Douglas Kelley | University of California, San Francisco (original) (raw)

Papers by Douglas Kelley

Research paper thumbnail of Quantitative Susceptibility Mapping: MRI at 7T versus 3T

Journal of Neuroimaging, 2019

ABSTRACTBACKGROUND AND PURPOSEUltrahigh‐field 7T promises more than doubling the signal‐to‐noise ... more ABSTRACTBACKGROUND AND PURPOSEUltrahigh‐field 7T promises more than doubling the signal‐to‐noise ratio (SNR) of 3T for magnetic resonance imaging (MRI), particularly for MRI of magnetic susceptibility effects induced by B0. Quantitative susceptibility mapping (QSM) is based on deconvolving the induced phase (or field) and would therefore benefit substantially from 7T. The purpose of this work was to compare QSM performance at 7T versus 3T in an intrascanner test‐retest experiment with varying echo numbers (5 and 10 echoes).METHODSA prospective study in N = 10 healthy subjects was carried out at both 3T and 7T field strengths. Gradient echo data using 5 and 10 echoes were acquired twice in each subject. Test‐retest reproducibility was assessed using Bland‐Altman and regression analysis of region of interest measurements. Image quality was scored by an experienced neuroradiologist.RESULTSIntrascanner bias was below 3.6 parts‐per‐billion (ppb) with correlation R2 > .85. Interscanner...

Research paper thumbnail of Ultrashort echo time MRI of cortical bone at 7 tesla field strength: A feasibility study

Journal of Magnetic Resonance Imaging, 2011

Purpose-To implement and examine the feasibility of a 3D ultra-short TE (UTE) sequence on a 7T cl... more Purpose-To implement and examine the feasibility of a 3D ultra-short TE (UTE) sequence on a 7T clinical MR scanner in comparison with 3T MRI at high isotropic resolution. Materials and Methods-Using an in-house built saddle coil at both field strengths we have imaged mid-diaphysial sections of five fresh cadaveric specimen of the distal tibia. An additional in vivo scan was performed at 7 Tesla using a quadrature knee coil. Results-Using the same type of saddle coil at both field strengths a significant increase in SNR at 7T compared to 3T (factor 1.7) was found. Significantly shorter T2* values were found at the higher field strength (T2*=552.2±126µs at 7T versus T2*=1163±391µs at 3T). Conclusions-UHF MRI at 7T has great potential for imaging tissues with short T2.

Research paper thumbnail of Multi-shot multi-channel diffusion data recovery using structured low-rank matrix completion

arXiv: Medical Physics, 2016

Purpose: To introduce a novel method for the recovery of multi-shot diffusion weighted (MS-DW) im... more Purpose: To introduce a novel method for the recovery of multi-shot diffusion weighted (MS-DW) images from echo-planar imaging (EPI) acquisitions. Methods: Current EPI-based MS-DW reconstruction methods rely on the explicit estimation of the motion- induced phase maps to recover the unaliased images. In the new formulation, the k-space data of the unaliased DWI is recovered using a structured low-rank matrix completion scheme, which does not require explicit estimation of the phase maps. The structured matrix is obtained as the lifting of the multi-shot data. The smooth phase-modulations between shots manifest as null-space vectors of this matrix, which implies that the structured matrix is low-rank. The missing entries of the structured matrix are filled in using a nuclear-norm minimization algorithm subject to the data-consistency. The formulation enables the natural introduction of smoothness regularization, thus enabling implicit motion-compensated recovery of fully-sampled as w...

Research paper thumbnail of Comprehensive reconstruction of multi-shot multi-channel diffusion data using mussels

2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2016

Echo planar imaging (EPI)-based magnetic resonance imaging (MRI) data are often corrupted by Nyqu... more Echo planar imaging (EPI)-based magnetic resonance imaging (MRI) data are often corrupted by Nyquist ghost artifacts resulting from odd-even shifts of the EPI read-outs. Algorithms that corrects for the Nyquist ghost artifacts rely on calibration scans that are collected prior to the data acquisition. However, a more complex pattern of ghosting artifacts arises when diffusion-weighted data are acquired using segmented k-space EPI read-outs. The additional under-sampling present in the segmented acquisitions and the inter-shot motion during diffusion weighted acquistion cause ghosting artifacts in addition to the EPI ghosting arising from odd-even shifts. We propose a comprehensive method that can remove the Nyquist-ghosting artifacts as well as the inter-shot motion-induced ghosting artifacts in diffusion weighted images in a single step from partial Fourier data without the need for a calibration scan. We show very high quality diffusion data recovery using the proposed method.

Research paper thumbnail of Clinically feasible NODDI characterization of glioma using multiband EPI at 7 T

NeuroImage: Clinical, 2015

Recent technological progress in the multiband echo planer imaging (MB EPI) technique enables acc... more Recent technological progress in the multiband echo planer imaging (MB EPI) technique enables accelerated MR diffusion weighted imaging (DWI) and allows whole brain, multi-b-value diffusion imaging to be acquired within a clinically feasible time. However, its applications at 7 T have been limited due to B1 field inhomogeneity and increased susceptibility artifact. It is an ongoing debate whether DWI at 7 T can be performed properly in patients, and a systematic SNR comparison for multiband spin-echo EPI between 3 T and 7 T has not been methodically studied. The goal of this study was to use MB EPI at 7 T in order to obtain 90-directional multi-shell DWI within a clinically feasible acquisition time for patients with glioma. This study included an SNR comparison between 3 T and 7 T, and the application of B1 mapping and distortion correction procedures for reducing the impact of variations in B0 and B1. The optimized multiband sequence was applied in 20 patients with glioma to generate both DTI and NODDI maps for comparison of values in tumor and normal appearing white matter (NAWM). Our SNR analysis showed that MB EPI at 7 T was comparable to that at 3 T, and the data quality acquired in patients was clinically acceptable. NODDI maps provided unique contrast within the T2 lesion that was not seen in anatomical images or DTI maps. Such contrast may reflect the complexity of tissue compositions associated with disease progression and treatment effects. The ability to consistently obtain high quality diffusion data at 7 T will contribute towards the implementation of a comprehensive brain MRI examination at ultra-high field.

