Compressed sensing for chemical shift‐based water–fat separation

Multi echo chemical shift‐based water–fat separation methods allow for uniform fat suppression in the presence of main field inhomogeneities. However, these methods require additional scan time for chemical shift encoding. This work presents a method for water–fat separation from undersampled data (CS‐WF), which combines compressed sensing and chemical shift‐based water–fat separation. Undersampling was applied in the k‐space and in the chemical shift encoding dimension to reduce the total scanning time. The method can reconstruct high quality water and fat images in 2D and 3D applications from undersampled data. As an extension, multipeak fat spectral models were incorporated into the CS‐WF reconstruction to improve the water–fat separation quality. In 3D MRI, reduction factors of above three can be achieved, thus fully compensating the additional time needed in three‐echo water–fat imaging. The method is demonstrated on knee and abdominal in vivo data. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.     

Regularized iterative reconstruction for undersampled BLADE and its applications in three‐point Dixon water–fat separation

In MRI, the suppression of fat signal is very important for many applications. Multipoint Dixon based water–fat separation methods are commonly used due to its robustness to B₀ homogeneity compared with other fat suppression methods, such as spectral fat saturation. The traditional Cartesian k‐space trajectory based multipoint Dixon technique is sensitive to motion, such as pulsatile blood flow, resulting in artifacts that compromise image quality. This work presents a three‐point Dixon water–fat separation method using undersampled BLADE (aka PROPELLER) for motion robustness and speed. A regularized iterative reconstruction method is then proposed for reducing the streaking artifacts coming from undersampling. In this study, the performance of the regularized iterative reconstruction method is first tested by simulations and on MR phantoms. The performance of the proposed technique is then evaluated in vivo by comparing it with conventional fat suppression methods on the human brain and knee. Experiments show that the presented method delivers reliable water–fat separation results. The reconstruction method suppresses streaking artifacts typical for undersampled BLADE acquisition schemes without missing fine structures in the image. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.     

Chemical shift encoding‐based water–fat separation methods

The suppression of signal from fat constitutes a basic requirement in many applications of magnetic resonance imaging. To date, this is predominantly achieved during data acquisition, using fat saturation, inversion recovery, or water excitation methods. Postponing the separation of signal from water and fat until image reconstruction holds the promise of resolving some of the problems associated with these methods, such as failure in the presence of field inhomogeneities or contrast agents. In this article, methods are reviewed that rely on the difference in chemical shift between the hydrogen atoms in water and fat to perform such a retrospective separation. The basic principle underlying these so‐called Dixon methods is introduced, and some fundamental implementations of the required chemical shift encoding in the acquisition and the subsequent water–fat separation in the reconstruction are described. Practical issues, such as the selection of key parameters and the appearance of typical artifacts, are illustrated, and a broad range of applications is demonstrated, including abdominal, cardiovascular, and musculoskeletal imaging. Finally, advantages and disadvantages of these Dixon methods are summarized, and emerging opportunities arising from the availability of information on the amount and distribution of fat are discussed. J. Magn. Reson. Imaging 2014;40:251–268 . © 2014 Wiley Periodicals, Inc .     

Accelerated water–fat imaging using restricted subspace field map estimation and compressed sensing

Water–fat separation techniques play an important role in a variety of clinical and research applications. In particular, multiecho separation methods remain a topic of great interest due to their ability to resolve water and fat images in the presence of B₀‐field inhomogeneity. However, these methods are inherently slow as they require multiple measurements. An accelerated technique with reduced k‐space sampling is desirable to decrease the scan time. This work presents a new method for water–fat separation from accelerated multiecho acquisitions. The proposed approach does not require the region‐growing or region‐merging schemes that are typically used for field map estimation. Instead, the water, fat, and field map signals are estimated directly from the undersampled k‐space measurements. In this work, up to 2.5×‐acceleration is demonstrated in a water–fat phantom, ankle, knee, and liver. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.     

Phase and amplitude correction for multi‐echo water–fat separation with bipolar acquisitions

Purpose:

To address phase and amplitude errors for multi‐point water–fat separation with “bipolar” acquisitions, which efficiently collect all echoes with alternating read‐out gradient polarities in one repetition.

