Academic Appointments

Administrative Appointments

  • Research Director, Stanford Center for Cognitive and Neurobiological Imaging (2017 - Present)

All Publications

  • Advantages of Short Repetition Time Resting-State Functional MRI Enabled by Simultaneous Multi-slice Imaging. Journal of neuroscience methods Jahanian, H., Holdsworth, S., Christen, T., Wu, H., Zhu, K., Kerr, A. B., Middione, M. J., Dougherty, R. F., Moseley, M., Zaharchuk, G. 2018


    BACKGROUND: Recent advancements in simultaneous multi-slice (SMS) imaging techniques have enabled whole-brain resting-state fMRI (rs-fMRI) scanning at sub-second temporal resolution, providing spectral ranges much wider than the typically used range of 0.01-0.1Hz. However, the advantages of this accelerated acquisition for rs-fMRI have not been evaluated.NEW METHOD: In this study, we used SMS Echo Planar Imaging (EPI) to probe whole-brain functional connectivity with a short repetition time (TR=350ms) and compared it with standard EPI with a longer TR of 2000ms. We determined the effect of scan length and investigated the temporal filtration strategies that optimize results based on metrics of signal-noise separation and test-retest reliability using both seed-based and independent component analysis (ICA).RESULTS: We found that use of either the entire frequency range of 0.01-1.4Hz or the entire frequency range with the exclusion of typical cardiac and respiratory frequency values tended to provide the best functional connectivity maps.COMPARISON WITH EXISTING METHODS: We found that the SMS-acquired rs-fMRI scans had improved the signal-noise separation, while preserving the same level of test-retest reliability compared to conventional EPI, and enabled the detection of reliable functional connectivity networks with scan times as short as 3minutes.CONCLUSIONS: Our findings suggest that whole-brain rs-fMRI studies may benefit from the increased temporal resolution enabled by the SMS-EPI acquisition, leading to drastic scan time reductions, which in turn should enable the more widespread use of rs-fMRI in clinical research protocols.

    View details for DOI 10.1016/j.jneumeth.2018.09.033

    View details for PubMedID 30300699

  • Body Diffusion Weighted Imaging Using Non-CPMG Fast Spin Echo IEEE TRANSACTIONS ON MEDICAL IMAGING Gibbons, E. K., Le Roux, P., Vasanawala, S. S., Pauly, J. M., Kerr, A. B. 2017; 36 (2): 549-559


    SS-FSE is a fast technique that does not suffer from off-resonance distortions to the degree that EPI does. Unlike EPI, SS-FSE is ill-suited to diffusion weighted imaging (DWI) due to the Carr-Purcell-Meiboom-Geill (CPMG) condition. Non- CPMG phase cycling does accommodate SS-FSE and DWI but places constraints on reconstruction, which are resolved here through parallel imaging. Additionally, improved echo stability can be achieved by using short duration and highly selective DIVERSE radiofrequency pulses. Here, signal-to-noise ratio (SNR) comparisons between EPI and nCPMG SS-FSE acquisitions and reconstruction techniques give similar values. Diffusion imaging with nCPMG SS-FSE gives similar SNR to an EPI acquisition, though apparent diffusion coefficient values are higher than seen with EPI. In vivo images have good image quality with little distortion. This method has the ability to capture distortionfree DWI images near areas of significant off-resonance as well as preserve adequate SNR. Parallel imaging and DIVERSE refocusing RF pulses allow shorter ETL compared to previous implementations and thus reduces phase encode direction blur and SAR accumulation.

    View details for DOI 10.1109/TMI.2016.2622238

    View details for Web of Science ID 000396115800019

  • Measuring B-1 distributions by B-1 phase encoding MAGNETIC RESONANCE IN MEDICINE Jordanova, K. V., Nishimura, D. G., Kerr, A. B. 2017; 77 (1): 229-236


    We propose a method to acquire B1 distribution plots by encoding in B1 instead of image space. Using this method, B1 data is acquired in a different way from traditional spatial B1 mapping, and allows for quick measurement of high dynamic range B1 data.To encode in B1, we acquire multiple projections of a slice, each along the same direction, but using a different phase sensitivity to B1. Using a convex optimization formulation, we reconstruct histograms of the B1 distribution estimates of the slice.We verify in vivo B1 distribution measurements by comparing measured distributions to distributions calculated from reference spatial B1 maps using the Earth Mover's Distance. Phantom measurements using a surface coil show that for increased spatial B1 variations, measured B1 distributions using the proposed method more accurately estimate the distribution than a low-resolution spatial B1 map, resulting in a 37% Earth Mover's Distance decrease while using fewer measurements.We propose and validate the performance of a method to acquire B1 distribution information directly without acquiring a spatial B1 map. The method may provide faster estimates of a B1 field for applications that do not require spatial B1 localization, such as the transmit gain calibration of the scanner, particularly for high dynamic B1 ranges. Magn Reson Med 77:229-236, 2017. © 2016 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.26114

    View details for Web of Science ID 000391038800024

    View details for PubMedCentralID PMC4947573

  • Lowering the B1 threshold for improved BEAR B1 mapping. Magnetic resonance in medicine Jordanova, K. V., Nishimura, D. G., Kerr, A. B. 2016; 75 (3): 1262-1268


