sequence faster. This results in sequence configurations that acquire more data per unit of time with SNR and mean of normalized absolute difference measurements close to its slower versions. CONCLUSION The optimization of the variable flip angle can be used to increase accuracy and precision, and to improve the speed of the typical imaging sequences used for quantitative 3D-T1ρ mapping of the knee joint.
Collapse
Affiliation(s)
- Marcelo V W Zibetti
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hector L. De Moura
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, NY, USA
| | | | - Ravinder R. Regatte
- Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, NY, USA
| |
Collapse
|
10
|
Xu Y, Farris CW, Anderson SW, Zhang X, Brown KA. Bayesian reconstruction of magnetic resonance images using Gaussian processes. Sci Rep 2023; 13:12527. [PMID: 37532743 PMCID: PMC10397278 DOI: 10.1038/s41598-023-39533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023] Open
Abstract
A central goal of modern magnetic resonance imaging (MRI) is to reduce the time required to produce high-quality images. Efforts have included hardware and software innovations such as parallel imaging, compressed sensing, and deep learning-based reconstruction. Here, we propose and demonstrate a Bayesian method to build statistical libraries of magnetic resonance (MR) images in k-space and use these libraries to identify optimal subsampling paths and reconstruction processes. Specifically, we compute a multivariate normal distribution based upon Gaussian processes using a publicly available library of T1-weighted images of healthy brains. We combine this library with physics-informed envelope functions to only retain meaningful correlations in k-space. This covariance function is then used to select a series of ring-shaped subsampling paths using Bayesian optimization such that they optimally explore space while remaining practically realizable in commercial MRI systems. Combining optimized subsampling paths found for a range of images, we compute a generalized sampling path that, when used for novel images, produces superlative structural similarity and error in comparison to previously reported reconstruction processes (i.e. 96.3% structural similarity and < 0.003 normalized mean squared error from sampling only 12.5% of the k-space data). Finally, we use this reconstruction process on pathological data without retraining to show that reconstructed images are clinically useful for stroke identification. Since the model trained on images of healthy brains could be directly used for predictions in pathological brains without retraining, it shows the inherent transferability of this approach and opens doors to its widespread use.
Collapse
Affiliation(s)
- Yihong Xu
- Department of Physics, Boston University, Boston, MA, 02215, USA
| | - Chad W Farris
- Department of Radiology, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Stephan W Anderson
- Department of Radiology, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Xin Zhang
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
- Department of Electrical & Computer Engineering, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science & Engineering, Boston University, Boston, MA, 02215, USA
| | - Keith A Brown
- Department of Physics, Boston University, Boston, MA, 02215, USA.
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA.
- Division of Materials Science & Engineering, Boston University, Boston, MA, 02215, USA.
| |
Collapse
|
11
|
Franceschiello B, Rumac S, Hilbert T, Nau M, Dziadosz M, Degano G, Roy CW, Gaglianese A, Petri G, Yerly J, Stuber M, Kober T, van Heeswijk RB, Murray MM, Fornari E. Hi-Fi fMRI: High-resolution, fast-sampled and sub-second whole-brain functional MRI at 3T in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.13.540663. [PMID: 37425913 PMCID: PMC10327135 DOI: 10.1101/2023.05.13.540663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Functional magnetic resonance imaging (fMRI) is a methodological cornerstone of neuroscience. Most studies measure blood-oxygen-level-dependent (BOLD) signal using echo-planar imaging (EPI), Cartesian sampling, and image reconstruction with a one-to-one correspondence between the number of acquired volumes and reconstructed images. However, EPI schemes are subject to trade-offs between spatial and temporal resolutions. We overcome these limitations by measuring BOLD with a gradient recalled echo (GRE) with 3D radial-spiral phyllotaxis trajectory at a high sampling rate (28.24ms) on standard 3T field-strength. The framework enables the reconstruction of 3D signal time courses with whole-brain coverage at simultaneously higher spatial (1mm 3 ) and temporal (up to 250ms) resolutions, as compared to optimized EPI schemes. Additionally, artifacts are corrected before image reconstruction; the desired temporal resolution is chosen after scanning and without assumptions on the shape of the hemodynamic response. By showing activation in the calcarine sulcus of 20 participants performing an ON-OFF visual paradigm, we demonstrate the reliability of our method for cognitive neuroscience research.
Collapse
|
12
|
Montez DF, Van AN, Miller RL, Seider NA, Marek S, Zheng A, Newbold DJ, Scheidter K, Feczko E, Perrone AJ, Miranda-Dominguez O, Earl EA, Kay BP, Jha AK, Sotiras A, Laumann TO, Greene DJ, Gordon EM, Tisdall MD, van der Kouwe A, Fair DA, Dosenbach NUF. Using synthetic MR images for distortion correction. Dev Cogn Neurosci 2023; 60:101234. [PMID: 37023632 PMCID: PMC10106483 DOI: 10.1016/j.dcn.2023.101234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Functional MRI (fMRI) data acquired using echo-planar imaging (EPI) are highly distorted by magnetic field inhomogeneities. Distortion and differences in image contrast between EPI and T1-weighted and T2-weighted (T1w/T2w) images makes their alignment a challenge. Typically, field map data are used to correct EPI distortions. Alignments achieved with field maps can vary greatly and depends on the quality of field map data. However, many public datasets lack field map data entirely. Additionally, reliable field map data is often difficult to acquire in high-motion pediatric or developmental cohorts. To address this, we developed Synth, a software package for distortion correction and cross-modal image registration that does not require field map data. Synth combines information from T1w and T2w anatomical images to construct an idealized undistorted synthetic image with similar contrast properties to EPI data. This synthetic image acts as an effective reference for individual-specific distortion correction. Using pediatric (ABCD: Adolescent Brain Cognitive Development) and adult (MSC: Midnight Scan Club; HCP: Human Connectome Project) data, we demonstrate that Synth performs comparably to field map distortion correction approaches, and often outperforms them. Field map-less distortion correction with Synth allows accurate and precise registration of fMRI data with missing or corrupted field map information.
Collapse
Affiliation(s)
- David F Montez
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America.
| | - Andrew N Van
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Ryland L Miller
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Nicole A Seider
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Scott Marek
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Annie Zheng
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Dillan J Newbold
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Neurology, New York University Langone Medical Center, New York, NY 10016, United States of America
| | - Kristen Scheidter
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Eric Feczko
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America; Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America
| | - Anders J Perrone
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America; Department of Psychiatry, Oregon Health and Science University, Portland, OR 97239, United States of America
| | - Oscar Miranda-Dominguez
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America; Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America
| | - Eric A Earl
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America; Department of Psychiatry, Oregon Health and Science University, Portland, OR 97239, United States of America
| | - Benjamin P Kay
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Abhinav K Jha
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Aristeidis Sotiras
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Timothy O Laumann
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Deanna J Greene
- Department of Cognitive Science, University of California, San Diego, La Jolla CA 92093, United States of America
| | - Evan M Gordon
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - M Dylan Tisdall
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Andre van der Kouwe
- Department of Radiology, Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA 02129, United States of America; Department of Radiology, Harvard Medical School, Boston, MA 02115, United States of America
| | - Damien A Fair
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America; Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America; Institute of Child Development, University of Minnesota Medical School, Minneapolis, MN 55455, United States of America
| | - Nico U F Dosenbach
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| |
Collapse
|
13
|
Li G, Ma X, Li S, Ye X, Börnert P, Zhou XJ, Guo H. Comparison of uniform-density, variable-density, and dual-density spiral samplings for multi-shot DWI. Magn Reson Med 2023; 90:133-149. [PMID: 36883748 DOI: 10.1002/mrm.29633] [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: 09/03/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/09/2023]
Abstract
PURPOSE To compare the performances of uniform-density spiral (UDS), variable-density spiral (VDS), and dual-density spiral (DDS) samplings in multi-shot diffusion imaging, and determine a sampling strategy that balances reliability of shot navigator and overall DWI image quality. THEORY AND METHODS UDS, VDS, and DDS trajectories were implemented to achieve four-shot diffusion-weighted spiral imaging. First, the static B0 off-resonance effects in UDS, VDS, and DDS acquisitions were analyzed based on a signal model. Then, in vivo experiments were performed to verify the theoretical analyses, and fractional anisotropy (FA) fitting residuals were used to quantitatively assess the quality of spiral diffusion data for tensor estimation. Finally, the SNR performances and g-factor behavior of the three spiral samplings were evaluated using a Monte Carlo-based pseudo multiple replica method. RESULTS Among the three spiral trajectories with the same readout duration, UDS sampling exhibited the least off-resonance artifacts. This was most evident when the static B0 off-resonance effect was severe. The UDS diffusion images had higher anatomical fidelity and lower FA fitting residuals than the other two counterparts. Furthermore, the four-shot UDS acquisition achieved the best SNR performance in diffusion imaging with 12.11% and 40.85% improvements over the VDS and DDS acquisitions with the same readout duration, respectively. CONCLUSION UDS sampling is an efficient spiral acquisition scheme for high-resolution diffusion imaging with reliable navigator information. It provides superior off-resonance performance and SNR efficiency over the VDS and DDS samplings for the tested scenarios.