Research paper thumbnail of Improved differentiation between knees with cartilage lesions and controls using 7T relaxation time mapping

Journal of Orthopaedic Translation, 2015

Research paper thumbnail of Very-High-Field Magnetic Resonance Imaging: Instrumentation and Safety Issues

Topics in Magnetic Resonance Imaging, 1999

Research paper thumbnail of Short-echo three-dimensional H-1 MR spectroscopic imaging of patients with glioma at 7 tesla for characterization of differences in metabolite levels

Journal of magnetic resonance imaging : JMRI, Jan 17, 2014

The purpose of this study was to evaluate the feasibility of using a short echo time, three-dimen... more The purpose of this study was to evaluate the feasibility of using a short echo time, three-dimensional H-1 magnetic resonance spectroscopic imaging (MRSI) sequence at 7 Tesla (T) to assess the metabolic signature of lesions for patients with glioma. Twenty-nine patients with glioma were studied. MRSI data were obtained using CHESS water suppression, spectrally selective adiabatic inversion-recovery pulses and automatically prescribed outer-volume-suppression for lipid suppression, and spin echo slice selection (echo time = 30 ms). An interleaved flyback echo-planar trajectory was applied to shorten the total acquisition time (∼10 min). Relative metabolite ratios were estimated in tumor and in normal-appearing white and gray matter (NAWM, GM). Levels of glutamine, myo-inositol, glycine, and glutathione relative to total creatine (tCr) were significantly increased in the T2 lesions for all tumor grades compared with those in the NAWM (P < 0.05), while N-acetyl aspartate to tCr wer...

Research paper thumbnail of Development of a robust method for generating 7.0 T multichannel phase images of the brain with application to normal volunteers and patients with neurological diseases

NeuroImage, 2008

The increased susceptibility effects and high signal-to-noise ratio at 7.0 T enable imaging of th... more The increased susceptibility effects and high signal-to-noise ratio at 7.0 T enable imaging of the brain using the phase of the magnetic resonance signal. This study describes and evaluates a robust method for calculating phase images from gradient-recalled echo (GRE) scans. The GRE scans were acquired at 7.0 T using an eight-channel receive coil at spatial resolutions up to 0.195 × 0.260 × 2.00 mm. The entire 7.0 T protocol took less than 10 min. Data were acquired from fortyseven subjects including clinical patients with multiple sclerosis (MS) or brain tumors. The phase images were post-processed using a fully automated phase unwrapping algorithm that combined the data from the different channels. The technique was used to create the first phase images of MS patients at any field strength and the first phase images of brain tumor patients above 1.5 T. The clinical images showed novel contrast in MS plaques and depicted microhemorrhages and abnormal vasculature in brain tumors with unsurpassed resolution and contrast.

Research paper thumbnail of Assessment of cartilage-dedicated sequences at ultra-high-field MRI: comparison of imaging performance and diagnostic confidence between 3.0 and 7.0 T with respect to osteoarthritis-induced changes at the knee joint

Skeletal Radiology, 2009

Objective The objectives of the study were to optimize three cartilage-dedicated sequences for in... more Objective The objectives of the study were to optimize three cartilage-dedicated sequences for in vivo knee imaging at 7.0 T ultra-high-field (UHF) magnetic resonance imaging (MRI) and to compare imaging performance and diagnostic confidence concerning osteoarthritis (OA)-induced changes at 7.0 and 3.0 T MRI. Materials and methods Optimized MRI sequences for cartilage imaging at 3.0 T were tailored for 7.0 T: an intermediate-weighted fast spin-echo (IM-w FSE), a fast imaging employing steady-state acquisition (FIESTA) and a T1-weighted 3D high-spatial-resolution volumetric fatsuppressed spoiled gradient-echo (SPGR) sequence. Three healthy subjects and seven patients with mild OA were examined. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diagnostic confidence in assessing cartilage abnormalities, and image quality were determined. Abnormalities were assessed with the whole organ magnetic resonance imaging score (WORMS). Focal cartilage lesions and bone marrow edema pattern (BMEP) were also quantified. Results At 7.0 T, SNR was increased (p<0.05) for all sequences. For the IM-w FSE sequence, limitations with the specific absorption rate (SAR) required modifications of the scan parameters yielding an incomplete coverage of the knee joint, extensive artifacts, and a less effective fat saturation. CNR and image quality were increased (p<0.05) for SPGR and FIESTA and decreased for IM-w FSE. Diagnostic confidence for cartilage lesions was highest (p<0.05) for FIESTA at 7.0 T. Evaluation of BMEP was decreased (p< 0.05) at 7.0 T due to limited performance of IM-w FSE. Conclusion Gradient echo-based pulse sequences like SPGR and FIESTA are well suited for imaging at UHF which may improve early detection of cartilage lesions. However, UHF IM-w FSE sequences are less feasible for clinical use.