    Accurate measurement of the nonuniform transmit radiofrequency field is necessary for magnetic resonance imaging applications. The radiofrequency field excitation amplitude (B1 ) is often obtained by acquiring a B1 map. We modify the B1 estimation using adiabatic refocusing (BEAR) method to extend its range to lower B1 magnitudes.The BEAR method is a phase-based B1 mapping method, wherein hyperbolic secant pulses induce a phase sensitivity to B1 . The measurable B1 range is limited due to the adiabatic threshold of the pulses. We redesign the method to use flattened hyperbolic secant pulses, which have lower adiabatic thresholds. We optimize the flattened hyperbolic secant parameters to minimize phase sensitivity to frequency variations.We validate the performance of the new method via simulation and in vivo at 3T, and show that for n≤8, accurate B1 maps can be acquired using reduced nominal peak B1 values.The adiabatic threshold for the BEAR method is reduced with flattened hyperbolic secant pulses, which are optimized for accurate phase-to-B1 mapping over a frequency range, and allow for lower nominal B1 values. At 3T, the nominal B1 is decreased by 52% and the sensitivity to B1 is increased by a factor of 3.8. This can improve the method's applicability for measurement of low B1 . Magn Reson Med 75:1262-1268, 2016. © 2015 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25711

    View details for PubMedID 25846905

  • B-1 Estimation Using Adiabatic Refocusing: BEAR MAGNETIC RESONANCE IN MEDICINE Jordanova, K. V., Nishimura, D. G., Kerr, A. B. 2014; 72 (5): 1302-1310


    Accurate measurement of the nonuniform transmit radiofrequency field is useful for many applications in magnetic resonance imaging, such as calibrating the scanner transmit system, evaluating coil performance, and improving image quality and quantitation. The radiofrequency field excitation amplitude (B(1)) is often obtained by acquiring a B(1) map. In this study, a new B(1) mapping method is proposed.The use of two adiabatic full passage pulses with different magnitudes applied as successive refocusing pulses results in a linear relationship between phase and B(1) field strength that is insensitive to the repetition time, off-resonance effects, T(1), and T(2). Using this method, B(1) mapping can be localized to a slice or three-dimensional (3D) volume, with a spin-echo acquisition that is appropriate for fast projection measurements.This new method is shown to agree well with the Bloch-Siegert B(1) mapping method for both phantom and in vivo B(1) measurements at 1.5T, 3T, and 7T. The method's ability to acquire accurate projection B(1) measurements is also demonstrated.This method's high dynamic range, ability to make fast projection measurements, and linear quantitative relationship between phase and B1 make it an ideal candidate for use in robust transmitter gain calibration.

    View details for DOI 10.1002/mrm.25049

    View details for Web of Science ID 000343873900012

    View details for PubMedCentralID PMC4031300

  • Adiabatic RF pulse design for Bloch-Siegert B-1(+) mapping MAGNETIC RESONANCE IN MEDICINE Khalighi, M. M., Rutt, B. K., Kerr, A. B. 2013; 70 (3): 829-835


    The Bloch-Siegert (B-S) B 1+ mapping method has been shown to be fast and accurate, yet it suffers from high Specific Absorption Rate (SAR) and moderately long echo time. An adiabatic RF pulse design is introduced here for optimizing the off-resonant B-S RF pulse to achieve more B-S B 1+ measurement sensitivity for a given pulse width. The extra sensitivity can be used for higher angle-to-noise ratio B 1+ maps or traded off for faster scans. Using numerical simulations and phantom experiments, it is shown that a numerically optimized 2-ms adiabatic B-S pulse is 2.5 times more efficient than a conventional 6-ms Fermi-shaped B-S pulse. The adiabatic B-S pulse performance is validated in a phantom, and in vivo brain B 1+ mapping at 3T and 7T are shown. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.24507

    View details for Web of Science ID 000323543600025

  • Reducing artifacts in one-dimensional Fourier velocity encoding for fast and pulsatile flow MAGNETIC RESONANCE IN MEDICINE Lee, D., Santos, J. M., Hu, B. S., Pauly, J. M., Kerr, A. B. 2012; 68 (6): 1876-1885


    When evaluating the severity of valvular stenosis, the peak velocity of the blood flow is routinely used to estimate the transvalvular pressure gradient. One-dimensional Fourier velocity encoding effectively detects the peak velocity with an ungated time series of spatially resolved velocity spectra in real time. However, measurement accuracy can be degraded by the pulsatile and turbulent nature of stenotic flow and the existence of spatially varying off-resonance. In this work, we investigate the feasibility of improving the peak velocity detection capability of one-dimensional Fourier velocity encoding for stenotic flow using a novel echo-shifted interleaved readout combined with a variable-density circular k-space trajectory. The shorter echo and readout times of the echo-shifted interleaved acquisitions are designed to reduce sensitivity to off-resonance. Preliminary results from limited phantom and in vivo results also indicate that some artifacts from pulsatile flow appear to be suppressed when using this trajectory compared to conventional single-shot readouts, suggesting that peak velocity detection may be improved. The efficiency of the new trajectory improves the temporal and spatial resolutions. To realize the proposed readout, a novel multipoint-traversing algorithm is introduced for flexible and automated gradient-waveform design.

    View details for DOI 10.1002/mrm.24212

    View details for Web of Science ID 000311398600021

    View details for PubMedID 22457248

    View details for PubMedCentralID PMC3499673

  • RF pulse optimization for Bloch-Siegert B-1(+) mapping MAGNETIC RESONANCE IN MEDICINE Khalighi, M. M., Rutt, B. K., Kerr, A. B. 2012; 68 (3): 857-862


    The Bloch-Siegert (B-S) method of B ₁⁺ mapping has been shown to be fast and accurate, yet has high SAR and moderately long TE. These limitations can lengthen scan times and incur signal loss due to B(0) inhomogeneity, particularly at high field. The B-S method relies on applying a band-limited off-resonant B-S radiofrequency pulse to induce a B ₁⁺-dependent frequency-shift for resonant spins. A method for optimizing the B-S radiofrequency pulse is presented here, which maximizes B-S B ₁⁺ measurement sensitivity for a given SAR and T(2) . A 4-ms optimized pulse is shown to have 35% less SAR compared with the conventional 6-ms Fermi pulse while still improving B ₁⁺ map angle-to-noise ratio by 22%. The optimized pulse performance is validated both in phantom and in vivo brain imaging at 7 T.

