pinecone/core-2020-05-10-deduplication huggingface dataset:
Using the robust principal component analysis algorithm to remove RF spike artifacts from MR images

Brief bursts of RF noise during MR data acquisition (“k-space spikes”) cause disruptive image artifacts, manifesting as stripes overlaid on the image. RF noise is often related to hardware problems, including vibrations during gradient-heavy sequences, such as diffusion-weighted imaging. In this study, we present an application of the Robust Principal Component Analysis (RPCA) algorithm to remove spike noise from k-space. Methods: Corrupted k-space matrices were decomposed into their low-rank and sparse components using the RPCA algorithm, such that spikes were contained within the sparse component and artifact-free k-space data remained in the low-rank component. Automated center refilling was applied to keep the peaked central cluster of k-space from misclassification in the sparse component. Results: This algorithm was demonstrated to effectively remove k-space spikes from four data types under conditions generating spikes: (i) mouse heart T1 mapping, (ii) mouse heart cine imaging, (iii) human kidney diffusion tensor imaging (DTI) data, and (iv) human brain DTI data. Myocardial T1 values changed by 86.1 ± 171 ms following despiking, and fractional anisotropy values were recovered following despiking of DTI data. Conclusion: The RPCA despiking algorithm will be a valuable postprocessing method for retrospectively removing stripe artifacts without affecting the underlying signal of interest. Magn Reson Med, 2015. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited
¹³C magnetic resonance spectroscopy measurements with hyperpolarized [1-¹³C] pyruvate can be used to detect the expression of transgenic pyruvate decarboxylase activity in vivo

Purpose Dissolution dynamic nuclear polarization can increase the sensitivity of the 13C magnetic resonance spectroscopy experiment by at least four orders of magnitude and offers a novel approach to the development of MRI gene reporters based on enzymes that metabolize 13C-labeled tracers. We describe here a gene reporter based on the enzyme Pyruvate Decarboxylase (EC 4.1.1.1), which catalyzes the decarboxylation of pyruvate to produce acetaldehyde and carbon dioxide. Methods Pyruvate Decarboxylase from Zymomonas mobilis (zmPDC), and a mutant that lacked enzyme activity, were expressed, using an inducible promoter, in human embryonic kidney (HEK293T) cells. Enzyme activity was measured in the cells, and in xenografts derived from the cells, using 13C MRS measurements of the conversion of hyperpolarized [1-13C] pyruvate to H13CO3 –. Results Induction of zmPDC expression in the cells and in the xenografts derived from them resulted in an approximately two-fold increase in the H13CO3 –/[1-13C] pyruvate signal ratio following intravenous injection of hyperpolarized [1-13C] pyruvate. Conclusion We have demonstrated the feasibility of using zmPDC as an in vivo reporter gene for use with hyperpolarized 13C MRS.PD was in receipt of a studentship funded by CRUK and S.-S.T. a Yousef Jameel studentship. TBR was in receipt of an Intra-European Marie Curie (FP7-PEOPLE- 2009-IEF, Imaging Lymphoma) and Long-term EMBO (EMBO-ALT-1145-2009) fellowships and E.M.S. and I.M.R were recipients of fellowships from the European Union Seventh Framework Programme (FP7/2007-2013) under the Marie Curie Initial Training Network METAFLUX (project number 264780). E.M.S. also acknowledges the educational support of Programme for Advanced Medical Education from Calouste Gulbenkian Foundation, Champalimaud Foundation, Ministerio de Saude and Fundacao para a Ciencia e Tecnologia, Portugal. The work was supported by a CRUK Programme Grant (17242) to KMB. The polarizer and related materials were provided by GE-Healthcare.This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/mrm.2587
Large dynamic range relative B1+ mapping.

