Estimation of undistorted images in brain echo-planar images with distortions using the conjugate gradient method with anatomical regularization

PURPOSE

Although echo-planar imaging (EPI) is widely used for diffusion magnetic resonance (MR) imaging, EPI images suffer from susceptibility-induced geometric distortions. We herein propose a new estimation method for undistorted EPI images using anatomical T₁ -weighted images (T₁ WIs) based on the physics of MR imaging.

METHODS

Our proposed method estimates the undistorted EPI image in the image domain while estimating the magnetic field inhomogeneity map using the conjugate gradient method with anatomical regularization. Our method synthesizes the distorted image to match the measured EPI image containing geometric distortions by alternately updating the undistorted EPI image and the magnetic field inhomogeneity map. We evaluated our proposed method and compared it with a nonrigid registration-based distortion correction method using simulated data and using real data. In the evaluation of the estimation of the magnetic field inhomogeneity map, we used the normalized root-mean-squared error (NRMSE) between the estimated results and the ground truth. In the evaluation of the estimation of undistorted images, we used mutual information (MI) between the undistorted EPI image and the anatomical T₁ WI.

RESULTS

Using the simulated data, the means and standard deviations of the NRMSE values in the nonrigid registration-based method and proposed method were 1.29 ± 0.63 and 0.64 ± 0.30, respectively. The MI values in the proposed method were larger than those in the nonrigid registration-based method in all evaluated slices. For the real data, the proposed method improved the distortion, and the MI values in the proposed method were larger than those in the nonrigid registration-based method. In the estimation of the magnetic field inhomogeneity map, the NRMSE values in our method were smaller than those in the nonrigid registration-based method.

CONCLUSIONS

We demonstrated that our proposed method can estimate the regions with compressed distortions that are not well represented by the nonrigid registration-based methods. The results suggest that the proposed method could be useful in analyses combining EPI images with T₁ WIs.

Integration of spatial distortion effects in a 4D computational phantom for simulation studies in extra-cranial MRI-guided radiation therapy: Initial results

PURPOSE

Spatial distortions in magnetic resonance imaging (MRI) are mainly caused by inhomogeneities of the static magnetic field, nonlinearities in the applied gradients, and tissue-specific magnetic susceptibility variations. These factors may significantly alter the geometrical accuracy of the reconstructed MR image, thus questioning the reliability of MRI for guidance in image-guided radiation therapy. In this work, we quantified MRI spatial distortions and created a quantitative model where different sources of distortions can be separated. The generated model was then integrated into a four-dimensional (4D) computational phantom for simulation studies in MRI-guided radiation therapy at extra-cranial sites.

METHODS

A geometrical spatial distortion phantom was designed in four modules embedding laser-cut PMMA grids, providing 3520 landmarks in a field of view of (345 × 260 × 480) mm³ . The construction accuracy of the phantom was verified experimentally. Two fast MRI sequences for extra-cranial imaging at 1.5 T were investigated, considering axial slices acquired with online distortion correction, in order to mimic practical use in MRI-guided radiotherapy. Distortions were separated into their sources by acquisition of images with gradient polarity reversal and dedicated susceptibility calculations. Such a separation yielded a quantitative spatial distortion model to be used for MR imaging simulations. Finally, the obtained spatial distortion model was embedded into an anthropomorphic 4D computational phantom, providing registered virtual CT/MR images where spatial distortions in MRI acquisition can be simulated.

RESULTS

The manufacturing accuracy of the geometrical distortion phantom was quantified to be within 0.2 mm in the grid planes and 0.5 mm in depth, including thickness variations and bending effects of individual grids. Residual spatial distortions after MRI distortion correction were strongly influenced by the applied correction mode, with larger effects in the trans-axial direction. In the axial plane, gradient nonlinearities caused the main distortions, with values up to 3 mm in a 1.5 T magnet, whereas static field and susceptibility effects were below 1 mm. The integration in the 4D anthropomorphic computational phantom highlighted that deformations can be severe in the region of the thoracic diaphragm, especially when using axial imaging with 2D distortion correction. Adaptation of the phantom based on patient-specific measurements was also verified, aiming at increased realism in the simulation.

