Publications

2015
Stephen F Cauley, Kawin Setsompop, Dan Ma, Yun Jiang, Huihui Ye, Elfar Adalsteinsson, Mark A Griswold, and Lawrence L Wald. 2015. “Fast group matching for MR fingerprinting reconstruction.” Magn Reson Med, 74, 2, Pp. 523-8.Abstract
PURPOSE: MR fingerprinting (MRF) is a technique for quantitative tissue mapping using pseudorandom measurements. To estimate tissue properties such as T1 , T2 , proton density, and B0 , the rapidly acquired data are compared against a large dictionary of Bloch simulations. This matching process can be a very computationally demanding portion of MRF reconstruction. THEORY AND METHODS: We introduce a fast group matching algorithm (GRM) that exploits inherent correlation within MRF dictionaries to create highly clustered groupings of the elements. During matching, a group specific signature is first used to remove poor matching possibilities. Group principal component analysis (PCA) is used to evaluate all remaining tissue types. In vivo 3 Tesla brain data were used to validate the accuracy of our approach. RESULTS: For a trueFISP sequence with over 196,000 dictionary elements, 1000 MRF samples, and image matrix of 128 × 128, GRM was able to map MR parameters within 2s using standard vendor computational resources. This is an order of magnitude faster than global PCA and nearly two orders of magnitude faster than direct matching, with comparable accuracy (1-2% relative error). CONCLUSION: The proposed GRM method is a highly efficient model reduction technique for MRF matching and should enable clinically relevant reconstruction accuracy and time on standard vendor computational resources.
Stephen F. Cauley, Yuanzhe Xi, Berkin Bilgic, Jianlin Xia, Elfar Adalsteinsson, Venkataramanan Balakrishnan, Lawrence L Wald, and Kawin Setsompop. 2015. “Fast reconstruction for multichannel compressed sensing using a hierarchically semiseparable solver.” Magnetic Resonance in Medicine, 73, Pp. 1034–1040. Publisher's VersionAbstract
PURPOSE: The adoption of multichannel compressed sensing (CS) for clinical magnetic resonance imaging (MRI) hinges on the ability to accurately reconstruct images from an undersampled dataset in a reasonable time frame. When CS is combined with SENSE parallel imaging, reconstruction can be computationally intensive. As an alternative to iterative methods that repetitively evaluate a forward CS+SENSE model, we introduce a technique for the fast computation of a compact inverse model solution. METHODS: A recently proposed hierarchically semiseparable (HSS) solver is used to compactly represent the inverse of the CS+SENSE encoding matrix to a high level of accuracy. To investigate the computational efficiency of the proposed HSS-Inverse method, we compare reconstruction time with the current state-of-the-art. In vivo 3T brain data at multiple image contrasts, resolutions, acceleration factors, and number of receive channels were used for this comparison. RESULTS: The HSS-Inverse method allows for \textgreater6× speedup when compared to current state-of-the-art reconstruction methods with the same accuracy. Efficient computational scaling is demonstrated for CS+SENSE with respect to image size. The HSS-Inverse method is also shown to have minimal dependency on the number of parallel imaging channels/acceleration factor. CONCLUSIONS: The proposed HSS-Inverse method is highly efficient and should enable real-time CS reconstruction on standard MRI vendors' computational hardware. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.
Stephen F Cauley, Yuanzhe Xi, Berkin Bilgic, Jianlin Xia, Elfar Adalsteinsson, Venkataramanan Balakrishnan, Lawrence L Wald, and Kawin Setsompop. 2015. “Fast reconstruction for multichannel compressed sensing using a hierarchically semiseparable solver.” Magn Reson Med, 73, 3, Pp. 1034-40.Abstract
PURPOSE: The adoption of multichannel compressed sensing (CS) for clinical magnetic resonance imaging (MRI) hinges on the ability to accurately reconstruct images from an undersampled dataset in a reasonable time frame. When CS is combined with SENSE parallel imaging, reconstruction can be computationally intensive. As an alternative to iterative methods that repetitively evaluate a forward CS+SENSE model, we introduce a technique for the fast computation of a compact inverse model solution. METHODS: A recently proposed hierarchically semiseparable (HSS) solver is used to compactly represent the inverse of the CS+SENSE encoding matrix to a high level of accuracy. To investigate the computational efficiency of the proposed HSS-Inverse method, we compare reconstruction time with the current state-of-the-art. In vivo 3T brain data at multiple image contrasts, resolutions, acceleration factors, and number of receive channels were used for this comparison. RESULTS: The HSS-Inverse method allows for >6× speedup when compared to current state-of-the-art reconstruction methods with the same accuracy. Efficient computational scaling is demonstrated for CS+SENSE with respect to image size. The HSS-Inverse method is also shown to have minimal dependency on the number of parallel imaging channels/acceleration factor. CONCLUSIONS: The proposed HSS-Inverse method is highly efficient and should enable real-time CS reconstruction on standard MRI vendors' computational hardware.