PURPOSE: Parallel transmission (PTx) requires knowledge of the B1+ produced by each element. However, B1+ mapping can be challenging when transmit fields exhibit large dynamic range. This study presents a method to produce high quality relative B1+ maps when this is the case. THEORY AND METHODS: The proposed technique involves the acquisition of spoiled gradient echo (SPGR) images at multiple radiofrequency drive levels for each transmitter. The images are combined using knowledge of the SPGR signal equation using maximum likelihood estimation, yielding an image for each channel whose signal is proportional to the B1+ field strength. Relative B1+ maps are then obtained by taking image ratios. The method was tested using numerical simulations, phantom imaging, and through in vivo experiments. RESULTS: The numerical simulations demonstrated that the proposed method can reconstruct relative transmit sensitivities over a wide range of B1+ amplitudes and at several SNR levels. The method was validated at 3 Tesla (T) by comparing it with an alternative B1+ mapping method, and demonstrated in vivo at 7T. CONCLUSION: Relative B1+ mapping in the presence of large dynamic range has been demonstrated through numerical simulations, phantom imaging at 3T and experimentally at 7T. The method will enable PTx to be applied in challenging imaging scenarios at ultrahigh field. Magn Reson Med 76:490-499, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited
Additional sampling directions improve detection range of wireless probes

Purpose:
While MRI is enhancing our knowledge about the structure and function of the human brain, subject motion remains a problem in many clinical applications. Recently, the use of wireless radio-frequency markers with three 1D navigators for prospective correction was demonstrated. This method is restricted in the range of motion that can be corrected, however, because of limited information in the 1D readouts.

Methods:
Here, the limitation of techniques for disambiguating marker locations was investigated. It was shown that including more sampling directions extends the tracking range for head rotations. The efficiency of trading readout resolution for speed was explored.

Results:
Tracking of head rotations was demonstrated from -19.2 to 34.4°, -2.7 to 10.0° and -60.9 to 70.9° in the x-, y- and z-directions respectively. In the presence of excessive head motion, the deviation of marker estimates from SPM8 was reduced by 17.1% over existing three-projection methods.
This was achieved by using an additional seven directions, extending the time needed for readouts by a factor of 3.3. Much of this increase may be circumvented by reducing resolution, without compromising accuracy.

Conclusion:
Including additional sampling directions extends the range in which markers can be used, for patients who move a lot.The project was supported by funding from the Isaac Newton Trust, the Wellcome Trust ISSF, and the Cusanuswerk funding body (Bonn, Germany).This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/mrm.2599
MR fingerprinting with simultaneous B1 estimation

Purpose

MR fingerprinting (MRF) can be used for quantitative estimation of physical parameters in MRI. Here, we extend the method to incorporate B1 estimation.

Methods

The acquisition is based on steady state free precession MR fingerprinting with a Cartesian trajectory. To increase the sensitivity to the B1 profile, abrupt changes in flip angle were introduced in the sequence. Slice profile and B1 effects were included in the dictionary and the results from two- and three-dimensional (3D) acquisitions were compared. Acceleration was demonstrated using retrospective undersampling in the phase encode directions of 3D data exploiting redundancy between MRF frames at the edges of k-space.

Results

Without B1 estimation, T2 and B1 were inaccurate by more than 20%. Abrupt changes in flip angle improved B1 maps. T1 and T2 values obtained with the new MRF methods agree with classical spin echo measurements and are independent of the B1 field profile. When using view sharing reconstruction, results remained accurate (error <10%) when sampling under 10% of k-space from the 3D data.

Conclusion

The methods demonstrated here can successfully measure T1, T2, and B1. Errors due to slice profile can be substantially reduced by including its effect in the dictionary or acquiring data in 3D. Magn Reson Med, 2015. © 2015 Wiley Periodicals, Inc.G.B. was funded by INFN CNS 5.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/mrm.2600
Optimal control design of turbo spin-echo sequences with applications to parallel-transmit systems