CONCLUSIONS

The implemented framework provides an integrated approach for MRI spatial distortion modeling, where different sources of distortion can be quantified in time-dependent geometries. The computational phantom represents a valuable platform to study motion management strategies in extra-cranial MRI-guided radiotherapy, where the effects of spatial distortions can be modeled on synthetic images in a virtual environment.

Deconvolution-based distortion correction of EPI using analytic single-voxel point-spread functions

PURPOSE

To develop a postprocessing algorithm that corrects geometric distortions due to spatial variations of the static magnetic field amplitude, B₀ , and effects from relaxation during signal acquisition in EPI.

THEORY AND METHODS

An analytic, complex point-spread function is deduced for k-space trajectories of EPI variants and applied to corresponding acquisitions in a resolution phantom and in human volunteers at 3 T. With the analytic point-spread function and experimental maps of B₀ (and, optionally, the effective transverse relaxation time, T 2 * ) as input, a point-spread function matrix operator is devised for distortion correction by a Thikonov-regularized deconvolution in image space. The point-spread function operator provides additional information for an appropriate correction of the signal intensity distribution. A previous image combination algorithm for acquisitions with opposite phase blip polarities is adapted to the proposed method to recover destructively interfering signal contributions.

RESULTS

Applications of the proposed deconvolution-based distortion correction ("DecoDisCo") algorithm demonstrate excellent distortion corrections and superior performance regarding the recovery of an undistorted intensity distribution in comparison to a multifrequency reconstruction. Examples include full and partial Fourier standard EPI scans as well as double-shot center-out trajectories. Compared with other distortion-correction approaches, DecoDisCo permits additional deblurring to obtain sharper images in cases of significant T 2 * effects.

CONCLUSION

Robust distortion corrections in EPI acquisitions are feasible with high quality by regularized deconvolution with an analytic point-spread function. The general algorithm, which is publicly released on GitHub, can be straightforwardly adapted for specific EPI variants or other acquisition schemes.

Diffusion-Weighted Echo Planar Imaging using MUltiplexed Sensitivity Encoding and Reverse Polarity Gradient in Head and Neck Cancer: An Initial Study

We aimed to compare the geometric distortion (GD) correction performance and apparent diffusion coefficient (ADC) measurements of single-shot diffusion-weighted echo-planar imaging (SS-DWEPI), multiplexed sensitivity encoding (MUSE)-DWEPI, and MUSE-DWEPI with reverse-polarity gradient (RPG) in phantoms and patients. We performed phantom studies at 3T magnetic resonance imaging (MRI) using the American College of Radiology phantom and Quantitative Imaging Biomarker Alliance DW-MRI ice-water phantom to assess GD and effect of distortion in the measurement of ADC, respectively. Institutional review board approved the prospective clinical component of this study. DW-MRI data were obtained from 11 patients with head and neck cancer using these three DW-MRI methods. Wilcoxon signed-rank (WSR) and Kruskal–Wallis (KW) tests were used to compare ADC values, and qualitative rating by radiologist between three DW-MRI methods. In the ACR phantom, GD of 0.17% was observed for the b = 0 s/mm² image of the MUSE-DWEPI with RPG method compared with that of 1.53% and 2.1% of MUSE-DWEPI and SS-DWEPI, respectively; The corresponding methods root-mean-square errors were 0.58, 3.37, and 5.07 mm. WSR and KW tests showed no significant difference in the ADC measurement between these three DW-MRI methods for both healthy masseter muscles and neoplasms (P > .05). We observed improvement in spatial accuracy for MUSE-DWEPI with RPG in the head and neck region with a higher correlation (R² = 0.791) compared with that for SS-DWEPI (R² = 0.707) and MUSE-DWEPI (R² = 0.745). MUSE-DWEPI with RPG significantly reduces the distortion compared with MUSE-DWEPI or conventional SS-DWEPI techniques, and the ADC values were similar.