Research paper thumbnail of Tissue Border Enhancement by inversion recovery MRI at 7.0 Tesla

Neuroradiology, 2014

Introduction This contribution presents a magnetic resonance imaging (MRI) acquisition technique ... more Introduction This contribution presents a magnetic resonance imaging (MRI) acquisition technique named Tissue Border Enhancement (TBE), whose purpose is to produce images with enhanced visualization of borders between two tissues of interest without any post-processing. Methods The technique is based on an inversion recovery sequence that employs an appropriate inversion time to produce images where the interface between two tissues of interest is hypo-intense; therefore, tissue borders are clearly represented by dark lines. This effect is achieved by setting imaging parameters such that two neighboring tissues of interest have magnetization with equal magnitude but opposite sign; therefore, the voxels containing a mixture of each tissue (that is, the tissue interface) possess minimal net signal. The technique was implemented on a 7.0 T MRI system. Results This approach can assist the definition of tissue borders, such as that between cortical gray matter and white matter; therefore, it could facilitate segmentation procedures, which are often challenging on ultra-high-field systems due to inhomogeneous radiofrequency distribution. TBE allows delineating the contours of structural abnormalities, and its capabilities were demonstrated with patients with focal cortical dysplasia, gray matter heterotopia, and polymicrogyria. Conclusion This technique provides a new type of image contrast and has several possible applications in basic neuroscience, neurogenetic research, and clinical practice, as it could improve the detection power of MRI in the characterization of cortical malformations, enhance the contour of small anatomical structures of interest, and facilitate cortical segmentation.

Research paper thumbnail of Hippocampal CA1 apical neuropil atrophy in mild Alzheimer disease visualized with 7-T MRI

Neurology, 2010

Objectives: In Alzheimer disease (AD), mounting evidence points to a greater role for synaptic lo... more Objectives: In Alzheimer disease (AD), mounting evidence points to a greater role for synaptic loss than neuronal loss. Supporting this notion, multiple postmortem studies have demonstrated that the hippocampal CA1 apical neuropil is one of the earliest sites of pathology, exhibiting tau aggregates and then atrophy before there is substantial loss of the CA1 pyramidal neurons themselves. In this cross-sectional study, we tested whether tissue loss in the CA1 apical neuropil layer can be observed in vivo in patients with mild AD. Methods: We performed ultra-high-field 7-T MRI on subjects with mild AD (n ϭ 14) and agematched normal controls (n ϭ 16). With a 2-dimensional T2*-weighted gradient-recalled echo sequence that was easily tolerated by subjects, we obtained cross-sectional slices of the hippocampus at an in-plane resolution of 195 m. Results: On images revealing the anatomic landmarks of hippocampal subfields and strata, we observed thinning of the CA1 apical neuropil in subjects with mild AD compared to controls. By contrast, the 2 groups exhibited no difference in the thickness of the CA1 cell body layer or of the entire CA1 subfield. Hippocampal volume, measured on a conventional T1-weighted sequence obtained at 3T, also did not differentiate these patients with mild AD from controls. Conclusions: CA1 apical neuropil atrophy is apparent in patients with mild AD. With its superior spatial resolution, 7-T MRI permits in vivo analysis of a very focal, early site of AD pathology.

Research paper thumbnail of Reduced field-of-view diffusion-weighted imaging of the brain at 7 T

Magnetic Resonance Imaging, 2010

Research paper thumbnail of Phased array 3D MR spectroscopic imaging of the brain at 7 T

Magnetic Resonance Imaging, 2008

Ultra-high-field 7 T magnetic resonance (MR) scanners offer the potential for greatly improved MR... more Ultra-high-field 7 T magnetic resonance (MR) scanners offer the potential for greatly improved MR spectroscopic imaging due to increased sensitivity and spectral resolution. Prior 7 T human single-voxel MR Spectroscopy (MRS) studies have shown significant increases in signal-to-noise ratio (SNR) and spectral resolution as compared to lower magnetic fields but have not demonstrated the increase in spatial resolution and multivoxel coverage possible with 7 T MR spectroscopic imaging. The goal of this study was to develop specialized radiofrequency (RF) pulses and sequences for three-dimensional (3D) MR spectroscopic imaging (MRSI) at 7 T to address the challenges of increased chemical shift misregistration, B1 power limitations, and increased spectral bandwidth. The new 7 T MRSI sequence was tested in volunteer studies and demonstrated the feasibility of obtaining high-SNR phased-array 3D MRSI from the human brain.

Research paper thumbnail of GRAPPA-based susceptibility-weighted imaging of normal volunteers and patients with brain tumor at 7 T

Magnetic Resonance Imaging, 2009

Susceptibility-weighted imaging (SWI) is a valuable technique for high-resolution imaging of brai... more Susceptibility-weighted imaging (SWI) is a valuable technique for high-resolution imaging of brain vasculature that greatly benefits from the emergence of higher field strength MR scanners. Autocalibrating partially parallel imaging techniques can be employed to reduce lengthy acquisition times as long as the decrease in signal-to-noise ratio does not significantly affect the contrast between vessels and brain parenchyma. This study assessed the feasibility of a Generalized Autocalibrating Partially Parallel Acquisition (GRAPPA)-based SWI technique at 7 T in both healthy volunteers and brain tumor patients. GRAPPA-based SWI allowed a twofold or more reduction in scan time without compromising vessel contrast and small vessel detection. Postprocessing parameters for the SWI needed to be modified for patients where the tumor causes high-frequency phase wrap artifacts but did not adversely affect vessel contrast. GRAPPA-based SWI at 7 T revealed regions of microvascularity, hemorrhage and calcification within heterogeneous brain tumors that may aid in characterizing active or necrotic tumor and monitoring treatment effects.