Collapse
Affiliation(s)
- Guangqi Li
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Xiaodong Ma
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Sisi Li
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Xinyu Ye
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Peter Börnert
- Radiology, C.J. Gorter Center for High-Field MRI, Leiden University Medical Center, Leiden, The Netherlands.,Philips Research, Hamburg, Germany
| | - Xiaohong Joe Zhou
- Center for MR Research and Departments of Radiology, Neurosurgery, and Biomedical Engineering, University of Illinois College of Medicine at Chicago, Chicago, Illinois, USA
| | - Hua Guo
- Center for Biomedical Imaging Research, Department of Biomedical Engineering, Tsinghua University, Beijing, China
| |
Collapse
|
14
|
Jwa AS, Goodman JS, Glover GH. Inconsistencies in mapping current distribution in transcranial direct current stimulation. FRONTIERS IN NEUROIMAGING 2023; 1:1069500. [PMID: 37555148 PMCID: PMC10406311 DOI: 10.3389/fnimg.2022.1069500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/28/2022] [Indexed: 08/10/2023]
Abstract
INTRODUCTION tDCS is a non-invasive neuromodulation technique that has been widely studied both as a therapy for neuropsychiatric diseases and for cognitive enhancement. However, recent meta-analyses have reported significant inconsistencies amongst tDCS studies. Enhancing empirical understanding of current flow in the brain may help elucidate some of these inconsistencies. METHODS We investigated tDCS-induced current distribution by injecting a low frequency current waveform in a phantom and in vivo. MR phase images were collected during the stimulation and a time-series analysis was used to reconstruct the magnetic field. A current distribution map was derived from the field map using Ampere's law. RESULTS The current distribution map in the phantom showed a clear path of current flow between the two electrodes, with more than 75% of the injected current accounted for. However, in brain, the results did evidence a current path between the two target electrodes but only some portion ( 25%) of injected current reached the cortex demonstrating that a significant fraction of the current is bypassing the brain and traveling from one electrode to the other external to the brain, probably due to conductivity differences in brain tissue types. Substantial inter-subject and intra-subject (across consecutive scans) variability in current distribution maps were also observed in human but not in phantom scans. DISCUSSIONS An in-vivo current mapping technique proposed in this study demonstrated that much of the injected current in tDCS was not accounted for in human brain and deviated to the edge of the brain. These findings would have ramifications in the use of tDCS as a neuromodulator and may help explain some of the inconsistencies reported in other studies.
Collapse
Affiliation(s)
- Anita S. Jwa
- Stanford University Law School, Stanford, CA, United States
| | - Jonathan S. Goodman
- Program in Biophysics, Stanford School of Medicine, Stanford, CA, United States
| | - Gary H. Glover
- Department of Radiology, Stanford University, Stanford, CA, United States
| |
Collapse
|
15
|
Abad N, Lee SK, Ajala A, In MH, Frigo LM, Bhushan C, Morris HD, Hua Y, Ho VB, Bernstein MA, Foo TKF. Calibration of concomitant field offsets using phase contrast MRI for asymmetric gradient coils. Magn Reson Med 2023; 89:262-275. [PMID: 36129000 PMCID: PMC9617788 DOI: 10.1002/mrm.29452] [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: 06/02/2022] [Revised: 07/25/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022]
Abstract
PURPOSE Asymmetric gradient coils introduce zeroth- and first-order concomitant field terms, in addition to higher-order terms common to both asymmetric and symmetric gradients. Salient to compensation strategies is the accurate calibration of the concomitant field spatial offset parameters for asymmetric coils. A method that allows for one-time calibration of the offset parameters is described. THEORY AND METHODS A modified phase contrast pulse sequence with single-sided bipolar flow encoding is proposed to calibrate the offsets for asymmetric, transverse gradient coils. By fitting the measured phase offsets to different gradient amplitudes, the spatial offsets were calculated by fitting the phase variation. This was used for calibrating real-time pre-emphasis compensation of the zeroth- and first-order concomitant fields. RESULTS Image quality improvement with the proposed corrections was demonstrated in phantom and healthy volunteers with non-Cartesian and Cartesian trajectory acquisitions. Concomitant field compensation using the calibrated offsets resulted in a residual phase error <3% at the highest gradient amplitude and demonstrated substantial reduction of image blur and slice position/selection artifacts. CONCLUSIONS The proposed implementation provides an accurate method for calibrating spatial offsets that can be used for real-time concomitant field compensation of zeroth and first-order terms, substantially reducing artifacts without retrospective correction or sequence specific waveform modifications.
Collapse
Affiliation(s)
| | | | | | | | | | | | - H. Douglas Morris
- Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Yihe Hua
- GE Research, Niskayuna, NY 12309, USA
| | - Vincent B. Ho
- Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Uniformed Services University, Bethesda, MD 20814, USA
| | | | - Thomas K. F. Foo
- GE Research, Niskayuna, NY 12309, USA
- Uniformed Services University, Bethesda, MD 20814, USA
| |
Collapse
|
16
|
Skorska MN, Lobaugh NJ, Lombardo MV, van Bruggen N, Chavez S, Thurston LT, Aitken M, Zucker KJ, Chakravarty MM, Lai MC, VanderLaan DP. Inter-Network Brain Functional Connectivity in Adolescents Assigned Female at Birth Who Experience Gender Dysphoria. Front Endocrinol (Lausanne) 2022; 13:903058. [PMID: 35937791 PMCID: PMC9353716 DOI: 10.3389/fendo.2022.903058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Gender dysphoria (GD) is characterized by distress due to an incongruence between experienced gender and sex assigned at birth. Brain functional connectivity in adolescents who experience GD may be associated with experienced gender (vs. assigned sex) and/or brain networks implicated in own-body perception. Furthermore, sexual orientation may be related to brain functional organization given commonalities in developmental mechanisms proposed to underpin GD and same-sex attractions. Here, we applied group independent component analysis to resting-state functional magnetic resonance imaging (rs-fMRI) BOLD timeseries data to estimate inter-network (i.e., between independent components) timeseries correlations, representing functional connectivity, in 17 GD adolescents assigned female at birth (AFAB) not receiving gender-affirming hormone therapy, 17 cisgender girls, and 15 cisgender boys (ages 12-17 years). Sexual orientation was represented by degree of androphilia-gynephilia and sexual attractions strength. Multivariate partial least squares analyses found that functional connectivity differed among cisgender boys, cisgender girls, and GD AFAB, with the largest difference between cisgender boys and GD AFAB. Regarding sexual orientation and age, the brain's intrinsic functional organization of GD AFAB was both similar to and different from cisgender girls, and both differed from cisgender boys. The pattern of group differences and the networks involved aligned with the hypothesis that brain functional organization is different among GD AFAB (vs. cisgender) adolescents, and certain aspects of this organization relate to brain areas implicated in own-body perception and self-referential thinking. Overall, brain functional organization of GD AFAB was generally more similar to that of cisgender girls than cisgender boys.
Collapse
Affiliation(s)
- Malvina N. Skorska
- Child and Youth Psychiatry, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Nancy J. Lobaugh
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Medicine, Division of Neurology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Michael V. Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Nina van Bruggen
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Sofia Chavez
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lindsey T. Thurston
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Madison Aitken
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Kenneth J. Zucker
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - M. Mallar Chakravarty
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, PQ, Canada
- Department of Psychiatry, McGill University, Montreal, PQ, Canada
- Department of Biological and Biomedical Engineering, McGill University, Montreal, PQ, Canada
| | - Meng-Chuan Lai
- Child and Youth Psychiatry, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- The Margaret and Wallace McCain Centre for Child, Youth & Family Mental Health and Azrieli Adult Neurodevelopmental Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry and Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Doug P. VanderLaan
- Child and Youth Psychiatry, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| |
Collapse
|
17
|
Mills-Finnerty C, Frangos E, Allen K, Komisaruk B, Wise N. Functional Magnetic Resonance Imaging Studies in Sexual Medicine: A Primer. J Sex Med 2022; 19:1073-1089. [DOI: 10.1016/j.jsxm.2022.03.217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 01/27/2022] [Accepted: 03/04/2022] [Indexed: 11/17/2022]
|
18
|
Paasonen E, Paasonen J, Lehto LJ, Pirttimäki T, Laakso H, Wu L, Ma J, Idiyatullin D, Tanila H, Mangia S, Michaeli S, Gröhn O. Event-recurring multiband SWIFT functional MRI with 200-ms temporal resolution during deep brain stimulation and isoflurane-induced burst suppression in rat. Magn Reson Med 2022; 87:2872-2884. [PMID: 34985145 PMCID: PMC9160777 DOI: 10.1002/mrm.29154] [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: 10/22/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022]
Abstract
PURPOSE To develop a high temporal resolution functional MRI method for tracking repeating events in the brain. METHODS We developed a novel functional MRI method using multiband sweep imaging with Fourier transformation (SWIFT), termed event-recurring SWIFT (EVER-SWIFT). The method is able to image similar repeating events with subsecond temporal resolution. Here, we demonstrate the use of EVER-SWIFT for detecting functional MRI responses during deep brain stimulation of the medial septal nucleus and during spontaneous isoflurane-induced burst suppression in the rat brain at 9.4 T with 200-ms temporal resolution. RESULTS The EVER-SWIFT approach showed that the shapes and time-to-peak values of the response curves to deep brain stimulation significantly differed between downstream brain regions connected to the medial septal nucleus, resembling findings obtained with traditional 2-second temporal resolution. In contrast, EVER-SWIFT allowed for detailed temporal measurement of a spontaneous isoflurane-induced bursting activity pattern, which was not achieved with traditional temporal resolution. CONCLUSION The EVER-SWIFT technique enables subsecond 3D imaging of both stimulated and spontaneously recurring brain activities, and thus holds great potential for studying the mechanisms of neuromodulation and spontaneous brain activity.
Collapse
Affiliation(s)
- E. Paasonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - J. Paasonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - LJ. Lehto
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - T. Pirttimäki
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
| | - H. Laakso
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - L. Wu
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - J. Ma
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - D. Idiyatullin
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - H. Tanila
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - S. Mangia
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - S. Michaeli
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - O. Gröhn
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
19
|
Evaluation of axial gradient Echo spiral MRI of the spine at 1.5 T. Magn Reson Imaging 2022; 89:24-32. [DOI: 10.1016/j.mri.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022]
|
20
|
McIlvain G, McGarry MDJ, Johnson CL. Quantitative effects of off-resonance related distortion on brain mechanical property estimation with magnetic resonance elastography. NMR IN BIOMEDICINE 2022; 35:e4616. [PMID: 34542196 PMCID: PMC8688217 DOI: 10.1002/nbm.4616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 07/01/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Off-resonance related geometric distortion can impact quantitative MRI techniques, such as magnetic resonance elastography (MRE), and result in errors to these otherwise sensitive metrics of brain health. MRE is a phase contrast technique to determine the mechanical properties of tissue by imaging shear wave displacements and estimating tissue stiffness through inverse solution of Navier's equation. In this study, we systematically examined the quantitative effects of distortion and corresponding correction approaches on MRE measurements through a series of simulations, phantom models, and in vivo brain experiments. We studied two different k-space trajectories, echo-planar imaging and spiral, and we determined that readout time, off-resonance gradient strength, and the combination of readout direction and off-resonance gradient direction, impact the estimated mechanical properties. Images were also processed through traditional distortion correction pipelines, and we found that each of the correction mechanisms works well for reducing stiffness errors, but are limited in cases of very large distortion. The ability of MRE to detect subtle changes to neural tissue health relies on accurate, artifact-free imaging, and thus off-resonance related geometric distortion must be considered when designing sequences and protocols by limiting readout time and applying correction where appropriate.