Tanguy Duval, Jennifer A McNab, Kawin Setsompop, Thomas Witzel, Torben Schneider, Susie Yi Huang, Boris Keil, Eric C Klawiter, Lawrence L Wald, and Julien Cohen-Adad. 2015. “In vivo mapping of human spinal cord microstructure at 300mT/m.” Neuroimage, 118, Pp. 494-507.Abstract
The ability to characterize white matter microstructure non-invasively has important applications for the diagnosis and follow-up of several neurological diseases. There exists a family of diffusion MRI techniques, such as AxCaliber, that provide indices of axon microstructure, such as axon diameter and density. However, to obtain accurate measurements of axons with small diameters (<5μm), these techniques require strong gradients, i.e. an order of magnitude higher than the 40-80mT/m currently available in clinical systems. In this study we acquired AxCaliber diffusion data at a variety of different q-values and diffusion times in the spinal cord of five healthy subjects using a 300mT/m whole body gradient system. Acquisition and processing were optimized using state-of-the-art methods (e.g., 64-channel coil, template-based analysis). Results consistently show an average axon diameter of 4.5+/-1.1μm in the spinal cord white matter. Diameters ranged from 3.0μm (gracilis) to 5.9μm (spinocerebellar tracts). Values were similar across laterality (left-right), but statistically different across spinal cord pathways (p<10(-5)). The observed trends are similar to those observed in animal histology. This study shows, for the first time, in vivo mapping of axon diameter in the spinal cord at 300mT/m, thus creating opportunities for applications in spinal cord diseases.
Borjan A Gagoski, Berkin Bilgic, Cornelius Eichner, Himanshu Bhat, Ellen P Grant, Lawrence L Wald, and Kawin Setsompop. 2015. “RARE/turbo spin echo imaging with Simultaneous Multislice Wave-CAIPI.” Magn Reson Med, 73, 3, Pp. 929-938.Abstract
PURPOSE: To enable highly accelerated RARE/Turbo Spin Echo (TSE) imaging using Simultaneous MultiSlice (SMS) Wave-CAIPI acquisition with reduced g-factor penalty. METHODS: SMS Wave-CAIPI incurs slice shifts across simultaneously excited slices while playing sinusoidal gradient waveforms during the readout of each encoding line. This results in an efficient k-space coverage that spreads aliasing in all three dimensions to fully harness the encoding power of coil sensitivities. The novel MultiPINS radiofrequency (RF) pulses dramatically reduce the power deposition of multiband (MB) refocusing pulse, thus allowing high MB factors within the Specific Absorption Rate (SAR) limit. RESULTS: Wave-CAIPI acquisition with MultiPINS permits whole brain coverage with 1 mm isotropic resolution in 70 s at effective MB factor 13, with maximum and average g-factor penalties of gmax  = 1.34 and gavg  = 1.12, and without √R penalty. With blipped-CAIPI, the g-factor performance was degraded to gmax  = 3.24 and gavg  = 1.42; a 2.4-fold increase in gmax relative to Wave-CAIPI. At this MB factor, the SAR of the MultiBand and PINS pulses are 4.2 and 1.9 times that of the MultiPINS pulse, while the peak RF power are 19.4 and 3.9 times higher. CONCLUSION: Combination of the two technologies, Wave-CAIPI and MultiPINS pulse, enables highly accelerated RARE/TSE imaging with low SNR penalty at reduced SAR.