Research paper thumbnail of Development and initial evaluation of 7-T q-ball imaging of the human brain

Magnetic Resonance Imaging, 2008

Diffusion tensor imaging (DTI) noninvasively depicts white matter connectivity in regions where t... more Diffusion tensor imaging (DTI) noninvasively depicts white matter connectivity in regions where the Gaussian model of diffusion is valid, but yields inaccurate results where diffusion has a more complex distribution, such as fiber crossings. Q-ball imaging (QBI) overcomes this limitation of DTI by more fully characterizing the angular dependence of intravoxel diffusion with larger numbers of diffusion-encoding directional measurements at higher diffusion-weighting factors (b values). However, the former results in longer acquisition times and the latter results in lower signal-to-noise ratio (SNR). In this project, we developed specialized 7 Tesla acquisition methods utilizing novel radiofrequency pulses, 8-channel parallel imaging EPI, and high-order shimming with a phase-sensitive multichannel B 0 field map reconstruction. These methods were applied in initial healthy adult volunteer studies which demonstrated the feasibility of performing 7T QBI. Preliminary comparisons of 3T with 7T within supratentorial crossing white matter tracts document a 79.5% SNR increase for b=3000 s/mm 2 (p=0.0001), and a 38.6% SNR increase for b=6000 s/mm 2 (p=0.015). Using spherical harmonic reconstruction of the q-ball orientation distribution function at b=3000 s/mm 2 , 7T QBI allowed accurate visualization of crossing fiber tracts with fewer diffusion-encoding acquisitions than at 3T. The improvement of 7T QBI at b factors as high as 6000 s/mm 2 resulted in better angular resolution than 3T for depicting fibers crossing at shallow angles. Although the increased susceptibility effects at 7T caused problematic distortions near brain-air interfaces at the skull base and posterior fossa, these initial 7T QBI studies demonstrated excellent quality in much of the supratentorial brain with significant improvements as compared to 3T acquisitions in the same individuals.

Research paper thumbnail of A dual-tuned quadrature volume coil with mixed λ/2 and λ/4 microstrip resonators for multinuclear MRSI at 7 T

Magnetic Resonance Imaging, 2012

In this work, an 8-element by 8-element dual-tuned quadrature volume coil with a mix of capacitor... more In this work, an 8-element by 8-element dual-tuned quadrature volume coil with a mix of capacitor terminated half-wavelength (λ/2) and quarter-wavelength (λ/4) microstrip resonators is proposed for multinuclear MRI/S studies at 7T. In the proton channel, λ/2 microstrip resonators with capacitive terminations on both ends are employed for operation at higher frequency of 298.1 MHz; in the heteronucleus channel, capacitor terminated λ/4 resonators, suitable for low frequency operations, are used to meet the low frequency requirement. This mixed structure design is particularly advantageous for high field heteronuclei MR applications with large difference in Larmor frequency of the nuclei in question. The proposed design method makes it much easier to perform frequency tuning for heteronucleus channel using a variable capacitor with a practical capacitance range. As an example, a dual-tuned volume coil for 1 H/ 13 C mouse spectroscopic imaging was proposed to demonstrate the feasibility of this method. The finite-difference timedomain (FDTD) method is first used to model this dual-tuned volume coil and calculate the B 1 field distributions at two frequencies. Transmission parameters (S 21) measured between the proton channel and the carbon channel are −50 dB at 75 MHz and −35 dB at 298 MHz, showing the excellent isolation between the two channels at 7T. The proton image and 13 C FID CSI image of a corn oil phantom on the axial plane at 7T demonstrate the feasibility of the proposed method. A preliminary proton image of a mouse on the sagittal plane is also acquired using the proposed dual-tuned volume coil at 7T, illustrating a fairly uniform B 1 field and sufficient image coverage for imaging in mice.

Research paper thumbnail of Lactate detection at 3T: Compensating J coupling effects with BASING

Journal of Magnetic Resonance Imaging, 1999

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Research paper thumbnail of High-speed 3T MR spectroscopic imaging of prostate with flyback echo-planar encoding

Journal of Magnetic Resonance Imaging, 2007

Prostate MR spectroscopic imaging (MRSI) at 3T may provide twofold higher spatial resolution over... more Prostate MR spectroscopic imaging (MRSI) at 3T may provide twofold higher spatial resolution over 1.5T, but this can result in longer acquisition times to cover the entire gland using conventional phase-encoding. In this study, flyback echo-planar readout trajectories were incorporated into a Malcolm Levitt's composite-pulse decoupling sequence (MLEV)-point-resolved spectroscopy sequence (PRESS) to accelerate the acquisition of large array (16 ϫ 16 ϫ 8), high spatial (0.154 cm 3) resolution MRSI data by eight-fold to just 8.5 minutes. Artifact free, high-quality MRSI data was obtained in nine prostate cancer patients. Easy data reconstruction and the robustness of the flyback echo-planar encoding make this technique particularly suitable for the clinical setting. The short acquisition time provided by this method reduces the 3T prostate MRI/ MRSI exam time, allows longer repetition times, and/or allows the acquisition of additional MR acquisitions within the same exam.

Research paper thumbnail of Compressed sensing for resolution enhancement of hyperpolarized 13C flyback 3D-MRSI

Journal of Magnetic Resonance, 2008

High polarization of nuclear spins in liquid state through dynamic nuclear polarization has enabl... more High polarization of nuclear spins in liquid state through dynamic nuclear polarization has enabled the direct monitoring of 13 C metabolites in vivo at very high signal to noise, allowing for rapid assessment of tissue metabolism. The abundant SNR afforded by this hyperpolarization technique makes high resolution 13 C 3D-MRSI feasible. However, the number of phase encodes that can be fit into the short acquisition time for hyperpolarized imaging limits spatial coverage and resolution. To take advantage of the high SNR available from hyperpolarization, we have applied compressed sensing to achieve a factor of 2 enhancement in spatial resolution without increasing acquisition time or decreasing coverage. In this paper, the design and testing of compressed sensing suited for a flyback 13 C 3D-MRSI sequence are presented. The key to this design was the undersampling of spectral k-space using a novel blipped scheme, thus taking advantage of the considerable sparsity in typical hyperpolarized 13 C spectra. Phantom tests validated the accuracy of the compressed sensing approach and initial mouse experiments demonstrated in vivo feasibility.