PURPOSE: The design of turbo spin-echo sequences is modeled as a dynamic optimization problem which includes the case of inhomogeneous transmit radiofrequency fields. This problem is efficiently solved by optimal control techniques making it possible to design patient-specific sequences online. THEORY AND METHODS: The extended phase graph formalism is employed to model the signal evolution. The design problem is cast as an optimal control problem and an efficient numerical procedure for its solution is given. The numerical and experimental tests address standard multiecho sequences and pTx configurations. RESULTS: Standard, analytically derived flip angle trains are recovered by the numerical optimal control approach. New sequences are designed where constraints on radiofrequency total and peak power are included. In the case of parallel transmit application, the method is able to calculate the optimal echo train for two-dimensional and three-dimensional turbo spin echo sequences in the order of 10 s with a single central processing unit (CPU) implementation. The image contrast is maintained through the whole field of view despite inhomogeneities of the radiofrequency fields. CONCLUSION: The optimal control design sheds new light on the sequence design process and makes it possible to design sequences in an online, patient-specific fashion. Magn Reson Med, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine
Single shot three-dimensional pulse sequence for hyperpolarized $^{13}$C MRI

Purpose

Metabolic imaging with hyperpolarized $^{13}$C-labeled cell substrates is a promising technique for imaging tissue metabolism in vivo. However, the transient nature of the hyperpolarization, and its depletion following excitation, limits the imaging time and the number of excitation pulses that can be used. We describe here a single-shot three-dimensional (3D) imaging sequence and demonstrate its capability to generate $^{13}$C MR images in tumor-bearing mice injected with hyperpolarized [1-$^{13}$C]pyruvate.

Methods

The pulse sequence acquires a stack-of-spirals at two spin echoes after a single excitation pulse and encodes the kz-dimension in an interleaved manner to enhance robustness to B$_{0}$ inhomogeneity. Spectral-spatial pulses are used to acquire dynamic 3D images from selected hyperpolarized $^{13}$C-labeled metabolites.

Results

A nominal spatial/temporal resolution of 1.25 × 1.25 × 2.5 mm3 × 2 s was achieved in tumor images of hyperpolarized [1-$^{13}$C]pyruvate and [1-$^{13}$C]lactate acquired in vivo. Higher resolution in the z-direction, with a different k-space trajectory, was demonstrated in measurements on a thermally polarized [1-$^{13}$C]lactate phantom.

Conclusion

The pulse sequence is capable of imaging hyperpolarized $^{13}$C-labeled substrates at relatively high spatial and temporal resolutions and is robust to moderate system imperfections.The work was supported by a Cancer Research UK Programme grant (17242) to KMB and by the CRUK-EPSRC Imaging Centre in Cambridge and Manchester (16465). JW was also supported, in part, by a grant from the Danish Strategic Research Council (LIFE-DNP: Hyperpolarized magnetic resonance for in vivo quantification of lipid, sugar and amino acid metabolism in lifestyle related diseases).This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1002/mrm.2616
A new paramagnetically shifted imaging probe for MRI.

Purpose\ud
To develop and characterize a new paramagnetic contrast agent for molecular imaging by MRI.\ud
\ud
Methods\ud
A contrast agent was developed for direct MRI detection through the paramagnetically shifted proton magnetic resonances of two chemically equivalent tert-butyl reporter groups within a dysprosium(III) complex. The complex was characterized in phantoms and imaged in physiologically intact mice at 7 Tesla (T) using three-dimensional (3D) gradient echo and spectroscopic imaging (MRSI) sequences to measure spatial distribution and signal frequency.\ud
\ud
Results\ud
The reporter protons reside ∼6.5 Å from the paramagnetic center, resulting in fast T1 relaxation (T1 = 8 ms) and a large paramagnetic frequency shift exceeding 60 ppm. Fast relaxation allowed short scan repetition times with high excitation flip angle, resulting in high sensitivity. The large dipolar shift allowed direct frequency selective excitation and acquisition of the dysprosium(III) complex, independent of the tissue water signal. The biokinetics of the complex were followed in vivo with a temporal resolution of 62 s following a single, low-dose intravenous injection. The lower concentration limit for detection was ∼23 μM. Through MRSI, the temperature dependence of the paramagnetic shift (0.28 ppm.K−1) was exploited to examine tissue temperature variation.\ud
\ud
Conclusions\ud
These data demonstrate a new MRI agent with the potential for physiological monitoring by MRI. Magn Reson Med 77:1307–1317, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited
Estimating Absolute-Phase Maps Using ESPIRiT and Virtual Conjugate Coils