Collapse
Affiliation(s)
- Grace McIlvain
- Department of Biomedical Engineering, University of Delaware; Newark, DE
| | | | - Curtis L Johnson
- Department of Biomedical Engineering, University of Delaware; Newark, DE
| |
Collapse
|
21
|
Kurban D, Ivanov D, Kashyap S, Huber L, Liberman G, Poser BA. Concurrent CBF and bold FMRI with dual-echo spiral simultaneous multi-slice acquisitions at 7T. Neuroimage 2021; 247:118820. [PMID: 34920086 DOI: 10.1016/j.neuroimage.2021.118820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022] Open
Abstract
Measurement of cerebral blood flow (CBF) using the Arterial Spin Labeling (ASL) technique is a desirable fMRI approach due to the higher specificity of CBF to the site of neural activation. However, ASL has inherent limitations, such as a low signal-to-noise ratio (SNR) and low coverage/resolution due to the limited readout window following the labeling. Recently, ASL has been implemented at ultra-high field (UHF) strengths in an attempt to mitigate the SNR challenges. Even though ASL intrinsically allows concurrent acquisition of CBF and BOLD contrasts, a compromise in the echo time (TE) for either of the contrasts is inevitable with single-echo acquisitions. Long durations of the Cartesian EPI readout do not allow for multi-echo acquisitions for resolutions ≤2 mm where both contrasts can be acquired at their optimal TE at UHF. With its higher acquisition efficiency, single-shot spiral imaging provides a promising alternative to EPI, and with a dual-echo, out-in trajectory allows both CBF and BOLD contrasts to be acquired at their respective optimal TE. In this work, we implemented a dual-echo spiral out-in ASL sequence with simultaneous multi-slice (SMS) readout for increased coverage, and validated its application to fMRI with a visuomotor paradigm. Conventional Cartesian EPI acquisitions with matched parameters served as a reference. The dual-echo spiral ASL acquisitions resulted in robust CBF and BOLD activations maps. The absolute and relative CBF changes measured with the dual-echo spiral readout were in agreement with previous reports in the literature as well as the reference Cartesian acquisitions. The BOLD response amplitude was higher compared to the Cartesian acquisitions, attributable to a more optimal TE of the second echo. In conclusion, dual-echo spiral out-in SMS acquisition shows promise for concurrent acquisitions of BOLD and non-BOLD contrasts that require a short TE, with no loss in temporal resolution.
Collapse
Affiliation(s)
- Denizhan Kurban
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht 6200MD, the Netherland.
| | - Dimo Ivanov
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht 6200MD, the Netherland
| | - Sriranga Kashyap
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht 6200MD, the Netherland
| | - Laurentius Huber
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht 6200MD, the Netherland
| | - Gilad Liberman
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht 6200MD, the Netherland; Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, United States
| | - Benedikt A Poser
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht 6200MD, the Netherland
| |
Collapse
|
22
|
Advances in spiral fMRI: A high-resolution study with single-shot acquisition. Neuroimage 2021; 246:118738. [PMID: 34800666 DOI: 10.1016/j.neuroimage.2021.118738] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 01/15/2023] Open
Abstract
Spiral fMRI has been put forward as a viable alternative to rectilinear echo-planar imaging, in particular due to its enhanced average k-space speed and thus high acquisition efficiency. This renders spirals attractive for contemporary fMRI applications that require high spatiotemporal resolution, such as laminar or columnar fMRI. However, in practice, spiral fMRI is typically hampered by its reduced robustness and ensuing blurring artifacts, which arise from imperfections in both static and dynamic magnetic fields. Recently, these limitations have been overcome by the concerted application of an expanded signal model that accounts for such field imperfections, and its inversion by iterative image reconstruction. In the challenging ultra-high field environment of 7 Tesla, where field inhomogeneity effects are aggravated, both multi-shot and single-shot 2D spiral imaging at sub-millimeter resolution was demonstrated with high depiction quality and anatomical congruency. In this work, we further these advances towards a time series application of spiral readouts, namely, single-shot spiral BOLD fMRI at 0.8 mm in-plane resolution. We demonstrate that high-resolution spiral fMRI at 7 T is not only feasible, but delivers both excellent image quality, BOLD sensitivity, and spatial specificity of the activation maps, with little artifactual blurring. Furthermore, we show the versatility of the approach with a combined in/out spiral readout at a more typical resolution (1.5 mm), where the high acquisition efficiency allows to acquire two images per shot for improved sensitivity by echo combination.
Collapse
|
23
|
Graedel NN, Kasper L, Engel M, Nussbaum J, Wilm BJ, Pruessmann KP, Vannesjo SJ. Feasibility of spiral fMRI based on an LTI gradient model. Neuroimage 2021; 245:118674. [PMID: 34718138 DOI: 10.1016/j.neuroimage.2021.118674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022] Open
Abstract
Spiral imaging is very well suited for functional MRI, however its use has been limited by the fact that artifacts caused by gradient imperfections and B0 inhomogeneity are more difficult to correct compared to EPI. Effective correction requires accurate knowledge of the traversed k-space trajectory. With the goal of making spiral fMRI more accessible, we have evaluated image reconstruction using trajectories predicted by the gradient impulse response function (GIRF), which can be determined in a one-time calibration step. GIRF-predicted reconstruction was tested for high-resolution (0.8 mm) fMRI at 7T. Image quality and functional results of the reconstructions using GIRF-prediction were compared to reconstructions using the nominal trajectory and concurrent field monitoring. The reconstructions using nominal spiral trajectories contain substantial artifacts and the activation maps contain misplaced activation. Image artifacts are substantially reduced when using the GIRF-predicted reconstruction, and the activation maps for the GIRF-predicted and monitored reconstructions largely overlap. The GIRF reconstruction provides a large increase in the spatial specificity of the activation compared to the nominal reconstruction. The GIRF-reconstruction generates image quality and fMRI results similar to using a concurrently monitored trajectory. The presented approach does not prolong or complicate the fMRI acquisition. Using GIRF-predicted trajectories has the potential to enable high-quality spiral fMRI in situations where concurrent trajectory monitoring is not available.
Collapse
Affiliation(s)
- Nadine N Graedel
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Lars Kasper
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland; Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Maria Engel
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Jennifer Nussbaum
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Bertram J Wilm
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Klaas P Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - S Johanna Vannesjo
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
24
|
Pipe JG, Borup DD. Generating spiral gradient waveforms with a compact frequency spectrum. Magn Reson Med 2021; 87:791-799. [PMID: 34519379 DOI: 10.1002/mrm.28993] [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: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/11/2022]
Abstract
PURPOSE To generate efficient gradient waveforms for spiral MRI which mitigate the high-frequency attenuation inherent in gradient systems. THEORY AND METHODS Spiral MRI has many clinical advantages, including high temporal and SNR efficiency. One of the challenges for robust spiral MRI is a high sensitivity to imperfections in the gradient system, which requires some form of correction in order to map data correctly in k-space. A previous numerical algorithm for generating spiral gradient waveforms was modified to reduce its high-frequency content with minimal increase in waveform duration. RESULTS Examples are shown of compact frequency gradient waveforms. Software implementing the algorithm is made available. CONCLUSION An algorithm to produce gradient waveforms with a compact frequency spectrum is described. This algorithm results in greatly reduced overall error and better compatibility with gradient systems than the original algorithm from which it was derived.
Collapse
Affiliation(s)
- James G Pipe
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | | |
Collapse
|
25
|
Sherwood MS, McIntire L, Madaris AT, Kim K, Ranganath C, McKinley RA. Intensity-Dependent Changes in Quantified Resting Cerebral Perfusion With Multiple Sessions of Transcranial DC Stimulation. Front Hum Neurosci 2021; 15:679977. [PMID: 34456695 PMCID: PMC8397582 DOI: 10.3389/fnhum.2021.679977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
Transcranial direct current stimulation (tDCS) to the left prefrontal cortex has been shown to produce broad behavioral effects including enhanced learning and vigilance. Still, the neural mechanisms underlying such effects are not fully understood. Furthermore, the neural underpinnings of repeated stimulation remain understudied. In this work, we evaluated the effects of the repetition and intensity of tDCS on cerebral perfusion [cerebral blood flow (CBF)]. A cohort of 47 subjects was randomly assigned to one of the three groups. tDCS of 1- or 2-mA was applied to the left prefrontal cortex on three consecutive days, and resting CBF was quantified before and after stimulation using the arterial spin labeling MRI and then compared with a group that received sham stimulation. A widespread decreased CBF was found in a group receiving sham stimulation across the three post-stimulation measures when compared with baseline. In contrast, only slight decreases were observed in the group receiving 2-mA stimulation in the second and third post-stimulation measurements, but more prominent increased CBF was observed across several brain regions including the locus coeruleus (LC). The LC is an integral region in the production of norepinephrine and the noradrenergic system, and an increased norepinephrine/noradrenergic activity could explain the various behavioral findings from the anodal prefrontal tDCS. A decreased CBF was observed in the 1-mA group across the first two post-stimulation measurements, similar to the sham group. This decreased CBF was apparent in only a few small clusters in the third post-stimulation scan but was accompanied by an increased CBF, indicating that the neural effects of stimulation may persist for at least 24 h and that the repeated stimulation may produce cumulative effects.