Research paper thumbnail of Quantitative Susceptibility Mapping: MRI at 7T versus 3T

Journal of Neuroimaging, 2019

ABSTRACTBACKGROUND AND PURPOSEUltrahigh‐field 7T promises more than doubling the signal‐to‐noise ... more ABSTRACTBACKGROUND AND PURPOSEUltrahigh‐field 7T promises more than doubling the signal‐to‐noise ratio (SNR) of 3T for magnetic resonance imaging (MRI), particularly for MRI of magnetic susceptibility effects induced by B0. Quantitative susceptibility mapping (QSM) is based on deconvolving the induced phase (or field) and would therefore benefit substantially from 7T. The purpose of this work was to compare QSM performance at 7T versus 3T in an intrascanner test‐retest experiment with varying echo numbers (5 and 10 echoes).METHODSA prospective study in N = 10 healthy subjects was carried out at both 3T and 7T field strengths. Gradient echo data using 5 and 10 echoes were acquired twice in each subject. Test‐retest reproducibility was assessed using Bland‐Altman and regression analysis of region of interest measurements. Image quality was scored by an experienced neuroradiologist.RESULTSIntrascanner bias was below 3.6 parts‐per‐billion (ppb) with correlation R2 > .85. Interscanner...

Research paper thumbnail of Ultrashort echo time MRI of cortical bone at 7 tesla field strength: A feasibility study

Journal of Magnetic Resonance Imaging, 2011

Purpose-To implement and examine the feasibility of a 3D ultra-short TE (UTE) sequence on a 7T cl... more Purpose-To implement and examine the feasibility of a 3D ultra-short TE (UTE) sequence on a 7T clinical MR scanner in comparison with 3T MRI at high isotropic resolution. Materials and Methods-Using an in-house built saddle coil at both field strengths we have imaged mid-diaphysial sections of five fresh cadaveric specimen of the distal tibia. An additional in vivo scan was performed at 7 Tesla using a quadrature knee coil. Results-Using the same type of saddle coil at both field strengths a significant increase in SNR at 7T compared to 3T (factor 1.7) was found. Significantly shorter T2* values were found at the higher field strength (T2*=552.2±126µs at 7T versus T2*=1163±391µs at 3T). Conclusions-UHF MRI at 7T has great potential for imaging tissues with short T2.

Research paper thumbnail of Multi-shot multi-channel diffusion data recovery using structured low-rank matrix completion

arXiv: Medical Physics, 2016

Purpose: To introduce a novel method for the recovery of multi-shot diffusion weighted (MS-DW) im... more Purpose: To introduce a novel method for the recovery of multi-shot diffusion weighted (MS-DW) images from echo-planar imaging (EPI) acquisitions. Methods: Current EPI-based MS-DW reconstruction methods rely on the explicit estimation of the motion- induced phase maps to recover the unaliased images. In the new formulation, the k-space data of the unaliased DWI is recovered using a structured low-rank matrix completion scheme, which does not require explicit estimation of the phase maps. The structured matrix is obtained as the lifting of the multi-shot data. The smooth phase-modulations between shots manifest as null-space vectors of this matrix, which implies that the structured matrix is low-rank. The missing entries of the structured matrix are filled in using a nuclear-norm minimization algorithm subject to the data-consistency. The formulation enables the natural introduction of smoothness regularization, thus enabling implicit motion-compensated recovery of fully-sampled as w...

Research paper thumbnail of Comprehensive reconstruction of multi-shot multi-channel diffusion data using mussels

2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2016

Echo planar imaging (EPI)-based magnetic resonance imaging (MRI) data are often corrupted by Nyqu... more Echo planar imaging (EPI)-based magnetic resonance imaging (MRI) data are often corrupted by Nyquist ghost artifacts resulting from odd-even shifts of the EPI read-outs. Algorithms that corrects for the Nyquist ghost artifacts rely on calibration scans that are collected prior to the data acquisition. However, a more complex pattern of ghosting artifacts arises when diffusion-weighted data are acquired using segmented k-space EPI read-outs. The additional under-sampling present in the segmented acquisitions and the inter-shot motion during diffusion weighted acquistion cause ghosting artifacts in addition to the EPI ghosting arising from odd-even shifts. We propose a comprehensive method that can remove the Nyquist-ghosting artifacts as well as the inter-shot motion-induced ghosting artifacts in diffusion weighted images in a single step from partial Fourier data without the need for a calibration scan. We show very high quality diffusion data recovery using the proposed method.

Research paper thumbnail of Clinically feasible NODDI characterization of glioma using multiband EPI at 7 T

NeuroImage: Clinical, 2015

Recent technological progress in the multiband echo planer imaging (MB EPI) technique enables acc... more Recent technological progress in the multiband echo planer imaging (MB EPI) technique enables accelerated MR diffusion weighted imaging (DWI) and allows whole brain, multi-b-value diffusion imaging to be acquired within a clinically feasible time. However, its applications at 7 T have been limited due to B1 field inhomogeneity and increased susceptibility artifact. It is an ongoing debate whether DWI at 7 T can be performed properly in patients, and a systematic SNR comparison for multiband spin-echo EPI between 3 T and 7 T has not been methodically studied. The goal of this study was to use MB EPI at 7 T in order to obtain 90-directional multi-shell DWI within a clinically feasible acquisition time for patients with glioma. This study included an SNR comparison between 3 T and 7 T, and the application of B1 mapping and distortion correction procedures for reducing the impact of variations in B0 and B1. The optimized multiband sequence was applied in 20 patients with glioma to generate both DTI and NODDI maps for comparison of values in tumor and normal appearing white matter (NAWM). Our SNR analysis showed that MB EPI at 7 T was comparable to that at 3 T, and the data quality acquired in patients was clinically acceptable. NODDI maps provided unique contrast within the T2 lesion that was not seen in anatomical images or DTI maps. Such contrast may reflect the complexity of tissue compositions associated with disease progression and treatment effects. The ability to consistently obtain high quality diffusion data at 7 T will contribute towards the implementation of a comprehensive brain MRI examination at ultra-high field.