    View details for DOI 10.1002/mrm.23271

    View details for Web of Science ID 000308098100022

    View details for PubMedID 22144397

    View details for PubMedCentralID PMC3297726

  • Generating Super Stimulated-Echoes in MRI and Their Application to Hyperpolarized C-13 Diffusion Metabolic Imaging IEEE TRANSACTIONS ON MEDICAL IMAGING Larson, P. E., Kerr, A. B., Reed, G. D., Hurd, R. E., Kurhanewicz, J., Pauly, J. M., Vigneron, D. B. 2012; 31 (2): 265-275


    Stimulated-echoes in MR can be used to provide high sensitivity to motion and flow, creating diffusion and perfusion weighting as well as T(1) contrast, but conventional approaches inherently suffer from a 50% signal loss. The super stimulated-echo, which uses a specialized radio-frequency (RF) pulse train, has been proposed in order to improve the signal while preserving motion and T(1) sensitivity. This paper presents a novel and straightforward method for designing the super stimulated-echo pulse train using inversion pulse design techniques. This method can also create adiabatic designs with an improved response to RF transmit field variations. The scheme was validated in phantom experiments and shown in vivo to improve signal-to-noise ratio (SNR). We have applied a super stimulated-echo to metabolic MRI with hyperpolarized (13)C-labeled molecules. For spectroscopic imaging of hyperpolarized agents, several repetition times are required but only a single stimulated-echo encoding is feasible, which can lead to unwanted motion blurring. To address this, a super stimulated-echo preparation scheme was used in which the diffusion weighting is terminated prior to the acquisition, and we observed a SNR increases of 60% in phantoms and 49% in vivo over a conventional stimulated-echo. Experiments following injection of hyperpolarized [1-(13)C] -pyruvate in murine transgenic cancer models have shown improved delineation for tumors since signals from metabolites within tumor tissues are retained while those from the vasculature are suppressed by the diffusion preparation scheme.

    View details for DOI 10.1109/TMI.2011.2168235

    View details for Web of Science ID 000300197500010

    View details for PubMedID 22027366

    View details for PubMedCentralID PMC3274664

  • Minimum Envelope Roughness Pulse Design for Reduced Amplifier Distortion in Parallel Excitation MAGNETIC RESONANCE IN MEDICINE Grissom, W. A., Kerr, A. B., Stang, P., Scott, G. C., Pauly, J. M. 2010; 64 (5): 1433-1440


    Parallel excitation uses multiple transmit channels and coils, each driven by independent waveforms, to afford the pulse designer an additional spatial encoding mechanism that complements gradient encoding. In contrast to parallel reception, parallel excitation requires individual power amplifiers for each transmit channel, which can be cost prohibitive. Several groups have explored the use of low-cost power amplifiers for parallel excitation; however, such amplifiers commonly exhibit nonlinear memory effects that distort radio frequency pulses. This is especially true for pulses with rapidly varying envelopes, which are common in parallel excitation. To overcome this problem, we introduce a technique for parallel excitation pulse design that yields pulses with smoother envelopes. We demonstrate experimentally that pulses designed with the new technique suffer less amplifier distortion than unregularized pulses and pulses designed with conventional regularization.

    View details for DOI 10.1002/mrm.22512

    View details for Web of Science ID 000283616900023

    View details for PubMedCentralID PMC3053148

  • Maximum Linear-Phase Spectral-Spatial Radiofrequency Pulses for Fat-Suppressed Proton Resonance Frequency-Shift MR Thermometry MAGNETIC RESONANCE IN MEDICINE Grissom, W. A., Kerr, A. B., Holbrook, A. B., Pauly, J. M., Butts-Pauly, K. 2009; 62 (5): 1242-1250


    Conventional spectral-spatial pulses used for water-selective excitation in proton resonance frequency-shift MR thermometry require increased sequence length compared to shorter wideband pulses. This is because spectral-spatial pulses are longer than wideband pulses, and the echo time period starts midway through them. Therefore, for a fixed echo time, one must increase sequence length to accommodate conventional spectral-spatial pulses in proton resonance frequency-shift thermometry. We introduce improved water-selective spectral-spatial pulses for which the echo time period starts near the beginning of excitation. Instead of requiring increased sequence length, these pulses extend into the long echo time periods common to PRF sequences. The new pulses therefore alleviate the traditional tradeoff between sequence length and fat suppression. We experimentally demonstrate an 11% improvement in frame rate in a proton resonance frequency imaging sequence compared to conventional spectral-spatial excitation. We also introduce a novel spectral-spatial pulse design technique that is a hybrid of previous model- and filter-based techniques and that inherits advantages from both. We experimentally validate the pulses' performance in suppressing lipid signal and in reducing sequence length compared to conventional spectral-spatial pulses.

    View details for DOI 10.1002/mrm.22118

    View details for Web of Science ID 000271431200018

    View details for PubMedID 19780177

    View details for PubMedCentralID PMC2795148

  • Technique development of 3D dynamic CS-EPSI for hyperpolarized C-13 pyruvate MR molecular imaging of human prostate cancer MAGNETIC RESONANCE IN MEDICINE Chen, H., Larson, P. Z., Gordon, J. W., Bok, R. A., Ferrone, M., van Criekinge, M., Carvajal, L., Cao, P., Pauly, J. M., Kerr, A. B., Park, I., Slater, J. B., Nelson, S. J., Munster, P. N., Aggarwal, R., Kurhanewicz, J., Vigneron, D. B. 2018; 80 (5): 2062–72