Characterization and Relaxation Properties of a Series of Monodispersed Magnetic Nanoparticles

Magnetic iron oxide nanoparticles are relatively advanced nanomaterials, and are widely used in biology, physics and medicine, especially as contrast agents for magnetic resonance imaging. Characterization of the properties of magnetic nanoparticles plays an important role in the application of magnetic particles. As a contrast agent, the relaxation rate directly affects image enhancement. We characterized a series of monodispersed magnetic nanoparticles using different methods and measured their relaxation rates using a 0.47 T low-field Nuclear Magnetic Resonance instrument. Generally speaking, the properties of magnetic nanoparticles are closely related to their particle sizes; however, neither longitudinal relaxation rate r1 nor transverse relaxation rate r2 changes monotonously with the particle size d. Therefore, size can affect the magnetism of magnetic nanoparticles, but it is not the only factor. Then, we defined the relaxation rates ri′ (i = 1 or 2) using the induced magnetization of magnetic nanoparticles, and found that the correlation relationship between r1′ relaxation rate and r1 relaxation rate is slightly worse, with a correlation coefficient of R2 = 0.8939, while the correlation relationship between r2′ relaxation rate and r2 relaxation rate is very obvious, with a correlation coefficient of R2 = 0.9983. The main reason is that r2 relaxation rate is related to the magnetic field inhomogeneity, produced by magnetic nanoparticles; however r1 relaxation rate is mainly a result of the direct interaction of hydrogen nucleus in water molecules and the metal ions in magnetic nanoparticles to shorten the T1 relaxation time, so it is not directly related to magnetic field inhomogeneity.

Designing 3D selective adiabatic radiofrequency pulses with single and parallel transmission

PURPOSE

To introduce a method of designing single and parallel transmit (pTx) 3D adiabatic π pulses for inverting and refocusing spins that are insensitive to transmit B1 ( B1+) inhomogeneity.

THEORY AND METHODS

A 3D adiabatic pulse is created by replacing each piece-wise constant element (or sub-pulse) of an adiabatic full passage (AFP) by a 2D selective pulse. In this study, the parent AFP is an HS1 and each sub-pulse is a 2D pulse derived from a jinc function designed using a spiral k-trajectory. Spatial selectivity in the third direction is achieved by blipping the slab-selective gradient between sub-pulses, yielding a rectangular slab profile identical to that of the parent AFP. The slew-rate limited sub-pulse can be undersampled utilizing pTx, thus shortening the overall pulse width. Simulations and experiments demonstrate the quality of spatial selectivity and adiabaticity achievable.

RESULTS

The 3D adiabatic pulse inverts and refocus spins in a sharply demarcated cylindrical volume. When stepping RF amplitude, an adiabatic threshold is observed above which the flip angle remains π. Experimental results demonstrate that pTx is an effective means to significantly improve pulse performance.

CONCLUSION

A method of designing 3D adiabatic pulses insensitive to B1 inhomogeneity has been developed. pTx can shorten these pulses while retaining their adiabatic character. Magn Reson Med 79:701-710, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

2D Pulses using spatially dependent frequency sweeping

PURPOSE

To introduce a method of designing two-dimensional (2D) frequency-modulated pulses that produce phase coherence in a spatiotemporal manner. Uniquely, this class of pulses provides the ability to compensate for field inhomogeneity using a spatiotemporally dependent trajectory of maximum coherence in a single-shot.

THEORY AND METHODS

A pulse design method based on a k-space description is developed. Bloch simulations and phantom experiments are used to demonstrate sequential spatiotemporal phase coherence and compensation for B1+ and B0 inhomogeneity.

RESULTS

In the presence of modulated gradients, the 2D frequency-modulated pulses were shown to excite a cylinder in a selective manner. With a surface coil transmitter, compensation of the effect of B1+ inhomogeneity was experimentally verified, in agreement with simulation results. In addition, simulations were used to demonstrate partial compensation for B0 inhomogeneity.