Materials and Methods:

With the bipolar acquisitions, eddy currents and other system nonidealities can induce inconsistent phase errors between echoes, disrupting water–fat separation. Previous studies have addressed phase correction in the read‐out direction. However, the bipolar acquisitions may be subject to spatially high order phase errors as well as an amplitude modulation in the read‐out direction. A method to correct for the 2D phase and amplitude errors is introduced. Low resolution reference data with reversed gradient polarities are collected. From the pair of low‐resolution data collected with opposite gradient polarities, the two‐dimensional phase errors are estimated and corrected. The pair of data are then combined for water–fat separation.

Results:

We demonstrate that the proposed method can effectively remove the high order errors with phantom and in vivo experiments, including obliquely oriented scans.

Conclusion:

For bipolar multi‐echo acquisitions, uniform water–fat separation can be achieved by removing high order phase errors with the proposed method. J. Magn. Reson. Imaging 2010;31:1264–1271. © 2010 Wiley‐Liss, Inc.     

Iterative decomposition of water and fat with echo asymmetry and least‐squares estimation (IDEAL): Application with fast spin‐echo imaging

Chemical shift based methods are often used to achieve uniform water–fat separation that is insensitive to B_o inhomogeneities. Many spin‐echo (SE) or fast SE (FSE) approaches acquire three echoes shifted symmetrically about the SE, creating time‐dependent phase shifts caused by water–fat chemical shift. This work demonstrates that symmetrically acquired echoes cause artifacts that degrade image quality. According to theory, the noise performance of any water–fat separation method is dependent on the proportion of water and fat within a voxel, and the position of echoes relative to the SE. To address this problem, we propose a method termed “iterative decomposition of water and fat with echo asymmetric and least‐squares estimation” (IDEAL). This technique combines asymmetrically acquired echoes with an iterative least‐squares decomposition algorithm to maximize noise performance. Theoretical calculations predict that the optimal echo combination occurs when the relative phase of the echoes is separated by 2π/3, with the middle echo centered at π/2+πk (k = any integer), i.e., (–π/6+πk, π/2+πk, 7π/6+πk). Only with these echo combinations can noise performance reach the maximum possible and be independent of the proportion of water and fat. Close agreement between theoretical and experimental results obtained from an oil–water phantom was observed, demonstrating that the iterative least‐squares decomposition method is an efficient estimator. Magn Reson Med, 2005. © 2005 Wiley‐Liss, Inc.     

Dual‐echo Dixon imaging with flexible choice of echo times

In this work, a new two‐point method for water–fat imaging is described and explored. It generalizes existing two‐point methods by eliminating some of the restrictions that these methods impose on the choice of echo times. Thus, the new two‐point method promises to provide more freedom in the selection of protocol parameters and to reach higher scan efficiency. Its performance was studied theoretically and was evaluated experimentally in abdominal imaging with a multigradient‐echo sequence. While depending on the choice of echo times, it is generally found to be favorable compared to existing two‐point methods. Notably, water images with higher spatial resolution and better signal‐to‐noise ratio were attained with it in single breathholds at 3.0 T and 1.5 T, respectively. The use of more accurate spectral models of fat is shown to substantially reduce observed variations in the extent of fat suppression. The acquisition of in‐ and opposed‐phase images is demonstrated to be replaceable by a synthesis from water and fat images. The new two‐point method is finally also applied to autocalibrate a multidimensional eddy current correction and to enhance the fat suppression achieved with three‐point methods in this way, especially toward the edges of larger field of views. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.     

Addressing phase errors in fat‐water imaging using a mixed magnitude/complex fitting method

Accurate, noninvasive measurements of liver fat content are needed for the early diagnosis and quantitative staging of nonalcoholic fatty liver disease. Chemical shift‐based fat quantification methods acquire images at multiple echo times using a multiecho spoiled gradient echo sequence, and provide fat fraction measurements through postprocessing. However, phase errors, such as those caused by eddy currents, can adversely affect fat quantification. These phase errors are typically most significant at the first echo of the echo train, and introduce bias in complex‐based fat quantification techniques. These errors can be overcome using a magnitude‐based technique (where the phase of all echoes is discarded), but at the cost of significantly degraded signal‐to‐noise ratio, particularly for certain choices of echo time combinations. In this work, we develop a reconstruction method that overcomes these phase errors without the signal‐to‐noise ratio penalty incurred by magnitude fitting. This method discards the phase of the first echo (which is often corrupted) while maintaining the phase of the remaining echoes (where phase is unaltered). We test the proposed method on 104 patient liver datasets (from 52 patients, each scanned twice), where the fat fraction measurements are compared to coregistered spectroscopy measurements. We demonstrate that mixed fitting is able to provide accurate fat fraction measurements with high signal‐to‐noise ratio and low bias over a wide choice of echo combinations. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.     