    The purpose of this study was to develop a new 3D dynamic carbon-13 compressed sensing echoplanar spectroscopic imaging (EPSI) MR sequence and test it in phantoms, animal models, and then in prostate cancer patients to image the metabolic conversion of hyperpolarized [1-13 C]pyruvate to [1-13 C]lactate with whole gland coverage at high spatial and temporal resolution.A 3D dynamic compressed sensing (CS)-EPSI sequence with spectral-spatial excitation was designed to meet the required spatial coverage, time and spatial resolution, and RF limitations of the 3T MR scanner for its clinical translation for prostate cancer patient imaging. After phantom testing, animal studies were performed in rats and transgenic mice with prostate cancers. For patient studies, a GE SPINlab polarizer (GE Healthcare, Waukesha, WI) was used to produce hyperpolarized sterile GMP [1-13 C]pyruvate. 3D dynamic 13 C CS-EPSI data were acquired starting 5 s after injection throughout the gland with a spatial resolution of 0.5 cm3 , 18 time frames, 2-s temporal resolution, and 36 s total acquisition time.Through preclinical testing, the 3D CS-EPSI sequence developed in this project was shown to provide the desired spectral, temporal, and spatial 5D HP 13 C MR data. In human studies, the 3D dynamic HP CS-EPSI approach provided first-ever simultaneously volumetric and dynamic images of the LDH-catalyzed conversion of [1-13 C]pyruvate to [1-13 C]lactate in a biopsy-proven prostate cancer patient with full gland coverage.The results demonstrate the feasibility to characterize prostate cancer metabolism in animals, and now patients using this new 3D dynamic HP MR technique to measure kPL , the kinetic rate constant of [1-13 C]pyruvate to [1-13 C]lactate conversion.

    View details for PubMedID 29575178

  • H-1 MR spectroscopic imaging of the prostate at 7T using spectral-spatial pulses MAGNETIC RESONANCE IN MEDICINE Lagemaat, M. W., Breukels, V., Vos, E. K., Kerr, A. B., van Uden, M. J., Orzada, S., Bitz, A. K., Maas, M. C., Scheenen, T. J. 2016; 75 (3): 933–45


    To assess the feasibility of prostate (1)H MR spectroscopic imaging (MRSI) using low-power spectral-spatial (SPSP) pulses at 7T, exploiting accurate spectral selection and spatial selectivity simultaneously.A double spin-echo sequence was equipped with SPSP refocusing pulses with a spectral selectivity of 1 ppm. Three-dimensional prostate (1)H-MRSI at 7T was performed with the SPSP-MRSI sequence using an 8-channel transmit array coil and an endorectal receive coil in three patients with prostate cancer and in one healthy subject. No additional water or lipid suppression pulses were used.Prostate (1)H-MRSI could be obtained well within specific absorption rate (SAR) limits in a clinically feasible time (10 min). Next to the common citrate signals, the prostate spectra exhibited high spermine signals concealing creatine and sometimes also choline. Residual lipid signals were observed at the edges of the prostate because of limitations in spectral and spatial selectivity.It is possible to perform prostate (1)H-MRSI at 7T with a SPSP-MRSI sequence while using separate transmit and receive coils. This low-SAR MRSI concept provides the opportunity to increase spatial resolution of MRSI within reasonable scan times.

    View details for DOI 10.1002/mrm.25569

    View details for Web of Science ID 000370593700002

    View details for PubMedID 25943445

  • Multiband RF pulses with improved performance via convex optimization JOURNAL OF MAGNETIC RESONANCE Shang, H., Larson, P. E., Kerr, A., Reed, G., Sukumar, S., Elkhaled, A., Gordon, J. W., Ohliger, M. A., Pauly, J. M., Lustig, M., Vigneron, D. B. 2016; 262: 81-90


    Selective RF pulses are commonly designed with the desired profile as a low pass filter frequency response. However, for many MRI and NMR applications, the spectrum is sparse with signals existing at a few discrete resonant frequencies. By specifying a multiband profile and releasing the constraint on "don't-care" regions, the RF pulse performance can be improved to enable a shorter duration, sharper transition, or lower peak B1 amplitude. In this project, a framework for designing multiband RF pulses with improved performance was developed based on the Shinnar-Le Roux (SLR) algorithm and convex optimization. It can create several types of RF pulses with multiband magnitude profiles, arbitrary phase profiles and generalized flip angles. The advantage of this framework with a convex optimization approach is the flexible trade-off of different pulse characteristics. Designs for specialized selective RF pulses for balanced SSFP hyperpolarized (HP) (13)C MRI, a dualband saturation RF pulse for (1)H MR spectroscopy, and a pre-saturation pulse for HP (13)C study were developed and tested.

    View details for DOI 10.1016/j.jmr.2015.11.010

    View details for Web of Science ID 000369877700013

    View details for PubMedID 26754063

    View details for PubMedCentralID PMC4716678

  • Controlling Radiofrequency-Induced Currents in Guidewires Using Parallel Transmit MAGNETIC RESONANCE IN MEDICINE Etezadi-Amoli, M., Stang, P., Kerr, A., Pauly, J., Scott, G. 2015; 74 (6): 1790-1802


    Elongated conductors, such as pacemaker leads, neurostimulator leads, and conductive guidewires used for interventional procedures can couple to the MRI radiofrequency (RF) transmit field, potentially causing dangerous tissue heating. The purpose of this study was to demonstrate the feasibility of using parallel transmit to control induced RF currents in elongated conductors, thereby reducing the RF heating hazard.Phantom experiments were performed on a four-channel parallel transmit system at 1.5T. Parallel transmit "null mode" excitations that induce minimal wire current were designed using coupling measurements derived from axial B1 (+) maps. The resulting current reduction performance was evaluated with B1 (+) maps, current sensor measurements, and fluoroptic temperature probe measurements.Null mode excitations reduced the maximum coupling mode current by factors ranging from 2 to 80. For the straight wire experiment, a current null imposed at a single wire location was sufficient to reduce tip heating below detectable levels. For longer insertion lengths and a curved geometry, imposing current nulls at two wire locations resulted in more distributed current reduction along the wire length.Parallel transmit can be used to create excitations that induce minimal RF current in elongated conductors, thereby decreasing the RF heating risk, while still allowing visualization of the surrounding volume.