Purpose: To develop an ESPIRiT-based method to estimate coil sensitivities
with image phase as a building block for efficient and robust image
reconstruction with phase constraints. Theory and Methods: ESPIRiT is a new
framework for calibration of the coil sensitivities and reconstruction in
parallel Magnetic Resonance Imaging (MRI). Applying ESPIRiT to a combined set
of physical and virtual conjugate coils (VCC-ESPIRiT) implicitly exploits
conjugate symmetry in k-space similar to VCC-GRAPPA. Based on this method, a
new post-processing step is proposed for the explicit computation of coil
sensitivities that include the absolute phase of the image. The accuracy of the
computed maps is directly validated using a test based on projection onto fully
sampled coil images and also indirectly in phase-constrained parallel-imaging
reconstructions. Results: The proposed method can estimate accurate
sensitivities which include low-resolution image phase. In case of
high-frequency phase variations VCC-ESPIRiT yields an additional set of maps
that indicates the existence of a high-frequency phase component. Taking this
additional set of maps into account can improve the robustness of
phase-constrained parallel imaging. Conclusion: The extended VCC-ESPIRiT is a
useful tool for phase-constrained imaging.Comment: 15 pages, 5 figure
A monte carlo study of restricted diffusion: Implications for diffusion MRI of prostate cancer

Purpose: Diffusion MRI is frequently used to assess prostate cancer. The prostate consists of cellular tissue surrounding fluid filled ducts. Here, the diffusion properties of the ductal fluid alone were studied. Monte Carlo simulations were used to investigate ductal residence times to determine whether ducts can be regarded as forming a separate compartment and whether ductal radius could determine the ADC of the ductal fluid. Methods: Random walks were simulated in cavities. Average residence times were estimated for permeable cavities. Signal reductions resulting from application of a Stejskal-Tanner pulse sequence were calculated in impermeable cavities. Simulations were repeated for cavities of different radii and different diffusion times. Results: Residence times are at least comparable with diffusion times even in relatively high grade tumours. ADCs asymptotically approach theoretical limiting values. At large radii and short diffusion times, ADCs are similar to free diffusion. At small radii and long diffusion times, ADCs are reduced towards zero, and kurtosis approaches a value of -1.2. Conclusions: Restricted diffusion in cavities of similar sizes to prostate ducts may reduce ductal ADCs. This may contribute to reductions in total ADC seen in prostate cancer
Characterization of perfluorocarbon relaxation times and their influence on the optimization of fluorine-19 MRI at 3 tesla.

To characterize and optimize javax.xml.bind.JAXBElement@7524a985 F MRI for different perfluorocarbons (PFCs) at 3T and quantify the loss of acquisition efficiency as a function of different temperature and cellular conditions.
The T javax.xml.bind.JAXBElement@1ef4ca84 and T javax.xml.bind.JAXBElement@295b7e6f relaxation times of the commonly used PFCs perfluoropolyether (PFPE), perfluoro-15-crown-5-ether (PFCE), and perfluorooctyl bromide (PFOB) were measured in phantoms and in several different conditions (cell types, presence of fixation agent, and temperatures). These relaxation times were used to optimize pulse sequences through numerical simulations. The acquisition efficiency in each cellular condition was then determined as the ratio of the signal after optimization with the reference relaxation times and after optimization with its proper relaxation times. Finally, PFC detection limits were determined.
The loss of acquisition efficiency due to parameter settings optimized for the wrong temperature and cellular condition was limited to 13%. The detection limits of all PFCs were lower at 24 °C than at 37 °C and varied from 11.8 ± 3.0 mM for PFCE at 24 °C to 379.9 ± 51.8 mM for PFOB at 37 °C.
Optimizing javax.xml.bind.JAXBElement@30187e57 F pulse sequences with a known phantom only leads to moderate loss in acquisition efficiency in cellular conditions that might be encountered in in vivo and in vitro experiments. Magn Reson Med 77:2263-2271, 2017. © 2016 International Society for Magnetic Resonance in Medicine
Evaluation of non-Gaussian diffusion in cardiac MRI.