Collapse
Affiliation(s)
| | | | - Aaron T. Madaris
- Infoscitex, Inc., Beavercreek, OH, United States
- Department of Biomedical, Industrial and Human Factors Engineering, Wright State University, Dayton, OH, United States
| | - Kamin Kim
- Department of Psychology, University of California, Davis, Davis, CA, United States
| | - Charan Ranganath
- Department of Psychology, University of California, Davis, Davis, CA, United States
- Center for Neuroscience, University of California, Davis, Davis, CA, United States
| | - R. Andy McKinley
- Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH, United States
| |
Collapse
|
26
|
Stephens TM, Young IM, O'Neal CM, Dadario NB, Briggs RG, Teo C, Sughrue ME. Akinetic mutism reversed by inferior parietal lobule repetitive theta burst stimulation: Can we restore default mode network function for therapeutic benefit? Brain Behav 2021; 11:e02180. [PMID: 34145791 PMCID: PMC8413751 DOI: 10.1002/brb3.2180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/24/2021] [Accepted: 04/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcranial magnetic stimulation is a noninvasive treatment used to modulate cortical excitability. Its use over the last two decades has expanded, ranging from psychiatric disorders to traumatic brain injury and poststroke rehabilitation. OBJECTIVES We present the case of a 59-year-old male patient who presented in a decreased state of consciousness due to a right frontal glioblastoma, wherein his state was not improved by a successful surgery and could not be explained by any other condition. Due to his poor prognosis, we examine the benefits of receiving transcranial magnetic stimulation treatment to improve his akinetic mutism. METHODS We utilized independent component analysis with resting-state functional magnetic resonance imaging (rsfMRI) to better understand his cortical functionality. The imaging suggested absence of the default mode network (DMN). The patient underwent five sessions of navigated intermittent theta burst stimulation to the ipsilesional inferior parietal lobule and inferior frontal gyrus, with the aim of improving his default mode network functionality. RESULTS No other treatments resulted in an improvement of this patient's condition; however, 3 weeks following transcranial magnetic stimulation treatment, the patient was more alert and interactive, and his follow-up rsfMRI scan demonstrated a partially intact default mode network. CONCLUSION This case raises important questions regarding the clinical utility of transcranial magnetic stimulation to improve the connectivity of important cerebral networks and subsequent related functional recovery.
Collapse
Affiliation(s)
- Tressie M Stephens
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, Japan
| | | | - Christen M O'Neal
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, Japan
| | | | - Robert G Briggs
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, Japan
| | - Charles Teo
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Sydney, NSW, Australia
| | - Michael E Sughrue
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Sydney, NSW, Australia
| |
Collapse
|
27
|
Khajehim M, Christen T, Tam F, Graham SJ. Streamlined magnetic resonance fingerprinting: Fast whole-brain coverage with deep-learning based parameter estimation. Neuroimage 2021; 238:118237. [PMID: 34091035 DOI: 10.1016/j.neuroimage.2021.118237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/26/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
Magnetic resonance fingerprinting (MRF) is a quantitative MRI (qMRI) framework that provides simultaneous estimates of multiple relaxation parameters as well as metrics of field inhomogeneity in a single acquisition. However, current challenges exist in the forms of (1) scan time; (2) need for custom image reconstruction; (3) large dictionary sizes; (4) long dictionary-matching time. This study aims to introduce a novel streamlined magnetic-resonance fingerprinting (sMRF) framework based on a single-shot echo-planar imaging (EPI) sequence to simultaneously estimate tissue T1, T2, and T2* with integrated B1+ correction. Encouraged by recent work on EPI-based MRF, we developed a method that combines spin-echo EPI with gradient-echo EPI to achieve T2 in addition to T1 and T2* quantification. To this design, we add simultaneous multi-slice (SMS) acceleration to enable full-brain coverage in a few minutes. Moreover, in the parameter-estimation step, we use deep learning to train a deep neural network (DNN) to accelerate the estimation process by orders of magnitude. Notably, due to the high image quality of the EPI scans, the training process can rely simply on Bloch-simulated data. The DNN also removes the need for storing large dictionaries. Phantom scans along with in-vivo multi-slice scans from seven healthy volunteers were acquired with resolutions of 1.1×1.1×3 mm3 and 1.7×1.7×3 mm3, and the results were validated against ground truth measurements. Excellent correspondence was found between our T1, T2, and T2* estimates and results obtained from standard approaches. In the phantom scan, a strong linear relationship (R = 1-1.04, R2>0.96) was found for all parameter estimates, with a particularly high agreement for T2 estimation (R2>0.99). Similar findings are reported for the in-vivo human data for all of our parameter estimates. Incorporation of DNN results in a reduction of parameter estimation time on the order of 1000 x and a reduction in storage requirements on the order of 2500 x while achieving highly similar results as conventional dictionary matching (%differences of 7.4 ± 0.4%, 3.6 ± 0.3% and 6.0 ± 0.4% error in T1, T2, and T2* estimation). Thus, sMRF has the potential to be the method of choice for future MRF studies by providing ease of implementation, fast whole-brain coverage, and ultra-fast T1/T2/T2* estimation.
Collapse
Affiliation(s)
- Mahdi Khajehim
- Department of Medical Biophysics, University of Toronto, 101 College St Suite 15-701, Toronto, ON M5G 1L7, Canada.
| | - Thomas Christen
- Grenoble Institute of Neuroscience, Inserm, Grenoble, France
| | - Fred Tam
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Simon J Graham
- Department of Medical Biophysics, University of Toronto, 101 College St Suite 15-701, Toronto, ON M5G 1L7, Canada; Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, ON, Canada
| |
Collapse
|
28
|
Wang X, Wang Q, Zhang P, Qian S, Liu S, Liu DQ. Reducing Inter-Site Variability for Fluctuation Amplitude Metrics in Multisite Resting State BOLD-fMRI Data. Neuroinformatics 2021; 19:23-38. [PMID: 32285299 DOI: 10.1007/s12021-020-09463-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
It has been reported that resting state fluctuation amplitude (RSFA) exhibits extremely large inter-site variability, which limits its application in multisite studies. Although global normalization (GN) based approaches are efficient in reducing the site effects, they may cause spurious results. In this study, our purpose was to find alternative strategies to minimize the substantial site effects for RSFA, without the risk of introducing artificial findings. We firstly modified the ALFF algorithm so that it is conceptually validated and insensitive to data length, then found that (a) global mean amplitude of low-frequency fluctuation (ALFF) covaried only with BOLD signal intensity, while global mean fractional ALFF (fALFF) was significantly correlated with TRs across different sites; (b) The inter-site variations in raw RSFA values were significant across the entire brain and exhibited similar trends between gray matter and white matter; (c) For ALFF, signal intensity rescaling could dramatically reduce inter-site variability by several orders, but could not fully removed the globally distributed inter-site variability. For fALFF, the global site effects could be completely removed by TR controlling; (d) Meanwhile, the magnitude of the inter-site variability of fALFF could also be reduced to an acceptable level, as indicated by the detection power of fALFF in multisite data quite close to that in monosite data. Thus our findings suggest GN based harmonization methods could be replaced with only controlling for confounding factors including signal scaling, TR and full-band power.
Collapse
Affiliation(s)
- Xinbo Wang
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, 116029, China
| | - Qing Wang
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, 116029, China
| | - Peiwen Zhang
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, 116029, China
| | - Shufang Qian
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, 116029, China
| | - Shiyu Liu
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, 116029, China
| | - Dong-Qiang Liu
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, 116029, China.
| |
Collapse
|
29
|
Abstract
OBJECTIVE. The purpose of this article is to review currently available and emerging techniques for pediatric lung MRI for general radiologists. CONCLUSION. MRI is a radiation-free alternative to CT, and clearly understanding the strengths and limitations of established and emerging techniques of pediatric lung MRI can allow practitioners to select and combine the optimal techniques, apply them in clinical practice, and potentially improve early diagnostic accuracy and patient management.
Collapse
|
30
|
King LS, Camacho MC, Montez DF, Humphreys KL, Gotlib IH. Naturalistic Language Input is Associated with Resting-State Functional Connectivity in Infancy. J Neurosci 2021; 41:424-434. [PMID: 33257324 PMCID: PMC7821865 DOI: 10.1523/jneurosci.0779-20.2020] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/11/2020] [Accepted: 10/30/2020] [Indexed: 12/14/2022] Open
Abstract
The quantity and quality of the language input that infants receive from their caregivers affects their future language abilities; however, it is unclear how variation in this input relates to preverbal brain circuitry. The current study investigated the relation between naturalistic language input and the functional connectivity (FC) of language networks in human infancy using resting-state functional magnetic resonance imaging (rsfMRI). We recorded the naturalistic language environments of five- to eight-month-old male and female infants using the Linguistic ENvironment Analysis (LENA) system and measured the quantity and consistency of their exposure to adult words (AWs) and adult-infant conversational turns (CTs). Infants completed an rsfMRI scan during natural sleep, and we examined FC among regions of interest (ROIs) previously implicated in language comprehension, including the auditory cortex, the left inferior frontal gyrus (IFG), and the bilateral superior temporal gyrus (STG). Consistent with theory of the ontogeny of the cortical language network (Skeide and Friederici, 2016), we identified two subnetworks posited to have distinct developmental trajectories: a posterior temporal network involving connections of the auditory cortex and bilateral STG and a frontotemporal network involving connections of the left IFG. Independent of socioeconomic status (SES), the quantity of CTs was uniquely associated with FC of these networks. Infants who engaged in a larger number of CTs in daily life had lower connectivity in the posterior temporal language network. These results provide evidence for the role of vocal interactions with caregivers, compared with overheard adult speech, in the function of language networks in infancy.
Collapse
Affiliation(s)
- Lucy S King
- Department of Psychology, Stanford University, Stanford, California 94305
| | - M Catalina Camacho
- Division of Biology and Biomedical Science, Washington University in St. Louis, St. Louis, Missouri 63110
| | - David F Montez
- Department of Neurology, Washington University in St. Louis, St. Louis, Missouri 63110
| | - Kathryn L Humphreys
- Department of Psychology and Human Development, Vanderbilt University, Nashville, Tennessee 37235
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, California 94305
| |
Collapse
|
31
|
Criaud M, Kim JH, Zurowski M, Lobaugh N, Chavez S, Houle S, Strafella AP. Anxiety in Parkinson's disease: Abnormal resting activity and connectivity. Brain Res 2021; 1753:147235. [PMID: 33412150 DOI: 10.1016/j.brainres.2020.147235] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 11/19/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022]
Abstract
Anxiety is a very common yet poorly understood symptom of Parkinson's disease. We investigated whether Parkinson's disease patients experiencing anxiety share neural mechanisms described in the general population with involvement of critical regions for the control of behaviour and movement. Thirty-nine patients with PD were recruited for this study, 20 with higher anxiety scores and 19 with lower anxiety scores. They all underwent a resting-state fMRI scan, while they were on medication. The amplitude of low-frequency fluctuation (ALFF) and seed-based connectivity were investigated to reveal the changes of the spontaneous activity and the interaction among different related regions. The results provided evidence that anxiety in Parkinson's disease is associated with the over-activation of the amygdala and impaired inter-relationship of regions involved in behavior (i.e. medial prefrontal cortex, insula) and motor control (i.e. basal ganglia).