    View details for DOI 10.1002/mrm.25543

    View details for Web of Science ID 000367737300031

    View details for PubMedCentralID PMC4470871

  • Chemical Shift Separation with Controlled Aliasing for Hyperpolarized C-13 Metabolic Imaging MAGNETIC RESONANCE IN MEDICINE Shin, P. J., Larson, P. E., Uecker, M., Reed, G. D., Kerr, A. B., Tropp, J., Ohliger, M. A., Nelson, S. J., Pauly, J. M., Lustig, M., Vigneron, D. B. 2015; 74 (4): 978-989


    A chemical shift separation technique for hyperpolarized (13) C metabolic imaging with high spatial and temporal resolution was developed. Specifically, a fast three-dimensional pulse sequence and a reconstruction method were implemented to acquire signals from multiple (13) C species simultaneously with subsequent separation into individual images.A stack of flyback echo-planar imaging readouts and a set of multiband excitation radiofrequency pulses were designed to spatially modulate aliasing patterns of the acquired metabolite images, which translated the chemical shift separation problem into parallel imaging reconstruction problem. An eight-channel coil array was used for data acquisition and a parallel imaging method based on nonlinear inversion was developed to separate the aliased images.Simultaneous acquisitions of pyruvate and lactate in a phantom study and in vivo rat experiments were performed. The results demonstrated successful separation of the metabolite distributions into individual images having high spatial resolution.This method demonstrated the ability to provide accelerated metabolite imaging in hyperpolarized (13) C MR using multichannel coils, tailored readout, and specialized RF pulses. Magn Reson Med 74:978-989, 2015. © 2014 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25473

    View details for PubMedID 25298086

  • Non-contrast-enhanced peripheral angiography using a sliding interleaved cylinder acquisition MAGNETIC RESONANCE IN MEDICINE Kwon, K. T., Kerr, A. B., Wu, H. H., Hu, B. S., Brittain, J. H., Nishimura, D. G. 2015; 74 (3): 727-738


    To develop a new sequence for non-contrast-enhanced peripheral angiography using a sliding interleaved cylinder (SLINCYL) acquisition.A venous saturation pulse was incorporated into a three-dimensional magnetization-prepared balanced steady-state free precession sequence for non-contrast-enhanced peripheral angiography to improve artery-vein contrast. The SLINCYL acquisition, which consists of a series of overlapped thin slabs for volumetric coverage similar to the original sliding interleaved ky (SLINKY) acquisition, was used to evenly distribute the venous-suppression effects over the field of view. In addition, the thin-slab-scan nature of SLINCYL and the centric-ordered sampling geometry of its readout trajectory were exploited to implement efficient fluid-suppression and parallel imaging schemes. The sequence was tested in healthy subjects and a patient.Compared to a multiple overlapped thin slab acquisition, both SLINKY and SLINCYL suppressed the venetian blind artifacts and provided similar artery-vein contrast. However, SLINCYL achieved this with shorter scan times and less noticeable artifacts from k-space amplitude modulation than SLINKY. The fluid-suppression and parallel imaging schemes were also validated. A patient study using the SLINCYL-based sequence well identified stenoses at the superficial femoral arteries, which were also confirmed with digital subtraction angiography.Non-contrast-enhanced angiography using SLINCYL can provide angiograms with improved artery-vein contrast in the lower extremities. Magn Reson Med 74:727-738, 2015. © 2014 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25452

    View details for Web of Science ID 000360222900014

    View details for PubMedCentralID PMC4362915

  • Interventional Device Visualization with Toroidal Transceiver and Optically Coupled Current Sensor for Radiofrequency Safety Monitoring MAGNETIC RESONANCE IN MEDICINE Etezadi-Amoli, M., Stang, P., Kerr, A., Pauly, J., Scott, G. 2015; 73 (3): 1315-1327


    The development of catheters and guidewires that are safe from radiofrequency (RF) -induced heating and clearly visible against background tissue is a major challenge in interventional MRI. An interventional imaging approach using a toroidal transmit-receive (transceive) coil is presented. This toroidal transceiver allows controlled, low levels of RF current to flow in the catheter/guidewire for visualization, and can be used with conductive interventional devices that have a localized low-impedance tip contact.Toroidal transceivers were built, and phantom experiments were performed to quantify transmit power levels required for device visibility and to detect heating hazards. Imaging experiments in a pig cadaver tested the extendibility to higher field strength and nonphantom settings. A photonically powered optically coupled toroidal current sensor for monitoring induced RF currents was built, calibrated, and tested using an independent image-based current estimation method.Results indicate that high signal-to-noise ratio visualization is achievable using milliwatts of transmit power-power levels orders of magnitude lower than levels that induce measurable heating in phantom tests. Agreement between image-based current estimates and RF current sensor measurements validates sensor accuracy.The toroidal transceiver, integrated with power and current sensing, could offer a promising platform for safe and effective interventional device visualization.