PURPOSE: The diffusion tensor model assumes Gaussian diffusion and is widely applied in cardiac diffusion MRI. However, diffusion in biological tissue deviates from a Gaussian profile as a result of hindrance and restriction from cell and tissue microstructure, and may be quantified better by non-Gaussian modeling. The aim of this study was to investigate non-Gaussian diffusion in healthy and hypertrophic hearts. METHODS: Thirteen rat hearts (five healthy, four sham, four hypertrophic) were imaged ex vivo. Diffusion-weighted images were acquired at b-values up to 10,000 s/mm(2) . Models of diffusion were fit to the data and ranked based on the Akaike information criterion. RESULTS: The diffusion tensor was ranked best at b-values up to 2000 s/mm(2) but reflected the signal poorly in the high b-value regime, in which the best model was a non-Gaussian "beta distribution" model. Although there was considerable overlap in apparent diffusivities between the healthy, sham, and hypertrophic hearts, diffusion kurtosis and skewness in the hypertrophic hearts were more than 20% higher in the sheetlet and sheetlet-normal directions. CONCLUSION: Non-Gaussian diffusion models have a higher sensitivity for the detection of hypertrophy compared with the Gaussian model. In particular, diffusion kurtosis may serve as a useful biomarker for characterization of disease and remodeling in the heart. Magn Reson Med, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited
Low Rank Alternating Direction Method of Multipliers Reconstruction for
  MR Fingerprinting

Purpose
  The proposed reconstruction framework addresses the reconstruction accuracy,
noise propagation and computation time for Magnetic Resonance Fingerprinting
(MRF).
  Methods
  Based on a singular value decomposition (SVD) of the signal evolution, MRF is
formulated as a low rank inverse problem in which one image is reconstructed
for each singular value under consideration. This low rank approximation of the
signal evolution reduces the computational burden by reducing the number of
Fourier transformations. Also, the low rank approximation improves the
conditioning of the problem, which is further improved by extending the low
rank inverse problem to an augmented Lagrangian that is solved by the
alternating direction method of multipliers (ADMM). The root mean square error
and the noise propagation are analyzed in simulations. For verification, in
vivo examples are provided.
  Results
  The proposed low rank ADMM approach shows a reduced root mean square error
compared to the original fingerprinting reconstruction, to a low rank
approximation alone and to an ADMM approach without a low rank approximation.
Incorporating sensitivity encoding allows for further artifact reduction.
  Conclusion
  The proposed reconstruction provides robust convergence, reduced
computational burden and improved image quality compared to other MRF
reconstruction approaches evaluated in this study.Comment: 47 Pages, 11 Figures, 1 Tabl
Simultaneous Multi-Slice MRI using Cartesian and Radial FLASH and
  Regularized Nonlinear Inversion: SMS-NLINV

Purpose: The development of a calibrationless parallel imaging method for
accelerated simultaneous multi-slice (SMS) MRI based on Regularized Nonlinear
Inversion (NLINV), evaluated using Cartesian and radial FLASH. Theory and
Methods: NLINV is a parallel imaging method that jointly estimates image
content and coil sensitivities using a Newton-type method with regularization.
Here, NLINV is extended to SMS-NLINV for reconstruction and separation of all
simultaneously acquired slices. The performance of the extended method is
evaluated for different sampling schemes using phantom and in-vivo experiments
based on Cartesian and radial SMS-FLASH sequences. Results: The basic algorithm
was validated in Cartesian experiments by comparison with ESPIRiT. For
Cartesian and radial sampling, improved results are demonstrated compared to
single-slice experiments, and it is further shown that sampling schemes using
complementary samples outperform schemes with the same samples in each
partition. Conclusion: The extension of the NLINV algorithm for SMS data was
implemented and successfully demonstrated in combination with a Cartesian and
radial SMS-FLASH sequence.Comment: Part of this work has been presented at the ISMRM Annual Conference
  2016 (Singapore) and 2017 (Honolulu). 25 pages, 8+4 figure