Cornelius Eichner, Stephen F Cauley, Julien Cohen-Adad, Harald E Möller, Robert Turner, Kawin Setsompop, and Lawrence L Wald. 2015. “Real diffusion-weighted MRI enabling true signal averaging and increased diffusion contrast.” Neuroimage, 122, Pp. 373-84.Abstract
This project aims to characterize the impact of underlying noise distributions on diffusion-weighted imaging. The noise floor is a well-known problem for traditional magnitude-based diffusion-weighted MRI (dMRI) data, leading to biased diffusion model fits and inaccurate signal averaging. Here, we introduce a total-variation-based algorithm to eliminate shot-to-shot phase variations of complex-valued diffusion data with the intention to extract real-valued dMRI datasets. The obtained real-valued diffusion data are no longer superimposed by a noise floor but instead by a zero-mean Gaussian noise distribution, yielding dMRI data without signal bias. We acquired high-resolution dMRI data with strong diffusion weighting and, thus, low signal-to-noise ratio. Both the extracted real-valued and traditional magnitude data were compared regarding signal averaging, diffusion model fitting and accuracy in resolving crossing fibers. Our results clearly indicate that real-valued diffusion data enables idealized conditions for signal averaging. Furthermore, the proposed method enables unbiased use of widely employed linear least squares estimators for model fitting and demonstrates an increased sensitivity to detect secondary fiber directions with reduced angular error. The use of phase-corrected, real-valued data for dMRI will therefore help to clear the way for more detailed and accurate studies of white matter microstructure and structural connectivity on a fine scale.
Marta Bianciardi, Nicola Toschi, Brian L Edlow, Cornelius Eichner, Kawin Setsompop, Jonathan R Polimeni, Emery N Brown, Hannah C Kinney, Bruce R Rosen, and Lawrence L Wald. 2015. “Toward an In Vivo Neuroimaging Template of Human Brainstem Nuclei of the Ascending Arousal, Autonomic, and Motor Systems.” Brain Connect, 5, 10, Pp. 597-607.Abstract
Brainstem nuclei (Bn) in humans play a crucial role in vital functions, such as arousal, autonomic homeostasis, sensory and motor relay, nociception, sleep, and cranial nerve function, and they have been implicated in a vast array of brain pathologies. However, an in vivo delineation of most human Bn has been elusive because of limited sensitivity and contrast for detecting these small regions using standard neuroimaging methods. To precisely identify several human Bn in vivo, we employed a 7 Tesla scanner equipped with multi-channel receive-coil array, which provided high magnetic resonance imaging sensitivity, and a multi-contrast (diffusion fractional anisotropy and T2-weighted) echo-planar-imaging approach, which provided complementary contrasts for Bn anatomy with matched geometric distortions and resolution. Through a combined examination of 1.3 mm(3) multi-contrast anatomical images acquired in healthy human adults, we semi-automatically generated in vivo probabilistic Bn labels of the ascending arousal (median and dorsal raphe), autonomic (raphe magnus, periaqueductal gray), and motor (inferior olivary nuclei, two subregions of the substantia nigra compatible with pars compacta and pars reticulata, two subregions of the red nucleus, and, in the diencephalon, two subregions of the subthalamic nucleus) systems. These labels constitute a first step toward the development of an in vivo neuroimaging template of Bn in standard space to facilitate future clinical and research investigations of human brainstem function and pathology. Proof-of-concept clinical use of this template is demonstrated in a minimally conscious patient with traumatic brainstem hemorrhages precisely localized to the raphe Bn involved in arousal.