    View details for DOI 10.1002/mrm.25187

    View details for Web of Science ID 000350279900046

    View details for PubMedID 24691876

    View details for PubMedCentralID PMC4182300

  • Quantitative Measurement of Cancer Metabolism Using Stimulated Echo Hyperpolarized Carbon-13 MRS MAGNETIC RESONANCE IN MEDICINE Swisher, C. L., Larson, P. E., Kruttwig, K., Kerr, A. B., Hu, S., Bok, R. A., Goga, A., Pauly, J. M., Nelson, S. J., Kurhanewicz, J., Vigneron, D. B. 2014; 71 (1): 1-11


    Magnetic resonance spectroscopy of hyperpolarized substrates allows for the observation of label exchange catalyzed by enzymes providing a powerful tool to investigate tissue metabolism and potentially kinetics in vivo. However, the accuracy of current methods to calculate kinetic parameters has been limited by T1 relaxation effects, extracellular signal contributions, and reduced precision at lower signal-to-noise ratio.To address these challenges, we investigated a new modeling technique using metabolic activity decomposition-stimulated echo acquisition mode. The metabolic activity decomposition-stimulated echo acquisition mode technique separates exchanging from nonexchanging metabolites providing twice the information as conventional techniques.This allowed for accurate measurements of rates of conversion and of multiple T1 values simultaneously using a single acquisition.The additional measurement of T1 values for the reaction metabolites provides further biological information about the cellular environment of the metabolites. The new technique was investigated through simulations and in vivo studies of transgenic mouse models of cancer demonstrating improved assessments of kinetic rate constants and new T1 relaxation value measurements for hyperpolarized (13) C-pyruvate, (13) C-lactate, and (13) C-alanine.

    View details for DOI 10.1002/mrm.24634

    View details for Web of Science ID 000328580300001

    View details for PubMedID 23412881

    View details for PubMedCentralID PMC3659200

  • Optimal variable flip angle schemes for dynamic acquisition of exchanging hyperpolarized substrates JOURNAL OF MAGNETIC RESONANCE Xing, Y., Reed, G. D., Pauly, J. M., Kerr, A. B., Larson, P. E. 2013; 234: 75-81


    In metabolic MRI with hyperpolarized contrast agents, the signal levels vary over time due to T1 decay, T2 decay following RF excitations, and metabolic conversion. Efficient usage of the nonrenewable hyperpolarized magnetization requires specialized RF pulse schemes. In this work, we introduce two novel variable flip angle schemes for dynamic hyperpolarized MRI in which the flip angle is varied between excitations and between metabolites. These were optimized to distribute the magnetization relatively evenly throughout the acquisition by accounting for T1 decay, prior RF excitations, and metabolic conversion. Simulation results are presented to confirm the flip angle designs and evaluate the variability of signal dynamics across typical ranges of T1 and metabolic conversion. They were implemented using multiband spectral-spatial RF pulses to independently modulate the flip angle at various chemical shift frequencies. With these schemes we observed increased SNR of [1-(13)C]lactate generated from [1-(13)C]pyruvate, particularly at later time points. This will allow for improved characterization of tissue perfusion and metabolic profiles in dynamic hyperpolarized MRI.

    View details for DOI 10.1016/j.jmr.2013.06.003

    View details for Web of Science ID 000323085800009

    View details for PubMedID 23845910

    View details for PubMedCentralID PMC3765634

  • Perfusion and diffusion sensitive C-13 stimulated-echo MRSI for metabolic imaging of cancer MAGNETIC RESONANCE IMAGING Larson, P. E., Hurd, R. E., Kerr, A. B., Pauly, J. M., Bok, R. A., Kurhanewicz, J., Vigneron, D. B. 2013; 31 (5): 635-642


    Metabolic imaging with hyperpolarized [1-(13)C]-pyruvate can rapidly probe tissue metabolic profiles in vivo and has been shown to provide cancer imaging biomarkers for tumor detection, progression, and response to therapy. This technique uses a bolus injection followed by imaging within 1-2 minutes. The observed metabolites include vascular components and their generation is also influenced by cellular transport. These factors complicate image interpretation, especially since [1-(13)C]lactate, a metabolic product that is a biomarker of cancer, is also produced by red blood cells. It would be valuable to understand the distribution of metabolites between the vasculature, interstitial space, and intracellular compartments. The purpose of this study was to better understand this compartmentalization by using a perfusion and diffusion-sensitive stimulated-echo acquisition mode (STEAM) MRSI acquisition method tailored to hyperpolarized substrates. Our results in mouse models showed that among metabolites, the injected substrate (13)C-pyruvate had the largest vascular fraction overall while (13)C-alanine had the smallest vascular fraction. We observed a larger vascular fraction of pyruvate and lactate in the kidneys and liver when compared to back muscle and prostate tumor tissue. Our data suggests that (13)C-lactate in prostate tumor tissue voxels was the most abundant labeled metabolite intracellularly. This was shown in STEAM images that highlighted abnormal cancer cell metabolism and suppressed vascular (13)C metabolite signals.

    View details for DOI 10.1016/j.mri.2012.10.020

    View details for Web of Science ID 000319103000001

    View details for PubMedID 23260391

    View details for PubMedCentralID PMC3626756

  • A rapid method for direct detection of metabolic conversion and magnetization exchange with application to hyperpolarized substrates JOURNAL OF MAGNETIC RESONANCE Larson, P. E., Kerr, A. B., Swisher, C. L., Pauly, J. M., Vigneron, D. B. 2012; 225: 71-80


    In this work, we present a new MR spectroscopy approach for directly observing nuclear spins that undergo exchange, metabolic conversion, or, generally, any frequency shift during a mixing time. Unlike conventional approaches to observe these processes, such as exchange spectroscopy (EXSY), this rapid approach requires only a single encoding step and thus is readily applicable to hyperpolarized MR in which the magnetization is not replenished after T(1) decay and RF excitations. This method is based on stimulated-echoes and uses phase-sensitive detection in conjunction with precisely chosen echo times in order to separate spins generated during the mixing time from those present prior to mixing. We are calling the method Metabolic Activity Decomposition Stimulated-echo Acquisition Mode or MAD-STEAM. We have validated this approach as well as applied it in vivo to normal mice and a transgenic prostate cancer mouse model for observing pyruvate-lactate conversion, which has been shown to be elevated in numerous tumor types. In this application, it provides an improved measure of cellular metabolism by separating [1-(13)C]-lactate produced in tissue by metabolic conversion from [1-(13)C]-lactate that has flowed into the tissue or is in the blood. Generally, MAD-STEAM can be applied to any system in which spins undergo a frequency shift.