Collapse
Affiliation(s)
- Marion Criaud
- Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada; Division of Brain, Imaging and Behaviour - Systems Neuroscience, Krembil Research Institute, UHN, University of Toronto, Ontario, Canada.
| | - Jin-Hee Kim
- Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada; Division of Brain, Imaging and Behaviour - Systems Neuroscience, Krembil Research Institute, UHN, University of Toronto, Ontario, Canada
| | - Mateusz Zurowski
- Division of Brain, Imaging and Behaviour - Systems Neuroscience, Krembil Research Institute, UHN, University of Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Ontario, Canada
| | - Nancy Lobaugh
- Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada; Division of Neurology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sofia Chavez
- Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada
| | - Sylvain Houle
- Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada
| | - Antonio P Strafella
- Morton and Gloria Shulman Movement Disorder Unit & E.J. Safra Parkinson Disease Program, Toronto Western Hospital, UHN, University of Toronto, Ontario, Canada; Research Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada; Division of Brain, Imaging and Behaviour - Systems Neuroscience, Krembil Research Institute, UHN, University of Toronto, Ontario, Canada; Division of Neurology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
32
|
Lee DH. Editorial for "Whole-Slab 3D MR Spectroscopic Imaging of the Human Brain With Spiral-Out-In Sampling at 7T". J Magn Reson Imaging 2020; 53:1251-1252. [PMID: 33190358 DOI: 10.1002/jmri.27443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Dong-Hoon Lee
- Department of Radiation Convergence Engineering, College of Health Sciences, Yonsei University, Wonju, Republic of Korea
| |
Collapse
|
33
|
Dehghani H, Oghabian MA, Batouli SAH, Arab Kheradmand J, Khatibi A. Effect of Physiological Noise on Thoracolumbar Spinal Cord Functional Magnetic Resonance Imaging in 3T Magnetic Field. Basic Clin Neurosci 2020; 11:737-751. [PMID: 33850611 PMCID: PMC8019845 DOI: 10.32598/bcn.11.6.1395.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/10/2018] [Accepted: 02/19/2019] [Indexed: 11/20/2022] Open
Abstract
Introduction: Functional Magnetic Resonance Imaging (fMRI) methods have been used to study sensorimotor processing in the spinal cord. However, these techniques confront unwanted noises to the measured signal from the physiological fluctuations. In the spinal cord imaging, most of the challenges are consequences of cardiac and respiratory movement artifacts that are considered as significant sources of noise, especially in the thoracolumbar region. In this study, we investigated the effect of each source of physiological noise and their contribution to the outcome of the analysis of the blood-oxygen-level-dependent signal in the human thoracolumbar spinal cord. Methods: Fifteen young healthy male volunteers participated in the study, and pain stimuli were delivered on the L5 dermatome between the two malleoli. Respiratory and cardiac signals were recorded during the imaging session, and the generated respiration and cardiac regressors were included in the general linear model for quantification of the effect of each of them on the task-analysis results. The sum of active voxels of the clusters was calculated in the spinal cord in three correction states (respiration correction only, cardiac correction only, and respiration and cardiac noise corrections) and analyzed with analysis of variance statistical test and receiver operating characteristic curve. Results: The results illustrated that cardiac noise correction had an effective role in increasing the active voxels (Mean±SD = 23.46±9.46) compared to other noise correction methods. Cardiac effects were higher than other physiological noise sources Conclusion: In summary, our results indicate great respiration effects on the lumbar and thoracolumbar spinal cord fMRI, and its contribution to the heartbeat effect can be a significant variable in the individual fMRI data analysis. Displacement of the spinal cord and the effects of this noise in the thoracolumbar and lumbar spinal cord fMRI results are significant and cannot be ignored.
Collapse
Affiliation(s)
- Hamed Dehghani
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Tehran University of Medical Science, Tehran, Iran.,Research Center for Molecular and Cellular Imaging (RCMCI), Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oghabian
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Tehran University of Medical Science, Tehran, Iran.,Research Center for Molecular and Cellular Imaging (RCMCI), Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Amir Hosein Batouli
- Research Center for Molecular and Cellular Imaging (RCMCI), Tehran University of Medical Sciences, Tehran, Iran.,Department of Neuroscience, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalil Arab Kheradmand
- Shefa Neuroscience Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Khatibi
- Centre of Precision Rehabilitation for Spinal Pain (CPR Spine), School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Birmingham, United Kingdom.,Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
34
|
Greve T, Sollmann N, Hock A, Zimmer C, Kirschke JS. Novel Ultrafast Spiral Head MR Angiography Compared to Standard MR and CT Angiography. J Neuroimaging 2020; 31:45-56. [PMID: 33118692 DOI: 10.1111/jon.12791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND AND PURPOSE Intracranial vessel imaging by time-of-flight MR angiography (TOF-MRA) is one of the most frequently performed investigations in clinical neuroradiology. Particularly in the acute setting, fast imaging is needed for diagnostics, with a sequence ideally depicting even small vessels. The purpose of this study was to compare image and diagnostic quality of a novel ultrashort TOF-MRA sequence accelerated by spiral imaging (TOF-Spiral-short) to a standard TOF-MRA sequence accelerated by compressed sensing (TOF-CS) and to CT angiography (CTA). METHODS Forty-one patients (36.6% showing vessel pathologies) who had undergone TOF-CS (acquisition duration: 4 minutes 8 seconds), TOF-Spiral-short (acquisition duration: 51 seconds; spiral imaging [accelerating factor 1.3], decreased field of view [accelerating factor 1.2], and increased voxel size [accelerating factor 3.3]), and CTA were retrospectively evaluated. Assessment of image quality, diagnostic confidence, and quantification of stenosis or aneurysm diameter were performed by two readers. RESULTS Image quality at the skull base was slightly reduced with TOF-Spiral-short compared to CTA and TOF-CS (P < .05). Delineation of small intracranial vessels was improved by TOF-Spiral-short compared to CTA (P < .0001). In TOF-Spiral-short, diagnostic confidence was not reduced compared to TOF-CS in patients with vessel pathologies. We observed no significant difference in quantitative pathology assessment between TOF-Spiral-short and the other two modalities. TOF-Spiral-short enabled the correct identification of all vessel pathologies. CONCLUSIONS Accelerating TOF-MRA of brain-feeding arteries by a novel ultrashort spiral imaging sequence shows adequate image quality and sufficient diagnostic performance. Thus, TOF-Spiral-short holds potential for fast and reliable diagnostics of vessel pathologies, particularly in the acute setting.
Collapse
Affiliation(s)
- Tobias Greve
- Department of Diagnostic and Interventional Neuroradiology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,Department of Neurosurgery, University Hospital, Ludwig-Maximilians-University, Campus Grosshadern, Munich, Germany
| | - Nico Sollmann
- Department of Diagnostic and Interventional Neuroradiology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,TUM-Neuroimaging Center, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Andreas Hock
- Health Systems Philips Switzerland, Horgen, Switzerland
| | - Claus Zimmer
- Department of Diagnostic and Interventional Neuroradiology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,TUM-Neuroimaging Center, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jan S Kirschke
- Department of Diagnostic and Interventional Neuroradiology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,TUM-Neuroimaging Center, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| |
Collapse
|
35
|
Bollmann S, Barth M. New acquisition techniques and their prospects for the achievable resolution of fMRI. Prog Neurobiol 2020; 207:101936. [PMID: 33130229 DOI: 10.1016/j.pneurobio.2020.101936] [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: 05/15/2020] [Revised: 09/10/2020] [Accepted: 10/18/2020] [Indexed: 01/17/2023]
Abstract
This work reviews recent advances in technologies for functional magnetic resonance imaging (fMRI) of the human brain and highlights the push for higher functional specificity based on increased spatial resolution and specific MR contrasts to reveal previously undetectable functional properties of small-scale cortical structures. We discuss how the combination of MR hardware, advanced acquisition techniques and various MR contrast mechanisms have enabled recent progress in functional neuroimaging. However, these advanced fMRI practices have only been applied to a handful of neuroscience questions to date, with the majority of the neuroscience community still using conventional imaging techniques. We thus discuss upcoming challenges and possibilities for fMRI technology development in human neuroscience. We hope that readers interested in functional brain imaging acquire an understanding of current and novel developments and potential future applications, even if they don't have a background in MR physics or engineering. We summarize the capabilities of standard fMRI acquisition schemes with pointers to relevant literature and comprehensive reviews and introduce more recent developments.
Collapse
Affiliation(s)
- Saskia Bollmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
| | - Markus Barth
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia; School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Australia; ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
36
|
Han C, Ress D, Ramos Nunez AI, de la Rosa N, Li S, Sulzer JS. Brainstem BOLD response to visual and acoustic stimuli. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2020:2889-2892. [PMID: 33018610 DOI: 10.1109/embc44109.2020.9175794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Understanding the fundamental roles of brainstem function resulting in proper motor control is critical to motor-rehabilitation after brain injuries. In particular, vestibular and reticular formation nuclei are thought to be associated with spasticity in chronic stroke patients. We used two kinds of stimuli in 10 healthy subjects to activate these nuclei while collecting high-resolution (1.5-mm) fMRI across the majority of brainstem. Optokinetic stimuli evoked illusory self-motion to activate the vestibular nuclei. Acoustic-startle stimuli were sets of loud tones designed to activate of the reticular formation. We summarized the response represented in a form of activation volume, mean percent signal change, and the phase delay (time lag) following the stimulus. We observed patterns of significant activations in the brainstem but did not find significant differences between the stimulus. We conclude that more sensitive measurement techniques are needed to reliably detect vestibular and reticular formation nuclei responses.