Simultaneous T2 and lipid quantitation using IDEAL‐CPMG

Muscle damage, edema, and fat infiltration are hallmarks of a range of neuromuscular diseases. The T₂ of water, T_2,w, in muscle lengthens with both myocellular damage and inflammation and is typically measured using multiple spin‐echo or Carr–Purcell–Meiboom–Gill acquisitions. However, microscopic fat infiltration in neuromuscular diseases prevents accurate T_2,w quantitation as the longer T₂ of fat, T_2,f, masks underlying changes in the water component. Fat saturation can be inconsistent across the imaging volume and removes valuable physiological fat information. A new method is presented that combines iterative decomposition of water and fat with echo asymmetry and least squares estimation with a Carr–Purcell–Meiboom–Gill–sequence. The sequence results in water and fat separated images at each echo time for use in T_2,w and T_2,f quantification. With knowledge of the T_2,w and T_2,f, a T₂‐corrected fat fraction map can also be calculated. Monte‐Carlo simulations and measurements in phantoms, volunteers, and a patient with inclusion body myositis are demonstrated. In healthy volunteers, uniform T_2,w and T₂‐corrected fat fraction maps are present within all muscle groups. However, muscle‐specific patterns of fat infiltration and edema are evident in inclusion body myositis, which demonstrates the power of separating and quantifying the fat and water components. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.     

Chemical shift encoded water–fat separation using parallel imaging and compressed sensing

Chemical shift encoded techniques have received considerable attention recently because they can reliably separate water and fat in the presence of off‐resonance. The insensitivity to off‐resonance requires that data be acquired at multiple echo times, which increases the scan time as compared to a single echo acquisition. The increased scan time often requires that a compromise be made between the spatial resolution, the volume coverage, and the tolerance to artifacts from subject motion. This work describes a combined parallel imaging and compressed sensing approach for accelerated water–fat separation. In addition, the use of multiscale cubic B‐splines for B₀ field map estimation is introduced. The water and fat images and the B₀ field map are estimated via an alternating minimization. Coil sensitivity information is derived from a calculated k‐space convolution kernel and l₁‐regularization is imposed on the coil‐combined water and fat image estimates. Uniform water–fat separation is demonstrated from retrospectively undersampled data in the liver, brachial plexus, ankle, and knee as well as from a prospectively undersampled acquisition of the knee at 8.6x acceleration. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.     

Frequency response of multipoint chemical shift‐based spectral decomposition

Purpose

To provide a framework for characterizing the frequency response of multipoint chemical shift based species separation techniques.

Materials and Methods

Multipoint chemical shift based species separation techniques acquire complex images at multiple echo times and perform maximum likelihood estimation to decompose signal from different species into separate images. In general, after a nonlinear process of estimating and demodulating the field map, these decomposition methods are linear transforms from the echo‐time domain to the chemical‐shift‐frequency domain, analogous to the discrete Fourier transform (DFT). In this work we describe a technique for finding the magnitude and phase of chemical shift decomposition for input signals over a range of frequencies using numerical and experimental modeling and examine several important cases of species separation.

Results

Simple expressions can be derived to describe the response to a wide variety of input signals. Agreement between numerical modeling and experimental results is very good.

Conclusion

Chemical shift‐based species separation is linear, and therefore can be fully described by the magnitude and phase curves of the frequency response. The periodic nature of the frequency response has important implications for the robustness of various techniques for resolving ambiguities in field inhomogeneity. J. Magn. Reson. Imaging 2010;32:943–952. © 2010 Wiley‐Liss, Inc.     

Homodyne reconstruction and IDEAL water-fat decomposition.

Multipoint water-fat separation methods have received renewed interest because they provide uniform separation of water and fat despite the presence of B0 and B1 field inhomogeneities. Unfortunately, full-resolution reconstruction of partial k-space acquisitions has been incompatible with these methods. Conventional homodyne reconstruction and related algorithms are commonly used to reconstruct partial k-space data sets by exploiting the Hermitian symmetry of k-space in order to maximize the spatial resolution of the image. In doing so, however, all phase information of the image is lost. The phase information of complex source images used in a water-fat separation acquisition is necessary to decompose water from fat. In this work, homodyne imaging is combined with the IDEAL (iterative decomposition of water and fat with echo asymmetry and least squares estimation) method to reconstruct full resolution water and fat images free of blurring. This method is extended to multicoil steady-state free precession and fast spin-echo applications and examples are shown.     