    View details for DOI 10.1016/j.jmr.2012.09.014

    View details for Web of Science ID 000312051700011

    View details for PubMedID 23143011

    View details for PubMedCentralID PMC3531583

  • RF Field Visualization of RF Ablation at the Larmor Frequency IEEE TRANSACTIONS ON MEDICAL IMAGING Shultz, K., Stang, P., Kerr, A., Pauly, J., Scott, G. 2012; 31 (4): 938-947


    Radio-frequency ablation (RFA) is an effective minimally invasive treatment for tumors. One primary source of difficulty is monitoring and controlling the ablation region. Currently, RFA is performed at 460 kHz, for which magnetic resonance imaging (MRI) could play a role given its capability for temperature monitoring and tumor visualization. If instead the ablation were to be performed at the MRI Larmor frequency, then the MR capability for B(1) field mapping could be used to directly visualize the radio-frequency (RF) fields created by the ablation currents. Visualizing the RF fields may enable better control of the ablation currents, enabling better control of lesion shape and size and improving repeatability. We demonstrate the feasibility of performing RFAs at 64 MHz and show preliminary results from imaging the RF fields from the ablation. The post-ablation RF fields show an increase in current density in the ablated region, consistent with an increase in conductivity of the ablated tissue.

    View details for DOI 10.1109/TMI.2011.2162248

    View details for Web of Science ID 000302547400008

    View details for PubMedID 21775256

    View details for PubMedCentralID PMC3321073

  • A method for simultaneous echo planar imaging of hyperpolarized C-13 pyruvate and C-13 lactate JOURNAL OF MAGNETIC RESONANCE Reed, G. D., Larson, P. E., Von Morze, C., Bok, R., Lustig, M., Kerr, A. B., Pauly, J. M., Kurhanewicz, J., Vigneron, D. B. 2012; 217: 41-47


    A rapid echo planar imaging sequence for dynamic imaging of [1-(13)C] lactate and [1-(13)C] pyruvate simultaneously was developed. Frequency-based separation of these metabolites was achieved by spatial shifting in the phase-encoded direction with the appropriate choice of echo spacing. Suppression of the pyruvate-hydrate and alanine resonances is achieved through an optimized spectral-spatial RF waveform. Signal sampling efficiency as a function of pyruvate and lactate excitation angle was simulated using two site exchange models. Dynamic imaging is demonstrated in a transgenic mouse model, and phantom validations of the RF pulse frequency selectivity were performed.

    View details for DOI 10.1016/j.jmr.2012.02.008

    View details for Web of Science ID 000303083500007

    View details for PubMedID 22405760

    View details for PubMedCentralID PMC3326401

  • VERSE-guided numerical RF pulse design: A fast method for peak RF power control MAGNETIC RESONANCE IN MEDICINE Lee, D., Grissom, W. A., Lustig, M., Kerr, A. B., Stang, P. P., Pauly, J. M. 2012; 67 (2): 353-362


    In parallel excitation, the computational speed of numerical radiofrequency (RF) pulse design methods is critical when subject dependencies and system nonidealities need to be incorporated on-the-fly. One important concern with optimization-based methods is high peak RF power exceeding hardware or safety limits. Hence, online controllability of the peak RF power is essential. Variable-rate selective excitation pulse reshaping is ideally suited to this problem due to its simplicity and low computational cost. In this work, we first improve the fidelity of variable-rate selective excitation implementation for discrete-time waveforms through waveform oversampling such that variable-rate selective excitation can be robustly applied to numerically designed RF pulses. Then, a variable-rate selective excitation-guided numerical RF pulse design is suggested as an online RF pulse design framework, aiming to simultaneously control peak RF power and compensate for off-resonance.

    View details for DOI 10.1002/mrm.23010

    View details for Web of Science ID 000299376500010

    View details for PubMedID 22135085

    View details for PubMedCentralID PMC3644517

  • Fast Dynamic 3D MR Spectroscopic Imaging With Compressed Sensing and Multiband Excitation Pulses for Hyperpolarized C-13 Studies MAGNETIC RESONANCE IN MEDICINE Larson, P. E., Hu, S., Lustig, M., Kerr, A. B., Nelson, S. J., Kurhanewicz, J., Pauly, J. M., Vigneron, D. B. 2011; 65 (3): 610-619


    Hyperpolarized 13C MR spectroscopic imaging can detect not only the uptake of the pre-polarized molecule but also its metabolic products in vivo, thus providing a powerful new method to study cellular metabolism. Imaging the dynamic perfusion and conversion of these metabolites provides additional tissue information but requires methods for efficient hyperpolarization usage and rapid acquisitions. In this work, we have developed a time-resolved 3D MR spectroscopic imaging method for acquiring hyperpolarized 13C data by combining compressed sensing methods for acceleration and multiband excitation pulses to efficiently use the magnetization. This method achieved a 2 sec temporal resolution with full volumetric coverage of a mouse, and metabolites were observed for up to 60 sec following injection of hyperpolarized [1-(13)C]-pyruvate. The compressed sensing acquisition used random phase encode gradient blips to create a novel random undersampling pattern tailored to dynamic MR spectroscopic imaging with sampling incoherency in four (time, frequency, and two spatial) dimensions. The reconstruction was also tailored to dynamic MR spectroscopic imaging by applying a temporal wavelet sparsifying transform to exploit the inherent temporal sparsity. Customized multiband excitation pulses were designed with a lower flip angle for the [1-(13)C]-pyruvate substrate given its higher concentration than its metabolic products ([1-(13)C]-lactate and [1-(13)C]-alanine), thus using less hyperpolarization per excitation. This approach has enabled the monitoring of perfusion and uptake of the pyruvate, and the conversion dynamics to lactate and alanine throughout a volume with high spatial and temporal resolution.