Research paper thumbnail of Improved differentiation between knees with cartilage lesions and controls using 7T relaxation time mapping

Journal of Orthopaedic Translation, 2015

Research paper thumbnail of Very-High-Field Magnetic Resonance Imaging: Instrumentation and Safety Issues

Topics in Magnetic Resonance Imaging, 1999

Research paper thumbnail of Short-echo three-dimensional H-1 MR spectroscopic imaging of patients with glioma at 7 tesla for characterization of differences in metabolite levels

Journal of magnetic resonance imaging : JMRI, Jan 17, 2014

The purpose of this study was to evaluate the feasibility of using a short echo time, three-dimen... more The purpose of this study was to evaluate the feasibility of using a short echo time, three-dimensional H-1 magnetic resonance spectroscopic imaging (MRSI) sequence at 7 Tesla (T) to assess the metabolic signature of lesions for patients with glioma. Twenty-nine patients with glioma were studied. MRSI data were obtained using CHESS water suppression, spectrally selective adiabatic inversion-recovery pulses and automatically prescribed outer-volume-suppression for lipid suppression, and spin echo slice selection (echo time = 30 ms). An interleaved flyback echo-planar trajectory was applied to shorten the total acquisition time (∼10 min). Relative metabolite ratios were estimated in tumor and in normal-appearing white and gray matter (NAWM, GM). Levels of glutamine, myo-inositol, glycine, and glutathione relative to total creatine (tCr) were significantly increased in the T2 lesions for all tumor grades compared with those in the NAWM (P < 0.05), while N-acetyl aspartate to tCr wer...

Research paper thumbnail of Development of a robust method for generating 7.0 T multichannel phase images of the brain with application to normal volunteers and patients with neurological diseases

NeuroImage, 2008

The increased susceptibility effects and high signal-to-noise ratio at 7.0 T enable imaging of th... more The increased susceptibility effects and high signal-to-noise ratio at 7.0 T enable imaging of the brain using the phase of the magnetic resonance signal. This study describes and evaluates a robust method for calculating phase images from gradient-recalled echo (GRE) scans. The GRE scans were acquired at 7.0 T using an eight-channel receive coil at spatial resolutions up to 0.195 × 0.260 × 2.00 mm. The entire 7.0 T protocol took less than 10 min. Data were acquired from fortyseven subjects including clinical patients with multiple sclerosis (MS) or brain tumors. The phase images were post-processed using a fully automated phase unwrapping algorithm that combined the data from the different channels. The technique was used to create the first phase images of MS patients at any field strength and the first phase images of brain tumor patients above 1.5 T. The clinical images showed novel contrast in MS plaques and depicted microhemorrhages and abnormal vasculature in brain tumors with unsurpassed resolution and contrast.

Research paper thumbnail of Assessment of cartilage-dedicated sequences at ultra-high-field MRI: comparison of imaging performance and diagnostic confidence between 3.0 and 7.0 T with respect to osteoarthritis-induced changes at the knee joint

Skeletal Radiology, 2009

Objective The objectives of the study were to optimize three cartilage-dedicated sequences for in... more Objective The objectives of the study were to optimize three cartilage-dedicated sequences for in vivo knee imaging at 7.0 T ultra-high-field (UHF) magnetic resonance imaging (MRI) and to compare imaging performance and diagnostic confidence concerning osteoarthritis (OA)-induced changes at 7.0 and 3.0 T MRI. Materials and methods Optimized MRI sequences for cartilage imaging at 3.0 T were tailored for 7.0 T: an intermediate-weighted fast spin-echo (IM-w FSE), a fast imaging employing steady-state acquisition (FIESTA) and a T1-weighted 3D high-spatial-resolution volumetric fatsuppressed spoiled gradient-echo (SPGR) sequence. Three healthy subjects and seven patients with mild OA were examined. Signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diagnostic confidence in assessing cartilage abnormalities, and image quality were determined. Abnormalities were assessed with the whole organ magnetic resonance imaging score (WORMS). Focal cartilage lesions and bone marrow edema pattern (BMEP) were also quantified. Results At 7.0 T, SNR was increased (p<0.05) for all sequences. For the IM-w FSE sequence, limitations with the specific absorption rate (SAR) required modifications of the scan parameters yielding an incomplete coverage of the knee joint, extensive artifacts, and a less effective fat saturation. CNR and image quality were increased (p<0.05) for SPGR and FIESTA and decreased for IM-w FSE. Diagnostic confidence for cartilage lesions was highest (p<0.05) for FIESTA at 7.0 T. Evaluation of BMEP was decreased (p< 0.05) at 7.0 T due to limited performance of IM-w FSE. Conclusion Gradient echo-based pulse sequences like SPGR and FIESTA are well suited for imaging at UHF which may improve early detection of cartilage lesions. However, UHF IM-w FSE sequences are less feasible for clinical use.