T2‐weighted 3D fast spin echo imaging with water–fat separation in a single acquisition

Purpose:

To develop a robust 3D fast spin echo (FSE) T₂‐weighted imaging method with uniform water and fat separation in a single acquisition, amenable to high‐quality multiplanar reformations.

Materials and Methods:

The Iterative Decomposition of water and fat with Echo Asymmetry and Least squares estimation (IDEAL) method was integrated with modulated refocusing flip angle 3D‐FSE. Echoes required for IDEAL processing were acquired by shifting the readout gradient with respect to the Carr‐Purcell‐Meiboom‐Gill echo. To reduce the scan time, an alternative data acquisition using two gradient echoes per repetition was implemented. Using the latter approach, a total of four gradient echoes were acquired in two repetitions and used in the modified IDEAL reconstruction.

Results:

3D‐FSE T₂‐weighted images with uniform water–fat separation were successfully acquired in various anatomies including breast, abdomen, knee, and ankle in clinically feasible scan times, ranging from 5:30–8:30 minutes. Using water‐only and fat‐only images, in‐phase and out‐of‐phase images were reconstructed.

Conclusion:

3D‐FSE‐IDEAL provides volumetric T₂‐weighted images with uniform water and fat separation in a single acquisition. High‐resolution images with multiple contrasts can be reformatted to any orientation from a single acquisition. This could potentially replace 2D‐FSE acquisitions with and without fat suppression and in multiple planes, thus improving overall imaging efficiency. J. Magn. Reson. Imaging 2010;32:745–751. © 2010 Wiley‐Liss, Inc.     

T1‐corrected fat quantification using chemical shift‐based water/fat separation: Application to skeletal muscle

Chemical shift‐based water/fat separation, like iterative decomposition of water and fat with echo asymmetry and least‐squares estimation, has been proposed for quantifying intermuscular adipose tissue. An important confounding factor in iterative decomposition of water and fat with echo asymmetry and least‐squares estimation‐based intermuscular adipose tissue quantification is the large difference in T₁ between muscle and fat, which can cause significant overestimation in the fat fraction. This T₁ bias effect is usually reduced by using small flip angles. T₁‐correction can be performed by using at least two different flip angles and fitting for T₁ of water and fat. In this work, a novel approach for the water/fat separation problem in a dual flip angle experiment is introduced and a new approach for the selection of the two flip angles, labeled as the unequal small flip angle approach, is developed, aiming to improve the noise efficiency of the T₁‐correction step relative to existing approaches. It is shown that the use of flip angles, selected such the muscle water signal is assumed to be T₁‐independent for the first flip angle and the fat signal is assumed to be T₁‐independent for the second flip angle, has superior noise performance to the use of equal small flip angles (no T₁ estimation required) and the use of large flip angles (T₁ estimation required). Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.     

Two‐point dixon method with flexible echo times

The two‐point Dixon method is a proton chemical shift imaging technique that produces separated water‐only and fat‐only images from a dual‐echo acquisition. It is shown how this can be achieved without the usual constraints on the echo times. A signal model considering spectral broadening of the fat peak is proposed for improved water/fat separation. Phase errors, mostly due to static field inhomogeneity, must be removed prior to least‐squares estimation of water and fat. To resolve ambiguity of the phase errors, a corresponding global optimization problem is formulated and solved using a message‐passing algorithm. It is shown that the noise in the water and fat estimates matches the Cramér‐Rao bounds, and feasibility is demonstrated for in vivo abdominal breath‐hold imaging. The water‐only images were found to offer superior fat suppression compared with conventional spectrally fat suppressed images. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.     

Turboprop IDEAL: A motion‐resistant fat–water separation technique

Suppression of the fat signal in MRI is very important for many clinical applications. Multi‐point water–fat separation methods, such as IDEAL (Iterative Decomposition of water and fat with Echo Asymmetry and Least‐squares estimation), can robustly separate water and fat signal, but inevitably increase scan time, making separated images more easily affected by patient motions. PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) and Turboprop techniques offer an effective approach to correct for motion artifacts. By combining these techniques together, we demonstrate that the new TP‐IDEAL method can provide reliable water–fat separation with robust motion correction. The Turboprop sequence was modified to acquire source images, and motion correction algorithms were adjusted to assure the registration between different echo images. Theoretical calculations were performed to predict the optimal shift and spacing of the gradient echoes. Phantom images were acquired, and results were compared with regular FSE‐IDEAL. Both T1‐ and T2‐weighted images of the human brain were used to demonstrate the effectiveness of motion correction. TP‐IDEAL images were also acquired for pelvis, knee, and foot, showing great potential of this technique for general clinical applications. Magn Reson Med 61:188–195, 2009. © 2008 Wiley‐Liss, Inc.     