Collapse
|
37
|
Sharma S, Coutino M, Chepuri SP, Leus G, Hari KVS. Towards a general framework for fast and feasible k-space trajectories for MRI based on projection methods. Magn Reson Imaging 2020; 72:122-134. [PMID: 32668272 DOI: 10.1016/j.mri.2020.06.016] [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: 02/20/2020] [Revised: 06/11/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
The design of feasible trajectories to traverse the k-space for sampling in magnetic resonance imaging (MRI) is important while considering ways to reduce the scan time. Over the recent years, non-Cartesian trajectories have been observed to result in benign artifacts and being less sensitive to motion. In this paper, we propose a generalized framework that encompasses projection-based methods to generate feasible non-Cartesian k-space trajectories. This framework allows to construct feasible trajectories from both random or structured initial trajectories, e.g., based on the traveling salesman problem (TSP). We evaluate the performance of the proposed methods by simulating the reconstruction of 128 × 128 and 256 × 256 phantom and brain MRI images in terms of structural similarity (SSIM) index and peak signal-to-noise ratio (PSNR) using compressed sensing techniques. It is observed that the TSP-based trajectories from the proposed projection method with constant acceleration parameterization (CAP) result in better reconstruction compared to the projection method with constant velocity parameterization (CVP) and this for a similar read-out time. Further, random-like trajectories are observed to be better than TSP-based trajectories as they reduce the read-out time while providing better reconstruction quality. A reduction in read-out time by upto 67% is achieved using the proposed projection with permutation (PP) method.
Collapse
Affiliation(s)
- Shubham Sharma
- Department of Electrical Communication Engineering, Indian Institute of Science, Bangalore, India.
| | - Mario Coutino
- Department of Microelectronics, Delft University of Technology, Netherlands
| | | | - Geert Leus
- Department of Microelectronics, Delft University of Technology, Netherlands
| | - K V S Hari
- Department of Electrical Communication Engineering, Indian Institute of Science, Bangalore, India
| |
Collapse
|
38
|
Deep residual network for highly accelerated fMRI reconstruction using variable density spiral trajectory. Neurocomputing 2020. [DOI: 10.1016/j.neucom.2019.02.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
39
|
Moeller S, Pisharady Kumar P, Andersson J, Akcakaya M, Harel N, Ma RE, Wu X, Yacoub E, Lenglet C, Ugurbil K. Diffusion Imaging in the Post HCP Era. J Magn Reson Imaging 2020; 54:36-57. [PMID: 32562456 DOI: 10.1002/jmri.27247] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
Diffusion imaging is a critical component in the pursuit of developing a better understanding of the human brain. Recent technical advances promise enabling the advancement in the quality of data that can be obtained. In this review the context for different approaches relative to the Human Connectome Project are compared. Significant new gains are anticipated from the use of high-performance head gradients. These gains can be particularly large when the high-performance gradients are employed together with ultrahigh magnetic fields. Transmit array designs are critical in realizing high accelerations in diffusion-weighted (d)MRI acquisitions, while maintaining large field of view (FOV) coverage, and several techniques for optimal signal-encoding are now available. Reconstruction and processing pipelines that precisely disentangle the acquired neuroanatomical information are established and provide the foundation for the application of deep learning in the advancement of dMRI for complex tissues. Level of Evidence: 3 Technical Efficacy Stage: Stage 3.
Collapse
Affiliation(s)
- Steen Moeller
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Pramod Pisharady Kumar
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jesper Andersson
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Mehmet Akcakaya
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA.,Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Noam Harel
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ruoyun Emily Ma
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Xiaoping Wu
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Essa Yacoub
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christophe Lenglet
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kamil Ugurbil
- Center for Magnetic Resonance Research; Department of Radiology, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
40
|
Ooi MB, Li Z, Robison RK, Wang D, Anderson AG, Zwart NR, Bakhru A, Nagaraj S, Mathews T, Hey S, Koonen JJ, Dimitrov IE, Friel HT, Lu Q, Obara M, Saha I, Wang H, Wang Y, Zhao Y, Temkit M, Hu HH, Chenevert TL, Togao O, Tkach JA, Nagaraj UD, Pinho MC, Gupta RK, Small JE, Kunst MM, Karis JP, Andre JB, Miller JH, Pinter NK, Pipe JG. Spiral T1 Spin-Echo for Routine Postcontrast Brain MRI Exams: A Multicenter Multireader Clinical Evaluation. AJNR Am J Neuroradiol 2020; 41:238-245. [PMID: 32029467 DOI: 10.3174/ajnr.a6409] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/10/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND AND PURPOSE Spiral MR imaging has several advantages compared with Cartesian MR imaging that can be leveraged for added clinical value. A multicenter multireader study was designed to compare spiral with standard-of-care Cartesian postcontrast structural brain MR imaging on the basis of relative performance in 10 metrics of image quality, artifact prevalence, and diagnostic benefit. MATERIALS AND METHODS Seven clinical sites acquired 88 total subjects. For each subject, sites acquired 2 postcontrast MR imaging scans: a spiral 2D T1 spin-echo, and 1 of 4 routine Cartesian 2D T1 spin-echo/TSE scans (fully sampled spin-echo at 3T, 1.5T, partial Fourier, TSE). The spiral acquisition matched the Cartesian scan for scan time, geometry, and contrast. Nine neuroradiologists independently reviewed each subject, with the matching pair of spiral and Cartesian scans compared side-by-side, and scored on 10 image-quality metrics (5-point Likert scale) focused on intracranial assessment. The Wilcoxon signed rank test evaluated relative performance of spiral versus Cartesian, while the Kruskal-Wallis test assessed interprotocol differences. RESULTS Spiral was superior to Cartesian in 7 of 10 metrics (flow artifact mitigation, SNR, GM/WM contrast, image sharpness, lesion conspicuity, preference for diagnosing abnormal enhancement, and overall intracranial image quality), comparable in 1 of 10 metrics (motion artifacts), and inferior in 2 of 10 metrics (susceptibility artifacts, overall extracranial image quality) related to magnetic susceptibility (P < .05). Interprotocol comparison confirmed relatively higher SNR and GM/WM contrast for partial Fourier and TSE protocol groups, respectively (P < .05). CONCLUSIONS Spiral 2D T1 spin-echo for routine structural brain MR imaging is feasible in the clinic with conventional scanners and was preferred by neuroradiologists for overall postcontrast intracranial evaluation.
Collapse
Affiliation(s)
- M B Ooi
- From Philips Healthcare (M.B.O., I.E.D., H.T.F., Q.L., H.W., Y.W., Y.Z.)
| | - Z Li
- Gainesville, Florida; Barrow Neurological Institute (Z.L., A.G.A., N.R.Z., J.P.K.)
| | - R K Robison
- Rochester, Minnesota; Phoenix Children's Hospital (R.K.R., M.T., H.H.H., J.H.M.)
| | - D Wang
- Phoenix, Arizona; Mayo Clinic (D.W., J.G.P.)
| | - A G Anderson
- Gainesville, Florida; Barrow Neurological Institute (Z.L., A.G.A., N.R.Z., J.P.K.)
| | - N R Zwart
- Gainesville, Florida; Barrow Neurological Institute (Z.L., A.G.A., N.R.Z., J.P.K.)
| | - A Bakhru
- Buffalo, New York; Philips Healthcare (A.B., S.N., T.M.)
| | - S Nagaraj
- Buffalo, New York; Philips Healthcare (A.B., S.N., T.M.)
| | - T Mathews
- Buffalo, New York; Philips Healthcare (A.B., S.N., T.M.)
| | - S Hey
- Bangalore, India; Philips Healthcare, (S.H., J.J.K.), Best, the Netherlands
| | - J J Koonen
- Bangalore, India; Philips Healthcare, (S.H., J.J.K.), Best, the Netherlands
| | - I E Dimitrov
- From Philips Healthcare (M.B.O., I.E.D., H.T.F., Q.L., H.W., Y.W., Y.Z.)
| | - H T Friel
- From Philips Healthcare (M.B.O., I.E.D., H.T.F., Q.L., H.W., Y.W., Y.Z.)
| | - Q Lu
- From Philips Healthcare (M.B.O., I.E.D., H.T.F., Q.L., H.W., Y.W., Y.Z.)
| | - M Obara
- Philips Healthcare (M.O.), Tokyo, Japan
| | - I Saha
- Philips Healthcare (I.S.), Gurgaon, India
| | - H Wang
- From Philips Healthcare (M.B.O., I.E.D., H.T.F., Q.L., H.W., Y.W., Y.Z.)
| | - Y Wang
- From Philips Healthcare (M.B.O., I.E.D., H.T.F., Q.L., H.W., Y.W., Y.Z.)
| | - Y Zhao
- From Philips Healthcare (M.B.O., I.E.D., H.T.F., Q.L., H.W., Y.W., Y.Z.)
| | - M Temkit
- Rochester, Minnesota; Phoenix Children's Hospital (R.K.R., M.T., H.H.H., J.H.M.)
| | - H H Hu
- Rochester, Minnesota; Phoenix Children's Hospital (R.K.R., M.T., H.H.H., J.H.M.)
| | - T L Chenevert
- University of Michigan (T.L.C.), Ann Arbor, Michigan
| | - O Togao
- Kyushu University Hospital (O.T.), Kyushu, Japan
| | - J A Tkach
- Cincinnati Children's Hospital (J.A.T., U.D.N.), Cincinnati, Ohio
| | - U D Nagaraj
- Cincinnati Children's Hospital (J.A.T., U.D.N.), Cincinnati, Ohio
| | - M C Pinho
- University of Texas Southwestern Medical Center (M.C.P.), Dallas, Texas
| | - R K Gupta
- Fortis Memorial Research Institute (R.K.G.), Gurgaon, India
| | - J E Small
- Lahey Hospital and Medical Center (J.E.S., M.M.K.), Burlington, Massachusetts
| | - M M Kunst
- Lahey Hospital and Medical Center (J.E.S., M.M.K.), Burlington, Massachusetts
| | - J P Karis
- Gainesville, Florida; Barrow Neurological Institute (Z.L., A.G.A., N.R.Z., J.P.K.)
| | - J B Andre
- University of Washington (J.B.A.), Seattle, Washington
| | - J H Miller
- Rochester, Minnesota; Phoenix Children's Hospital (R.K.R., M.T., H.H.H., J.H.M.)
| | - N K Pinter
- Phoenix, Arizona; DENT Neurologic Institute (N.K.P.)
| | - J G Pipe
- Phoenix, Arizona; Mayo Clinic (D.W., J.G.P.)
| |
Collapse
|
41
|
Gupta CN, Turner JA, Calhoun VD. Source-based morphometry: a decade of covarying structural brain patterns. Brain Struct Funct 2019; 224:3031-3044. [PMID: 31701266 DOI: 10.1007/s00429-019-01969-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/16/2019] [Indexed: 12/24/2022]
Abstract
In this paper, we review and discuss brain imaging studies which have used the source-based morphometry (SBM) approach over the past decade. SBM is a data-driven linear multivariate approach for decomposing structural brain imaging data into commonly covarying imaging components and subject-specific loading parameters. It is a well-established technique which has predominantly been used to study neuroanatomic differences between healthy controls and patients with neuropsychiatric diseases. We start by discussing the advantages of this technique over univariate analysis for imaging studies, followed by a discussion of results from recent studies which have successfully applied this methodology. We also present recent extensions of this framework including nonlinear SBM, biclustered independent component analysis (B-ICA) and conclude with the possible directions of work for future.