Research paper thumbnail of Tissue Border Enhancement by inversion recovery MRI at 7.0 Tesla

Neuroradiology, 2014

Introduction This contribution presents a magnetic resonance imaging (MRI) acquisition technique ... more Introduction This contribution presents a magnetic resonance imaging (MRI) acquisition technique named Tissue Border Enhancement (TBE), whose purpose is to produce images with enhanced visualization of borders between two tissues of interest without any post-processing. Methods The technique is based on an inversion recovery sequence that employs an appropriate inversion time to produce images where the interface between two tissues of interest is hypo-intense; therefore, tissue borders are clearly represented by dark lines. This effect is achieved by setting imaging parameters such that two neighboring tissues of interest have magnetization with equal magnitude but opposite sign; therefore, the voxels containing a mixture of each tissue (that is, the tissue interface) possess minimal net signal. The technique was implemented on a 7.0 T MRI system. Results This approach can assist the definition of tissue borders, such as that between cortical gray matter and white matter; therefore, it could facilitate segmentation procedures, which are often challenging on ultra-high-field systems due to inhomogeneous radiofrequency distribution. TBE allows delineating the contours of structural abnormalities, and its capabilities were demonstrated with patients with focal cortical dysplasia, gray matter heterotopia, and polymicrogyria. Conclusion This technique provides a new type of image contrast and has several possible applications in basic neuroscience, neurogenetic research, and clinical practice, as it could improve the detection power of MRI in the characterization of cortical malformations, enhance the contour of small anatomical structures of interest, and facilitate cortical segmentation.

Research paper thumbnail of Hippocampal CA1 apical neuropil atrophy in mild Alzheimer disease visualized with 7-T MRI

Neurology, 2010

Objectives: In Alzheimer disease (AD), mounting evidence points to a greater role for synaptic lo... more Objectives: In Alzheimer disease (AD), mounting evidence points to a greater role for synaptic loss than neuronal loss. Supporting this notion, multiple postmortem studies have demonstrated that the hippocampal CA1 apical neuropil is one of the earliest sites of pathology, exhibiting tau aggregates and then atrophy before there is substantial loss of the CA1 pyramidal neurons themselves. In this cross-sectional study, we tested whether tissue loss in the CA1 apical neuropil layer can be observed in vivo in patients with mild AD. Methods: We performed ultra-high-field 7-T MRI on subjects with mild AD (n ϭ 14) and agematched normal controls (n ϭ 16). With a 2-dimensional T2*-weighted gradient-recalled echo sequence that was easily tolerated by subjects, we obtained cross-sectional slices of the hippocampus at an in-plane resolution of 195 m. Results: On images revealing the anatomic landmarks of hippocampal subfields and strata, we observed thinning of the CA1 apical neuropil in subjects with mild AD compared to controls. By contrast, the 2 groups exhibited no difference in the thickness of the CA1 cell body layer or of the entire CA1 subfield. Hippocampal volume, measured on a conventional T1-weighted sequence obtained at 3T, also did not differentiate these patients with mild AD from controls. Conclusions: CA1 apical neuropil atrophy is apparent in patients with mild AD. With its superior spatial resolution, 7-T MRI permits in vivo analysis of a very focal, early site of AD pathology.

Research paper thumbnail of Reduced field-of-view diffusion-weighted imaging of the brain at 7 T

Magnetic Resonance Imaging, 2010

Research paper thumbnail of Phased array 3D MR spectroscopic imaging of the brain at 7 T

Magnetic Resonance Imaging, 2008

Ultra-high-field 7 T magnetic resonance (MR) scanners offer the potential for greatly improved MR... more Ultra-high-field 7 T magnetic resonance (MR) scanners offer the potential for greatly improved MR spectroscopic imaging due to increased sensitivity and spectral resolution. Prior 7 T human single-voxel MR Spectroscopy (MRS) studies have shown significant increases in signal-to-noise ratio (SNR) and spectral resolution as compared to lower magnetic fields but have not demonstrated the increase in spatial resolution and multivoxel coverage possible with 7 T MR spectroscopic imaging. The goal of this study was to develop specialized radiofrequency (RF) pulses and sequences for three-dimensional (3D) MR spectroscopic imaging (MRSI) at 7 T to address the challenges of increased chemical shift misregistration, B1 power limitations, and increased spectral bandwidth. The new 7 T MRSI sequence was tested in volunteer studies and demonstrated the feasibility of obtaining high-SNR phased-array 3D MRSI from the human brain.

Research paper thumbnail of GRAPPA-based susceptibility-weighted imaging of normal volunteers and patients with brain tumor at 7 T

Magnetic Resonance Imaging, 2009

Susceptibility-weighted imaging (SWI) is a valuable technique for high-resolution imaging of brai... more Susceptibility-weighted imaging (SWI) is a valuable technique for high-resolution imaging of brain vasculature that greatly benefits from the emergence of higher field strength MR scanners. Autocalibrating partially parallel imaging techniques can be employed to reduce lengthy acquisition times as long as the decrease in signal-to-noise ratio does not significantly affect the contrast between vessels and brain parenchyma. This study assessed the feasibility of a Generalized Autocalibrating Partially Parallel Acquisition (GRAPPA)-based SWI technique at 7 T in both healthy volunteers and brain tumor patients. GRAPPA-based SWI allowed a twofold or more reduction in scan time without compromising vessel contrast and small vessel detection. Postprocessing parameters for the SWI needed to be modified for patients where the tumor causes high-frequency phase wrap artifacts but did not adversely affect vessel contrast. GRAPPA-based SWI at 7 T revealed regions of microvascularity, hemorrhage and calcification within heterogeneous brain tumors that may aid in characterizing active or necrotic tumor and monitoring treatment effects.