Berkin Bilgic, Borjan A Gagoski, Stephen F Cauley, Audrey P Fan, Jonathan R Polimeni, Ellen P Grant, Lawrence L Wald, and Kawin Setsompop. 2015. “Wave-CAIPI for highly accelerated 3D imaging.” Magn Reson Med, 73, 6, Pp. 2152-62.Abstract
PURPOSE: To introduce the wave-CAIPI (controlled aliasing in parallel imaging) acquisition and reconstruction technique for highly accelerated 3D imaging with negligible g-factor and artifact penalties. METHODS: The wave-CAIPI 3D acquisition involves playing sinusoidal gy and gz gradients during the readout of each kx encoding line while modifying the 3D phase encoding strategy to incur interslice shifts as in 2D-CAIPI acquisitions. The resulting acquisition spreads the aliasing evenly in all spatial directions, thereby taking full advantage of 3D coil sensitivity distribution. By expressing the voxel spreading effect as a convolution in image space, an efficient reconstruction scheme that does not require data gridding is proposed. Rapid acquisition and high-quality image reconstruction with wave-CAIPI is demonstrated for high-resolution magnitude and phase imaging and quantitative susceptibility mapping. RESULTS: Wave-CAIPI enables full-brain gradient echo acquisition at 1 mm isotropic voxel size and R = 3 × 3 acceleration with maximum g-factors of 1.08 at 3T and 1.05 at 7T. Relative to the other advanced Cartesian encoding strategies (2D-CAIPI and bunched phase encoding) wave-CAIPI yields up to two-fold reduction in maximum g-factor for nine-fold acceleration at both field strengths. CONCLUSION: Wave-CAIPI allows highly accelerated 3D acquisitions with low artifact and negligible g-factor penalties, and may facilitate clinical application of high-resolution volumetric imaging.
Berkin Bilgic, Borjan A. Gagoski, Stephen F. Cauley, Audrey P Fan, Jonathan R. Polimeni, Ellen P Grant, Lawrence L Wald, and Kawin Setsompop. 2015. “Wave-CAIPI for highly accelerated 3D imaging.” Magnetic Resonance in Medicine, 73, 6, Pp. 2152–62. Publisher's VersionAbstract
PURPOSE: To introduce the wave-CAIPI (controlled aliasing in parallel imaging) acquisition and reconstruction technique for highly accelerated 3D imaging with negligible g-factor and artifact penalties. METHODS: The wave-CAIPI 3D acquisition involves playing sinusoidal gy and gz gradients during the readout of each kx encoding line while modifying the 3D phase encoding strategy to incur interslice shifts as in 2D-CAIPI acquisitions. The resulting acquisition spreads the aliasing evenly in all spatial directions, thereby taking full advantage of 3D coil sensitivity distribution. By expressing the voxel spreading effect as a convolution in image space, an efficient reconstruction scheme that does not require data gridding is proposed. Rapid acquisition and high-quality image reconstruction with wave-CAIPI is demonstrated for high-resolution magnitude and phase imaging and quantitative susceptibility mapping. RESULTS: Wave-CAIPI enables full-brain gradient echo acquisition at 1 mm isotropic voxel size and R = 3 × 3 acceleration with maximum g-factors of 1.08 at 3T and 1.05 at 7T. Relative to the other advanced Cartesian encoding strategies (2D-CAIPI and bunched phase encoding) wave-CAIPI yields up to two-fold reduction in maximum g-factor for nine-fold acceleration at both field strengths. CONCLUSION: Wave-CAIPI allows highly accelerated 3D acquisitions with low artifact and negligible g-factor penalties, and may facilitate clinical application of high-resolution volumetric imaging. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.
2014
Itthi Chatnuntawech, Borjan A. Gagoski, Berkin Bilgic, Stephen F. Cauley, Kawin Setsompop, and Elfar Adalsteinsson. 2014. “Accelerated (1) H MRSI using randomly undersampled spiral-based k-space trajectories.” Magnetic Resonance in Medicine, In press. Publisher's VersionAbstract
PURPOSE: To develop and evaluate the performance of an acquisition and reconstruction method for accelerated MR spectroscopic imaging (MRSI) through undersampling of spiral trajectories. THEORY AND METHODS: A randomly undersampled spiral acquisition and sensitivity encoding (SENSE) with total variation (TV) regularization, random SENSE+TV, is developed and evaluated on single-slice numerical phantom, in vivo single-slice MRSI, and in vivo three-dimensional (3D)-MRSI at 3 Tesla. Random SENSE+TV was compared with five alternative methods for accelerated MRSI. RESULTS: For the in vivo single-slice MRSI, random SENSE+TV yields up to 2.7 and 2 times reduction in root-mean-square error (RMSE) of reconstructed N-acetyl aspartate (NAA), creatine, and choline maps, compared with the denoised fully sampled and uniformly undersampled SENSE+TV methods with the same acquisition time, respectively. For the in vivo 3D-MRSI, random SENSE+TV yields up to 1.6 times reduction in RMSE, compared with uniform SENSE+TV. Furthermore, by using random SENSE+TV, we have demonstrated on the in vivo single-slice and 3D-MRSI that acceleration factors of 4.5 and 4 are achievable with the same quality as the fully sampled data, as measured by RMSE of reconstructed NAA map, respectively. CONCLUSION: With the same scan time, random SENSE+TV yields lower RMSEs of metabolite maps than other methods evaluated. Random SENSE+TV achieves up to 4.5-fold acceleration with comparable data quality as the fully sampled acquisition. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.