    View details for DOI 10.1002/mrm.22650

    View details for Web of Science ID 000287929800002

    View details for PubMedID 20939089

    View details for PubMedCentralID PMC3021589

  • Frequency-Offset Cartesian Feedback for MRI Power Amplifier Linearization IEEE TRANSACTIONS ON MEDICAL IMAGING Zanchi, M. G., Stang, P., Kerr, A., Pauly, J. M., Scott, G. C. 2011; 30 (2): 512-522


    High-quality magnetic resonance imaging (MRI) requires precise control of the transmit radio-frequency (RF) field. In parallel excitation applications such as transmit SENSE, high RF power linearity is essential to cancel aliased excitations. In widely-employed class AB power amplifiers, gain compression, cross-over distortion, memory effects, and thermal drift all distort the RF field modulation and can degrade image quality. Cartesian feedback (CF) linearization can mitigate these effects in MRI, if the quadrature mismatch and dc offset imperfections inherent in the architecture can be minimized. In this paper, we present a modified Cartesian feedback technique called "frequency-offset Cartesian feedback" (FOCF) that significantly reduces these problems. In the FOCF architecture, the feedback control is performed at a low intermediate frequency rather than dc, so that quadrature ghosts and dc errors are shifted outside the control bandwidth. FOCF linearization is demonstrated with a variety of typical MRI pulses. Simulation of the magnetization obtained with the Bloch equation demonstrates that high-fidelity RF reproduction can be obtained even with inexpensive class AB amplifiers. Finally, the enhanced RF fidelity of FOCF over CF is demonstrated with actual images obtained in a 1.5 T MRI system.

    View details for DOI 10.1109/TMI.2010.2087768

    View details for Web of Science ID 000286931000029

    View details for PubMedID 20959264

    View details for PubMedCentralID PMC3155726

  • Fast Large-Tip-Angle Multidimensional and Parallel RF Pulse Design in MRI IEEE TRANSACTIONS ON MEDICAL IMAGING Grissom, W. A., Xu, D., Kerr, A. B., Fessler, J. A., Noll, D. C. 2009; 28 (10): 1548-1559


    Large-tip-angle multidimensional radio-frequency (RF) pulse design is a difficult problem, due to the nonlinear response of magnetization to applied RF at large tip-angles. In parallel excitation, multidimensional RF pulse design is further complicated by the possibility for transmit field patterns to change between subjects, requiring pulses to be designed rapidly while a subject lies in the scanner. To accelerate pulse design, we introduce a fast version of the optimal control method for large-tip-angle parallel excitation. The new method is based on a novel approach to analytically linearizing the Bloch equation about a large-tip-angle RF pulse, which results in an approximate linear model for the perturbations created by adding a small-tip-angle pulse to a large-tip-angle pulse. The linear model can be evaluated rapidly using nonuniform fast Fourier transforms, and we apply it iteratively to produce a sequence of pulse updates that improve excitation accuracy. We achieve drastic reductions in design time and memory requirements compared to conventional optimal control, while producing pulses of similar accuracy. The new method can also compensate for nonidealities such as main field inhomogeneties.

    View details for DOI 10.1109/TMI.2009.2020064

    View details for Web of Science ID 000270226100004

    View details for PubMedID 19447704

    View details for PubMedCentralID PMC2763429

  • Spiral Imaging Artifact Reduction: A Comparison of Two k-Trajectory Measurement Methods JOURNAL OF MAGNETIC RESONANCE IMAGING Lechner, S. M., Sipilae, P. T., Wiesinger, F., Kerr, A. B., Vogel, M. W. 2009; 29 (6): 1485-1492


    To compare an external sensor-based k-space calibration technique with a routine precalibration method for quantification of method accuracy and reduction of spiral imaging artifacts to obtain improved image quality.Recently, magnetic field monitoring (MFM) has been introduced as a new calibration technique of gradient field-related imperfections. External sensors are placed near the observed object to measure magnetic field variations during image acquisition. The measured field data are used to determine the actual k-space trajectory and for image reconstruction to reduce artifacts. In the past, precalibration techniques have been proposed where the k-space trajectory is measured by means of special calibration sequences directly in the object of interest. In this study, MFM is introduced as an effective correction technique for spiral imaging. On the basis of a comparison, whether MFM is as viable as the chosen reference method presented by Duyn et al (J Magn Reson [1998] 132:150-153) is analyzed in terms of detecting imperfections of spatial encoding gradients in order to correct for these in image reconstruction. As this technique is used as a reference method, it is given the acronym Duyn calibration technique (DCT). MFM and DCT are compared and timing delays, k-space offsets, eddy current effects, k-trajectory error propagation, image distortions, and signal-to-noise ratio were determined for different spiral sequences in two different phantoms.Both techniques effectively detect k-space offsets and k-trajectory error propagation and correct for general error sources like timing delays. In object border areas, artifacts such as deformations and blurring were dramatically reduced. Within all tested categories, MFM performed as well as DCT. In terms of k-trajectory error propagation and image distortion quantification, MFM was more accurate.We introduce MFM as an effective and accurate correction technique for spiral imaging, where a comparison of MFM and DCT has shown that both techniques are accurate correction techniques for spiral imaging.

    View details for DOI 10.1002/jmri.21782

    View details for Web of Science ID 000266673200032

    View details for PubMedID 19472426