Research paper thumbnail of Development and initial evaluation of 7-T q-ball imaging of the human brain

Magnetic Resonance Imaging, 2008

Diffusion tensor imaging (DTI) noninvasively depicts white matter connectivity in regions where t... more Diffusion tensor imaging (DTI) noninvasively depicts white matter connectivity in regions where the Gaussian model of diffusion is valid, but yields inaccurate results where diffusion has a more complex distribution, such as fiber crossings. Q-ball imaging (QBI) overcomes this limitation of DTI by more fully characterizing the angular dependence of intravoxel diffusion with larger numbers of diffusion-encoding directional measurements at higher diffusion-weighting factors (b values). However, the former results in longer acquisition times and the latter results in lower signal-to-noise ratio (SNR). In this project, we developed specialized 7 Tesla acquisition methods utilizing novel radiofrequency pulses, 8-channel parallel imaging EPI, and high-order shimming with a phase-sensitive multichannel B 0 field map reconstruction. These methods were applied in initial healthy adult volunteer studies which demonstrated the feasibility of performing 7T QBI. Preliminary comparisons of 3T with 7T within supratentorial crossing white matter tracts document a 79.5% SNR increase for b=3000 s/mm 2 (p=0.0001), and a 38.6% SNR increase for b=6000 s/mm 2 (p=0.015). Using spherical harmonic reconstruction of the q-ball orientation distribution function at b=3000 s/mm 2 , 7T QBI allowed accurate visualization of crossing fiber tracts with fewer diffusion-encoding acquisitions than at 3T. The improvement of 7T QBI at b factors as high as 6000 s/mm 2 resulted in better angular resolution than 3T for depicting fibers crossing at shallow angles. Although the increased susceptibility effects at 7T caused problematic distortions near brain-air interfaces at the skull base and posterior fossa, these initial 7T QBI studies demonstrated excellent quality in much of the supratentorial brain with significant improvements as compared to 3T acquisitions in the same individuals.

Research paper thumbnail of A dual-tuned quadrature volume coil with mixed λ/2 and λ/4 microstrip resonators for multinuclear MRSI at 7 T

Magnetic Resonance Imaging, 2012

In this work, an 8-element by 8-element dual-tuned quadrature volume coil with a mix of capacitor... more In this work, an 8-element by 8-element dual-tuned quadrature volume coil with a mix of capacitor terminated half-wavelength (λ/2) and quarter-wavelength (λ/4) microstrip resonators is proposed for multinuclear MRI/S studies at 7T. In the proton channel, λ/2 microstrip resonators with capacitive terminations on both ends are employed for operation at higher frequency of 298.1 MHz; in the heteronucleus channel, capacitor terminated λ/4 resonators, suitable for low frequency operations, are used to meet the low frequency requirement. This mixed structure design is particularly advantageous for high field heteronuclei MR applications with large difference in Larmor frequency of the nuclei in question. The proposed design method makes it much easier to perform frequency tuning for heteronucleus channel using a variable capacitor with a practical capacitance range. As an example, a dual-tuned volume coil for 1 H/ 13 C mouse spectroscopic imaging was proposed to demonstrate the feasibility of this method. The finite-difference timedomain (FDTD) method is first used to model this dual-tuned volume coil and calculate the B 1 field distributions at two frequencies. Transmission parameters (S 21) measured between the proton channel and the carbon channel are −50 dB at 75 MHz and −35 dB at 298 MHz, showing the excellent isolation between the two channels at 7T. The proton image and 13 C FID CSI image of a corn oil phantom on the axial plane at 7T demonstrate the feasibility of the proposed method. A preliminary proton image of a mouse on the sagittal plane is also acquired using the proposed dual-tuned volume coil at 7T, illustrating a fairly uniform B 1 field and sufficient image coverage for imaging in mice.

Research paper thumbnail of Lactate detection at 3T: Compensating J coupling effects with BASING

Journal of Magnetic Resonance Imaging, 1999

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Research paper thumbnail of High-speed 3T MR spectroscopic imaging of prostate with flyback echo-planar encoding

Journal of Magnetic Resonance Imaging, 2007

Prostate MR spectroscopic imaging (MRSI) at 3T may provide twofold higher spatial resolution over... more Prostate MR spectroscopic imaging (MRSI) at 3T may provide twofold higher spatial resolution over 1.5T, but this can result in longer acquisition times to cover the entire gland using conventional phase-encoding. In this study, flyback echo-planar readout trajectories were incorporated into a Malcolm Levitt's composite-pulse decoupling sequence (MLEV)-point-resolved spectroscopy sequence (PRESS) to accelerate the acquisition of large array (16 ϫ 16 ϫ 8), high spatial (0.154 cm 3) resolution MRSI data by eight-fold to just 8.5 minutes. Artifact free, high-quality MRSI data was obtained in nine prostate cancer patients. Easy data reconstruction and the robustness of the flyback echo-planar encoding make this technique particularly suitable for the clinical setting. The short acquisition time provided by this method reduces the 3T prostate MRI/ MRSI exam time, allows longer repetition times, and/or allows the acquisition of additional MR acquisitions within the same exam.

Research paper thumbnail of Compressed sensing for resolution enhancement of hyperpolarized 13C flyback 3D-MRSI

Journal of Magnetic Resonance, 2008

High polarization of nuclear spins in liquid state through dynamic nuclear polarization has enabl... more High polarization of nuclear spins in liquid state through dynamic nuclear polarization has enabled the direct monitoring of 13 C metabolites in vivo at very high signal to noise, allowing for rapid assessment of tissue metabolism. The abundant SNR afforded by this hyperpolarization technique makes high resolution 13 C 3D-MRSI feasible. However, the number of phase encodes that can be fit into the short acquisition time for hyperpolarized imaging limits spatial coverage and resolution. To take advantage of the high SNR available from hyperpolarization, we have applied compressed sensing to achieve a factor of 2 enhancement in spatial resolution without increasing acquisition time or decreasing coverage. In this paper, the design and testing of compressed sensing suited for a flyback 13 C 3D-MRSI sequence are presented. The key to this design was the undersampling of spectral k-space using a novel blipped scheme, thus taking advantage of the considerable sparsity in typical hyperpolarized 13 C spectra. Phantom tests validated the accuracy of the compressed sensing approach and initial mouse experiments demonstrated in vivo feasibility.