Collapse
Affiliation(s)
- Cota Navin Gupta
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, US.
- Neural Engineering Lab, Department of Biosciences and Bioengineering (BSBE), Indian Institute of Technology Guwahati, Guwahati, India.
| | - Jessica A Turner
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, US
- Department of Psychology and Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, US
- Department of Psychology and Neuroscience Institute, Georgia State University, Atlanta, GA, USA
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, USA
| |
Collapse
|
42
|
O'Neil EB, Lee ACH. Examining the representational content of perirhinal cortex and posterior ventral visual pathway regions when maintenance of visual information is interrupted. Cortex 2019; 121:16-26. [PMID: 31539829 DOI: 10.1016/j.cortex.2019.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 11/30/2022]
Abstract
The perirhinal cortex (PRC) is known to support recognition memory, working memory, and perception for objects. Often, information must be maintained in working memory in the face of ongoing visual perception, raising the question of how PRC and other regions supporting object representation deal with this conflict. Here, we used functional MRI to examine the representational content of human ventral visual pathway (VVP) regions, including perirhinal cortex (PRC), during a visual delayed match-to-sample task. Critically, interfering items from a different stimulus category to the target were presented to participants during the maintenance phase, creating conflict between the contents of working memory and ongoing perception. Using representational similarity analysis, we compared information content across study, interference and test phases to models that differed in the extent to which they predicted that information content would be maintained during the delay period and perturbed by interference. This revealed that lateral occipital and fusiform regions are best fit by models that reflect the stimulus content of the item currently being viewed, whereas PRC reflects the information content of the studied item, even when an interfering stimulus is presented during the delay. This division of labor within the VVP sheds light on the specialized nature of representations in VVP regions, including PRC. Our findings support a representational hierarchical understanding of medial temporal lobe function which posits that representations at the most anterior aspect of the VVP are more robust to ongoing perceptual activity.
Collapse
Affiliation(s)
- Edward B O'Neil
- Department of Psychology (Scarborough), University of Toronto, Toronto, Canada.
| | - Andy C H Lee
- Department of Psychology (Scarborough), University of Toronto, Toronto, Canada; Rotman Research Institute, Baycrest Centre, Toronto, Ontario, Canada
| |
Collapse
|
43
|
van Zijl P, Knutsson L. In vivo magnetic resonance imaging and spectroscopy. Technological advances and opportunities for applications continue to abound. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:55-65. [PMID: 31377150 PMCID: PMC6703925 DOI: 10.1016/j.jmr.2019.07.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/19/2019] [Accepted: 07/08/2019] [Indexed: 05/07/2023]
Abstract
Over the past decades, the field of in vivo magnetic resonance (MR) has built up an impressive repertoire of data acquisition and analysis technologies for anatomical, functional, physiological, and molecular imaging, the description of which requires many book volumes. As such it is impossible for a few authors to have an authoritative overview of the field and for a brief article to be inclusive. We will therefore focus mainly on data acquisition and attempt to give some insight into the principles underlying current advanced methods in the field and the potential for further innovation. In our view, the foreseeable future is expected to show continued rapid progress, for instance in imaging of microscopic tissue properties in vivo, assessment of functional and anatomical connectivity, higher resolution physiologic and metabolic imaging, and even imaging of receptor binding. In addition, acquisition speed and information content will continue to increase due to the continuous development of approaches for parallel imaging (including simultaneous multi-slice imaging), compressed sensing, and MRI fingerprinting. Finally, artificial intelligence approaches are becoming more realistic and will have a tremendous effect on both acquisition and analysis strategies. Together, these developments will continue to provide opportunity for scientific discovery and, in combination with large data sets from other fields such as genomics, allow the ultimate realization of precision medicine in the clinic.
Collapse
Affiliation(s)
- Peter van Zijl
- Department of Radiology, Johns Hopkins University, F.M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA.
| | - Linda Knutsson
- Department of Medical Radiation Physics, Lund University, Lund, Sweden
| |
Collapse
|
44
|
Maknojia S, Churchill NW, Schweizer TA, Graham SJ. Resting State fMRI: Going Through the Motions. Front Neurosci 2019; 13:825. [PMID: 31456656 PMCID: PMC6700228 DOI: 10.3389/fnins.2019.00825] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/23/2019] [Indexed: 11/19/2022] Open
Abstract
Resting state functional magnetic resonance imaging (rs-fMRI) has become an indispensable tool in neuroscience research. Despite this, rs-fMRI signals are easily contaminated by artifacts arising from movement of the head during data collection. The artifacts can be problematic even for motions on the millimeter scale, with complex spatiotemporal properties that can lead to substantial errors in functional connectivity estimates. Effective correction methods must be employed, therefore, to distinguish true functional networks from motion-related noise. Research over the last three decades has produced numerous correction methods, many of which must be applied in combination to achieve satisfactory data quality. Subject instruction, training, and mild restraints are helpful at the outset, but usually insufficient. Improvements come from applying multiple motion correction algorithms retrospectively after rs-fMRI data are collected, although residual artifacts can still remain in cases of elevated motion, which are especially prevalent in patient populations. Although not commonly adopted at present, “real-time” correction methods are emerging that can be combined with retrospective methods and that promise better correction and increased rs-fMRI signal sensitivity. While the search for the ideal motion correction protocol continues, rs-fMRI research will benefit from good disclosure practices, such as: (1) reporting motion-related quality control metrics to provide better comparison between studies; and (2) including motion covariates in group-level analyses to limit the extent of motion-related confounds when studying group differences.
Collapse
Affiliation(s)
- Sanam Maknojia
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Nathan W Churchill
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Tom A Schweizer
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.,Division of Neurosurgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Institute of Biomaterials and Biomedical Engineering, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - S J Graham
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
45
|
Ilovitsh A, Fite BZ, Ilovitsh T, Ferrara KW. Acoustic radiation force imaging using a single-shot spiral readout. Phys Med Biol 2019; 64:125004. [PMID: 31039549 DOI: 10.1088/1361-6560/ab1e21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The purpose of this study is to develop and validate rapid magnetic resonance acoustic radiation force imaging (MR-ARFI) using a single shot spiral readout for focused ultrasound (FUS) guidance and for local tissue displacement measurements. A magnetic resonance guided FUS system was used to focus a 3 MHz ultrasound beam to a predetermined position. MR-ARFI was performed with a Bruker 7 T MRI using a modified single-shot spiral readout, with additional motion encoding gradients that convert local displacement into the phase image. Post processing was then used to analyze the resulting displacement and to evaluate the method's performance for the detection of tissue changes resulting from thermal ablation. The single-shot spiral readout acquires a single MR-ARFI image in one second, which is up to two orders of magnitude faster than conventional 2D spin-warp spin echo that acquires the k-space data line by line. The ARFI displacement in tissue mimicking phantoms was detected and localized with less than 5% geometric distortion. The ARFI displacement was also measured pre and post thermal ablation in an ex vivo chicken breast. For transmitted peak negative pressure of 8.6 MPa, the maximum displacement of the tissue that was ablated to 70 °C was 78% lower than the pre-ablated tissue. Since spiral readout is not prone to geometrical distortion, it is well-suited for FUS guidance, without generating undesired temperature elevation. Additionally, local displacement measurements of tissues can be performed rapidly during thermal ablation procedures and may help to assess the success of the treatment.
Collapse
Affiliation(s)
- Asaf Ilovitsh
- Department of Radiology, Stanford University, Palo Alto, CA 94305, United States of America
| | | | | | | |
Collapse
|
46
|
Zeng DY, Shaikh J, Holmes S, Brunsing RL, Pauly JM, Nishimura DG, Vasanawala SS, Cheng JY. Deep residual network for off-resonance artifact correction with application to pediatric body MRA with 3D cones. Magn Reson Med 2019; 82:1398-1411. [PMID: 31115936 DOI: 10.1002/mrm.27825] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023]
Abstract
PURPOSE To enable rapid imaging with a scan time-efficient 3D cones trajectory with a deep-learning off-resonance artifact correction technique. METHODS A residual convolutional neural network to correct off-resonance artifacts (Off-ResNet) was trained with a prospective study of pediatric MRA exams. Each exam acquired a short readout scan (1.18 ms ± 0.38) and a long readout scan (3.35 ms ± 0.74) at 3 T. Short readout scans, with longer scan times but negligible off-resonance blurring, were used as reference images and augmented with additional off-resonance for supervised training examples. Long readout scans, with greater off-resonance artifacts but shorter scan time, were corrected by autofocus and Off-ResNet and compared with short readout scans by normalized RMS error, structural similarity index, and peak SNR. Scans were also compared by scoring on 8 anatomical features by two radiologists, using analysis of variance with post hoc Tukey's test and two one-sided t-tests. Reader agreement was determined with intraclass correlation. RESULTS The total scan time for long readout scans was on average 59.3% shorter than short readout scans. Images from Off-ResNet had superior normalized RMS error, structural similarity index, and peak SNR compared with uncorrected images across ±1 kHz off-resonance (P < .01). The proposed method had superior normalized RMS error over -677 Hz to +1 kHz and superior structural similarity index and peak SNR over ±1 kHz compared with autofocus (P < .01). Radiologic scoring demonstrated that long readout scans corrected with Off-ResNet were noninferior to short readout scans (P < .05). CONCLUSION The proposed method can correct off-resonance artifacts from rapid long-readout 3D cones scans to a noninferior image quality compared with diagnostically standard short readout scans.