2014. “Accelerated 1H MRSI using randomly undersampled spiral‐based k‐space trajectories.” Magnetic łdots}. Publisher's Version
Bastien Guérin, Kawin Setsompop, Huihui Ye, Benedikt A Poser, Andrew V Stenger, and Lawrence L Wald. 2014. “Design of parallel transmission pulses for simultaneous multislice with explicit control for peak power and local specific absorption rate.” Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 00, Pp. 1–8. Publisher's VersionAbstract
PURPOSE: To design parallel transmit (pTx) simultaneous multislice (SMS) spokes pulses with explicit control for peak power and local and global specific absorption rate (SAR). METHODS: We design SMS pTx least-squares and magnitude least squares spokes pulses while constraining local SAR using the virtual observation points (VOPs) compression of SAR matrices. We evaluate our approach in simulations of a head (7T) and a body (3T) coil with eight channels arranged in two z-rows. RESULTS: For many of our simulations, control of average power by Tikhonov regularization of the SMS pTx spokes pulse design yielded pulses that violated hardware and SAR safety limits. On the other hand, control of peak power alone yielded pulses that violated local SAR limits. Pulses optimized with control of both local SAR and peak power satisfied all constraints and therefore had the best excitation performance under limited power and SAR constraints. These results extend our previous results for single slice pTx excitations but are more pronounced because of the large power demands and SAR of SMS pulses. CONCLUSIONS: Explicit control of local SAR and peak power is required to generate optimal SMS pTx excitations satisfying both the system's hardware limits and regulatory safety limits. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.
Stephen F Cauley, Kawin Setsompop, Dan Ma, Yun Jiang, Huihui Ye, Elfar Adalsteinsson, Mark A Griswold, and Lawrence L Wald. 2014. “Fast group matching for MR fingerprinting reconstruction.” Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine. Publisher's VersionAbstract
PURPOSE: MR fingerprinting (MRF) is a technique for quantitative tissue mapping using pseudorandom measurements. To estimate tissue properties such as T1 , T2 , proton density, and B0 , the rapidly acquired data are compared against a large dictionary of Bloch simulations. This matching process can be a very computationally demanding portion of MRF reconstruction. THEORY AND METHODS: We introduce a fast group matching algorithm (GRM) that exploits inherent correlation within MRF dictionaries to create highly clustered groupings of the elements. During matching, a group specific signature is first used to remove poor matching possibilities. Group principal component analysis (PCA) is used to evaluate all remaining tissue types. In vivo 3 Tesla brain data were used to validate the accuracy of our approach. RESULTS: For a trueFISP sequence with over 196,000 dictionary elements, 1000 MRF samples, and image matrix of 128 × 128, GRM was able to map MR parameters within 2s using standard vendor computational resources. This is an order of magnitude faster than global PCA and nearly two orders of magnitude faster than direct matching, with comparable accuracy (1-2% relative error). CONCLUSION: The proposed GRM method is a highly efficient model reduction technique for MRF matching and should enable clinically relevant reconstruction accuracy and time on standard vendor computational resources. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.