CONCLUSION

The 2D frequency-modulated pulses are a new class of pulses that generate phase coherence sequentially along a spatial trajectory determined by gradient- and frequency-modulated functions. By exploiting their spatiotemporal nature, 2D frequency-modulated pulses can compensate for spatial variation of the radiofrequency field in a single-shot excitation. Preliminary results shown suggest extensions might also be used to compensate for static field inhomogeneity. Magn Reson Med 76:1364-1374, 2016. © 2015 International Society for Magnetic Resonance in Medicine.

Technical challenges in 3 T magnetic resonance spectroscopic imaging of the prostate-A single-institution experience

The magnetic resonance spectroscopic imaging (MRSI) is the only technique that is currently available in the clinical practice to provide the metabolic status of prostate tissue at the cellular level with a great potential to improve the clinical patient care. Increasing the field strength from 1.5 to 3 T can theoretically provide proportionately higher signal-to-noise ratio (SNR) and improve spectral separation between prostatic metabolite peaks. The technique, however, has been limited to a few academic institutions that are equipped with a team of experts primarily due to due to serious technical challenges in optimizing the spectral quality. High quality shimming is key to the successful MRSI acquisition. Without optimization of the increased field inhomogeneity and radiofrequency (RF) dielectric effect at 3 T, the spectral peak broadening and residual signal from the periprostatic fat tissue may render the overall spectra non-diagnostic. The purpose of this technical note is to present the practical steps of successful acquisition of 3 T MRSI and to address several important technical challenges in minimizing the effect of the increased magnetic field and RF field inhomogeneity in order to obtain highest possible spectral quality based on our initial experience in using 3 T MRSI prototype software.

Shift-driven modulations of spin-echo signals

Since the pioneering works of Carr-Purcell and Meiboom-Gill [Carr HY, Purcell EM (1954) Phys Rev 94:630; Meiboom S, Gill D (1985) Rev Sci Instrum 29:688], trains of π-pulses have featured amongst the main tools of quantum control. Echo trains find widespread use in nuclear magnetic resonance spectroscopy (NMR) and imaging (MRI), thanks to their ability to free the evolution of a spin-1/2 from several sources of decoherence. Spin echoes have also been researched in dynamic decoupling scenarios, for prolonging the lifetimes of quantum states or coherences. Inspired by this search we introduce a family of spin-echo sequences, which can still detect site-specific interactions like the chemical shift. This is achieved thanks to the presence of weak environmental fluctuations of common occurrence in high-field NMR--such as homonuclear spin-spin couplings or chemical/biochemical exchanges. Both intuitive and rigorous derivations of the resulting "selective dynamical recoupling" sequences are provided. Applications of these novel experiments are given for a variety of NMR scenarios including determinations of shift effects under inhomogeneities overwhelming individual chemical identities, and model-free characterizations of chemically exchanging partners.

Associations of age, gender and body mass with 1H MR-observed brain metabolites and tissue distributions

Recent reports have indicated that a measure of adiposity, the body mass index (BMI), is associated with MR-observed brain metabolite concentrations and tissue volume measures. In addition to indicating possible associations between brain metabolism, BMI and cognitive function, the inclusion of BMI as an additional subject selection criterion could potentially improve the detection of metabolic and structural differences between subjects and study groups. In this study, a retrospective analysis of 140 volumetric MRSI datasets was carried out to investigate the value of including BMI in the subject selection relative to age and gender. The findings replicate earlier reports of strong associations of N-acetylaspartate, creatine, choline and gray matter with age and gender, with additional observations of slightly increased spectral linewidth with age and in female relative to male subjects. Associations of metabolite levels, linewidth and gray matter volume with BMI were also observed, although only in some regions. Using voxel-based analyses, it was also observed that the patterns of the relative changes of metabolites with BMI matched those of linewidth with BMI or weight, and that residual magnetic field inhomogeneity and measures of spectral quality were influenced by body weight. It is concluded that, although associations of metabolite levels and tissue distributions with BMI occur, these may be attributable to issues associated with data acquisition and analysis; however, an organic origin for these findings cannot be specifically excluded. There is, however, sufficient evidence to warrant the inclusion of body weight as a subject selection parameter, secondary to age, and as a factor in data analysis for MRS studies of some brain regions.