Collapse
Affiliation(s)
- David Y Zeng
- Department of Electrical Engineering, Stanford University, Stanford, California
| | - Jamil Shaikh
- Department of Radiology, Stanford University, Stanford, California
| | - Signy Holmes
- Department of Radiology, Stanford University, Stanford, California
| | - Ryan L Brunsing
- Department of Radiology, Stanford University, Stanford, California
| | - John M Pauly
- Department of Electrical Engineering, Stanford University, Stanford, California
| | - Dwight G Nishimura
- Department of Electrical Engineering, Stanford University, Stanford, California
| | | | - Joseph Y Cheng
- Department of Radiology, Stanford University, Stanford, California
| |
Collapse
|
47
|
Sherwood MS, Parker JG, Diller EE, Ganapathy S, Bennett KB, Esquivel CR, Nelson JT. Self-directed down-regulation of auditory cortex activity mediated by real-time fMRI neurofeedback augments attentional processes, resting cerebral perfusion, and auditory activation. Neuroimage 2019; 195:475-489. [PMID: 30954710 DOI: 10.1016/j.neuroimage.2019.03.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/23/2019] [Accepted: 03/31/2019] [Indexed: 12/18/2022] Open
Abstract
In this work, we investigated the use of real-time functional magnetic resonance imaging (fMRI) with neurofeedback training (NFT) to teach volitional down-regulation of the auditory cortex (AC) using directed attention strategies as there is a growing interest in the application of fMRI-NFT to treat neurologic disorders. Healthy participants were separated into two groups: the experimental group received real feedback regarding activity in the AC; the control group was supplied sham feedback yoked from a random participant in the experimental group and matched for fMRI-NFT experience. Each participant underwent five fMRI-NFT sessions. Each session contained 2 neurofeedback runs where participants completed alternating blocks of "rest" and "lower" conditions while viewing a continuously-updated bar representing AC activation and listening to continuous noise. Average AC deactivation was extracted from each closed-loop neuromodulation run and used to quantify the control over AC (AC control), which was found to significantly increase across training in the experimental group. Additionally, behavioral testing was completed outside of the MRI on sessions 1 and 5 consisting of a subjective questionnaire to assess attentional control and two quantitative tests of attention. No significant changes in behavior were observed; however, there was a significant correlation between changes in AC control and attentional control. Also, in a neural assessment before and after fMRI-NFT, AC activity in response to continuous noise stimulation was found to significantly decrease across training while changes in AC resting perfusion were found to be significantly greater in the experimental group. These results may be useful in formulating effective therapies outside of the MRI, specifically for chronic tinnitus which is often characterized by hyperactivity of the primary auditory cortex and altered attentional processes. Furthermore, the modulation of attention may be useful in developing therapies for other disorders such as chronic pain.
Collapse
Affiliation(s)
- Matthew S Sherwood
- Department of Biomedical, Industrial & Human Factors Engineering, Wright State University, Dayton, OH, USA.
| | - Jason G Parker
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indiana University, IN, USA
| | - Emily E Diller
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indiana University, IN, USA; College of Health and Human Services, Purdue University, West Lafayette, IN, USA
| | - Subhashini Ganapathy
- Department of Biomedical, Industrial & Human Factors Engineering, Wright State University, Dayton, OH, USA; Department of Trauma Care, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Kevin B Bennett
- Department of Psychology, Wright State University, Dayton, OH, USA
| | - Carlos R Esquivel
- Department of Defense Hearing Center of Excellence, JBSA-Lackland, USA
| | - Jeremy T Nelson
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indiana University, IN, USA; Department of Defense Hearing Center of Excellence, JBSA-Lackland, USA; Ho-Chunk Inc., Alexandria, VA, USA
| |
Collapse
|
48
|
Huotari N, Raitamaa L, Helakari H, Kananen J, Raatikainen V, Rasila A, Tuovinen T, Kantola J, Borchardt V, Kiviniemi VJ, Korhonen VO. Sampling Rate Effects on Resting State fMRI Metrics. Front Neurosci 2019; 13:279. [PMID: 31001071 PMCID: PMC6454039 DOI: 10.3389/fnins.2019.00279] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/08/2019] [Indexed: 01/21/2023] Open
Abstract
Low image sampling rates used in resting state functional magnetic resonance imaging (rs-fMRI) may cause aliasing of the cardiorespiratory pulsations over the very low frequency (VLF) BOLD signal fluctuations which reflects to functional connectivity (FC). In this study, we examine the effect of sampling rate on currently used rs-fMRI FC metrics. Ultra-fast fMRI magnetic resonance encephalography (MREG) data, sampled with TR 0.1 s, was downsampled to different subsampled repetition times (sTR, range 0.3–3 s) for comparisons. Echo planar k-space sampling (TR 2.15 s) and interleaved slice collection schemes were also compared against the 3D single shot trajectory at 2.2 s sTR. The quantified connectivity metrics included stationary spatial, time, and frequency domains, as well as dynamic analyses. Time domain methods included analyses of seed-based functional connectivity, regional homogeneity (ReHo), coefficient of variation, and spatial domain group level probabilistic independent component analysis (ICA). In frequency domain analyses, we examined fractional and amplitude of low frequency fluctuations. Aliasing effects were spatially and spectrally analyzed by comparing VLF (0.01–0.1 Hz), respiratory (0.12–0.35 Hz) and cardiac power (0.9–1.3 Hz) FFT maps at different sTRs. Quasi-periodic pattern (QPP) of VLF events were analyzed for effects on dynamic FC methods. The results in conventional time and spatial domain analyses remained virtually unchanged by the different sampling rates. In frequency domain, the aliasing occurred mainly in higher sTR (1–2 s) where cardiac power aliases over respiratory power. The VLF power maps suffered minimally from increasing sTRs. Interleaved data reconstruction induced lower ReHo compared to 3D sampling (p < 0.001). Gradient recalled echo-planar imaging (EPI BOLD) data produced both better and worse metrics. In QPP analyses, the repeatability of the VLF pulse detection becomes linearly reduced with increasing sTR. In conclusion, the conventional resting state metrics (e.g., FC, ICA) were not markedly affected by different TRs (0.1–3 s). However, cardiorespiratory signals showed strongest aliasing in central brain regions in sTR 1–2 s. Pulsatile QPP and other dynamic analyses benefit linearly from short TR scanning.
Collapse
Affiliation(s)
- Niko Huotari
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Lauri Raitamaa
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Heta Helakari
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Janne Kananen
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Ville Raatikainen
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Aleksi Rasila
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Timo Tuovinen
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Jussi Kantola
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Viola Borchardt
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Vesa J Kiviniemi
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Vesa O Korhonen
- Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland.,Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
| |
Collapse
|
49
|
Abstract
Purpose: To develop a fast 3D MRI simulator for arbitrary k-space sampling using a graphical processing unit (GPU) and demonstrate its performance by comparing simulation and experimental results in a real MRI system. Materials and Methods: A fast 3D MRI simulator using a GeForce GTX 1080 GPU (NVIDIA Corporation, Santa Clara, CA, USA) was developed using C++ and the CUDA 8.0 platform (NVIDIA Corporation). The unique advantage of this simulator was that it could use the same pulse sequence as used in the experiment. The performance of the MRI simulator was measured using two GTX 1080 GPUs and 3D Cones sequences. The MRI simulation results for 3D non-Cartesian sampling trajectories like 3D Cones sequences using a numerical 3D phantom were compared with the experimental results obtained with a real MRI system and a real 3D phantom. Results: The performance of the MRI simulator was about 3800–4900 gigaflops for 128- to 4-shot 3D Cones sequences with 2563 voxels, which was about 60% of the performance of the previous MRI simulator optimized for Cartesian sampling calculated for a Cartesian sampling gradient-echo sequence with 2563 voxels. The effects of the static magnetic field inhomogeneity, radio-frequency field inhomogeneity, gradient field nonlinearity, and fast repetition times on the MR images were reproduced in the simulated images as observed in the experimental images. Conclusion: The 3D MRI simulator developed for arbitrary k-space sampling optimized using GPUs is a powerful tool for the development and evaluation of advanced imaging sequences including both Cartesian and non-Cartesian k-space sampling.
Collapse
Affiliation(s)
| | - Ayana Setoi
- Institute of Applied Physics, University of Tsukuba
| | - Katsumi Kose
- Institute of Applied Physics, University of Tsukuba
| |
Collapse
|
50
|
Jiang W, Larson PE, Lustig M. Simultaneous auto-calibration and gradient delays estimation (SAGE) in non-Cartesian parallel MRI using low-rank constraints. Magn Reson Med 2018; 80:2006-2016. [PMID: 29524244 PMCID: PMC6107389 DOI: 10.1002/mrm.27168] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/10/2018] [Accepted: 02/13/2018] [Indexed: 11/09/2022]
Abstract
PURPOSE To correct gradient timing delays in non-Cartesian MRI while simultaneously recovering corruption-free auto-calibration data for parallel imaging, without additional calibration scans. METHODS The calibration matrix constructed from multi-channel k-space data should be inherently low-rank. This property is used to construct reconstruction kernels or sensitivity maps. Delays between the gradient hardware across different axes and RF receive chain, which are relatively benign in Cartesian MRI (excluding EPI), lead to trajectory deviations and hence data inconsistencies for non-Cartesian trajectories. These in turn lead to higher rank and corrupted calibration information which hampers the reconstruction. Here, a method named Simultaneous Auto-calibration and Gradient delays Estimation (SAGE) is proposed that estimates the actual k-space trajectory while simultaneously recovering the uncorrupted auto-calibration data. This is done by estimating the gradient delays that result in the lowest rank of the calibration matrix. The Gauss-Newton method is used to solve the non-linear problem. The method is validated in simulations using center-out radial, projection reconstruction and spiral trajectories. Feasibility is demonstrated on phantom and in vivo scans with center-out radial and projection reconstruction trajectories. RESULTS SAGE is able to estimate gradient timing delays with high accuracy at a signal to noise ratio level as low as 5. The method is able to effectively remove artifacts resulting from gradient timing delays and restore image quality in center-out radial, projection reconstruction, and spiral trajectories. CONCLUSION The low-rank based method introduced simultaneously estimates gradient timing delays and provides accurate auto-calibration data for improved image quality, without any additional calibration scans.
Collapse
Affiliation(s)
- Wenwen Jiang
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
| | - Peder E.Z. Larson
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, California, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Michael Lustig
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
| |
Collapse
|