SF Cauley, K Setsompop, and D Ma. 2014. “Fast group matching for MR fingerprinting reconstruction.” Magnetic łdots}. Publisher's Version
Berkin Bilgic, Itthi Chatnuntawech, Audrey P Fan, Kawin Setsompop, Stephen F Cauley, Lawrence L Wald, and Elfar Adalsteinsson. 2014. “Fast image reconstruction with L2-regularization.” J Magn Reson Imaging, 40, 1, Pp. 181-91.Abstract
PURPOSE: We introduce L2-regularized reconstruction algorithms with closed-form solutions that achieve dramatic computational speed-up relative to state of the art L1- and L2-based iterative algorithms while maintaining similar image quality for various applications in MRI reconstruction. MATERIALS AND METHODS: We compare fast L2-based methods to state of the art algorithms employing iterative L1- and L2-regularization in numerical phantom and in vivo data in three applications; (i) Fast Quantitative Susceptibility Mapping (QSM), (ii) Lipid artifact suppression in Magnetic Resonance Spectroscopic Imaging (MRSI), and (iii) Diffusion Spectrum Imaging (DSI). In all cases, proposed L2-based methods are compared with the state of the art algorithms, and two to three orders of magnitude speed up is demonstrated with similar reconstruction quality. RESULTS: The closed-form solution developed for regularized QSM allows processing of a three-dimensional volume under 5 s, the proposed lipid suppression algorithm takes under 1 s to reconstruct single-slice MRSI data, while the PCA based DSI algorithm estimates diffusion propagators from undersampled q-space for a single slice under 30 s, all running in Matlab using a standard workstation. CONCLUSION: For the applications considered herein, closed-form L2-regularization can be a faster alternative to its iterative counterpart or L1-based iterative algorithms, without compromising image quality.
Berkin Bilgic, Itthi Chatnuntawech, Audrey P Fan, Kawin Setsompop, Stephen F Cauley, Lawrence L Wald, and Elfar Adalsteinsson. 2014. “Fast image reconstruction with L2-regularization.” Journal of magnetic resonance imaging : JMRI, 40, 1, Pp. 181–91. Publisher's VersionAbstract
PURPOSE: We introduce L2-regularized reconstruction algorithms with closed-form solutions that achieve dramatic computational speed-up relative to state of the art L1- and L2-based iterative algorithms while maintaining similar image quality for various applications in MRI reconstruction. MATERIALS AND METHODS: We compare fast L2-based methods to state of the art algorithms employing iterative L1- and L2-regularization in numerical phantom and in vivo data in three applications; (i) Fast Quantitative Susceptibility Mapping (QSM), (ii) Lipid artifact suppression in Magnetic Resonance Spectroscopic Imaging (MRSI), and (iii) Diffusion Spectrum Imaging (DSI). In all cases, proposed L2-based methods are compared with the state of the art algorithms, and two to three orders of magnitude speed up is demonstrated with similar reconstruction quality. RESULTS: The closed-form solution developed for regularized QSM allows processing of a three-dimensional volume under 5 s, the proposed lipid suppression algorithm takes under 1 s to reconstruct single-slice MRSI data, while the PCA based DSI algorithm estimates diffusion propagators from undersampled q-space for a single slice under 30 s, all running in Matlab using a standard workstation. CONCLUSION: For the applications considered herein, closed-form L2-regularization can be a faster alternative to its iterative counterpart or L1-based iterative algorithms, without compromising image quality.
Berkin Bilgic, Audrey P Fan, Jonathan R. Polimeni, Stephen F Cauley, Marta Bianciardi, Elfar Adalsteinsson, Lawrence L Wald, and Kawin Setsompop. 2014. “Fast quantitative susceptibility mapping with L1-regularization and automatic parameter selection.” Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 72, 5, Pp. 1444–59. Publisher's VersionAbstract
PURPOSE: To enable fast reconstruction of quantitative susceptibility maps with total variation penalty and automatic regularization parameter selection. METHODS: ℓ1 -Regularized susceptibility mapping is accelerated by variable splitting, which allows closed-form evaluation of each iteration of the algorithm by soft thresholding and fast Fourier transforms. This fast algorithm also renders automatic regularization parameter estimation practical. A weighting mask derived from the magnitude signal can be incorporated to allow edge-aware regularization. RESULTS: Compared with the nonlinear conjugate gradient (CG) solver, the proposed method is 20 times faster. A complete pipeline including Laplacian phase unwrapping, background phase removal with SHARP filtering, and ℓ1 -regularized dipole inversion at 0.6 mm isotropic resolution is completed in 1.2 min using MATLAB on a standard workstation compared with 22 min using the CG solver. This fast reconstruction allows estimation of regularization parameters with the L-curve method in 13 min, which would have taken 4 h with the CG algorithm. The proposed method also permits magnitude-weighted regularization, which prevents smoothing across edges identified on the magnitude signal. This more complicated optimization problem is solved 5 times faster than the nonlinear CG approach. Utility of the proposed method is also demonstrated in functional blood oxygen level-dependent susceptibility mapping, where processing of the massive time series dataset would otherwise be prohibitive with the CG solver. CONCLUSION: Online reconstruction of regularized susceptibility maps may become feasible with the proposed dipole inversion. Magn Reson Med 72:1444-1459, 2014. © 2013 Wiley Periodicals, Inc.
Berkin Bilgic, Audrey P Fan, Jonathan R Polimeni, Stephen F Cauley, Marta Bianciardi, Elfar Adalsteinsson, Lawrence L Wald, and Kawin Setsompop. 2014. “Fast quantitative susceptibility mapping with L1-regularization and automatic parameter selection.” Magn Reson Med, 72, 5, Pp. 1444-59.Abstract
PURPOSE: To enable fast reconstruction of quantitative susceptibility maps with total variation penalty and automatic regularization parameter selection. METHODS: ℓ(1) -Regularized susceptibility mapping is accelerated by variable splitting, which allows closed-form evaluation of each iteration of the algorithm by soft thresholding and fast Fourier transforms. This fast algorithm also renders automatic regularization parameter estimation practical. A weighting mask derived from the magnitude signal can be incorporated to allow edge-aware regularization. RESULTS: Compared with the nonlinear conjugate gradient (CG) solver, the proposed method is 20 times faster. A complete pipeline including Laplacian phase unwrapping, background phase removal with SHARP filtering, and ℓ(1) -regularized dipole inversion at 0.6 mm isotropic resolution is completed in 1.2 min using MATLAB on a standard workstation compared with 22 min using the CG solver. This fast reconstruction allows estimation of regularization parameters with the L-curve method in 13 min, which would have taken 4 h with the CG algorithm. The proposed method also permits magnitude-weighted regularization, which prevents smoothing across edges identified on the magnitude signal. This more complicated optimization problem is solved 5 times faster than the nonlinear CG approach. Utility of the proposed method is also demonstrated in functional blood oxygen level-dependent susceptibility mapping, where processing of the massive time series dataset would otherwise be prohibitive with the CG solver. CONCLUSION: Online reconstruction of regularized susceptibility maps may become feasible with the proposed dipole inversion.
2014. “Fast reconstruction for multichannel compressed sensing using a hierarchically semiseparable solver.” Magnetic łdots}. Publisher's Version
Wei-Tang Chang, Kawin Setsompop, Jyrki Ahveninen, John W Belliveau, Thomas Witzel, and Fa-Hsuan Lin. 2014. “Improving the spatial resolution of magnetic resonance inverse imaging via the blipped-CAIPI acquisition scheme.” NeuroImage, 91, Pp. 401–11. Publisher's VersionAbstract
Using simultaneous acquisition from multiple channels of a radio-frequency (RF) coil array, magnetic resonance inverse imaging (InI) achieves functional MRI acquisitions at a rate of 100ms per whole-brain volume. InI accelerates the scan by leaving out partition encoding steps and reconstructs images by solving under-determined inverse problems using RF coil sensitivity information. Hence, the correlated spatial information available in the coil array causes spatial blurring in the InI reconstruction. Here, we propose a method that employs gradient blips in the partition encoding direction during the acquisition to provide extra spatial encoding in order to better differentiate signals from different partitions. According to our simulations, this blipped-InI (bInI) method can increase the average spatial resolution by 15.1% (1.3mm) across the whole brain and from 32.6% (4.2mm) in subcortical regions, as compared to the InI method. In a visual fMRI experiment, we demonstrate that, compared to InI, the spatial distribution of bInI BOLD response is more consistent with that of a conventional echo-planar imaging (EPI) at the level of individual subjects. With the improved spatial resolution, especially in subcortical regions, bInI can be a useful fMRI tool for obtaining high spatiotemporal information for clinical and cognitive neuroscience studies.

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