Water-fat separation with IDEAL gradient-echo imaging

Purpose

To combine gradient‐echo (GRE) imaging with a multipoint water–fat separation method known as “iterative decomposition of water and fat with echo asymmetry and least squares estimation” (IDEAL) for uniform water–fat separation. Robust fat suppression is necessary for many GRE imaging applications; unfortunately, uniform fat suppression is challenging in the presence of B₀ inhomogeneities. These challenges are addressed with the IDEAL technique.

Materials and Methods

Echo shifts for three‐point IDEAL were chosen to optimize noise performance of the water–fat estimation, which is dependent on the relative proportion of water and fat within a voxel. Phantom experiments were performed to validate theoretical SNR predictions. Theoretical echo combinations that maximize noise performance are discussed, and examples of clinical applications at 1.5T and 3.0T are shown.

Results

The measured SNR performance validated theoretical predictions and demonstrated improved image quality compared to unoptimized echo combinations. Clinical examples of the liver, breast, heart, knee, and ankle are shown, including the combination of IDEAL with parallel imaging. Excellent water–fat separation was achieved in all cases. The utility of recombining water and fat images into “in‐phase,” “out‐of‐phase,” and “fat signal fraction” images is also discussed.

Conclusion

IDEAL‐SPGR provides robust water–fat separation with optimized SNR performance at both 1.5T and 3.0T with multicoil acquisitions and parallel imaging in multiple regions of the body. J. Magn. Reson. Imaging 2007;25:644–652. © 2007 Wiley‐Liss, Inc.     

Linear phase‐error correction for improved water and fat separation in dual‐echo dixon techniques

Large and spatially‐linear phase errors along the frequency‐encode direction may be induced by several common and hard‐to‐avoid system imperfections such as eddy currents. For data acquired in dual‐echo Dixon techniques, the linear phase error can be more aggravated when compared to that acquired in a single echo and can pose challenges to a phase‐correction algorithm necessary for successful Dixon processing. In this work, we propose a two‐step process that first corrects the linear component of the phase errors with a modified Ahn‐Cho algorithm (Ahn CB and Cho ZH, IEEE Trans. Med. Imaging 6:32, 1987) and then corrects the residual phase errors with a previously‐developed region‐growing algorithm (Ma J, Magn. Res. Med. 52:415, 2004). We demonstrate that successive application of the two‐step process to data from a dual‐echo Dixon technique provides a “1‐2 punch” to the overall phase errors and can overcome local water and fat separation failures that are observed when the region‐growing–based algorithm is applied alone. Magn Reson Med 60:1250–1255, 2008. © 2008 Wiley‐Liss, Inc.     

Quantification of hepatic steatosis with MRI: The effects of accurate fat spectral modeling

Purpose

To develop a chemical‐shift–based imaging method for fat quantification that accounts for the complex spectrum of fat, and to compare this method with MR spectroscopy (MRS). Quantitative noninvasive biomarkers of hepatic steatosis are urgently needed for the diagnosis and management of nonalcoholic fatty liver disease (NAFLD).

Materials and Methods

Hepatic steatosis was measured with “fat‐fraction” images in 31 patients using a multiecho chemical‐shift–based water‐fat separation method at 1.5T. Fat‐fraction images were reconstructed using a conventional signal model that considers fat as a single peak at –210 Hz relative to water (“single peak” reconstruction). Fat‐fraction images were also reconstructed from the same source images using two methods that account for the complex spectrum of fat; precalibrated and self‐calibrated “multipeak” reconstruction. Single‐voxel MRS that was coregistered with imaging was performed for comparison.

Results

Imaging and MRS demonstrated excellent correlation with single peak reconstruction (r² = 0.91), precalibrated multipeak reconstruction (r² = 0.94), and self‐calibrated multipeak reconstruction (r² = 0.91). However, precalibrated multipeak reconstruction demonstrated the best agreement with MRS, with a slope statistically equivalent to 1 (0.96 ± 0.04; P = 0.4), compared to self‐calibrated multipeak reconstruction (0.83 ± 0.05, P = 0.001) and single‐peak reconstruction (0.67 ± 0.04, P < 0.001).

Conclusion

Accurate spectral modeling is necessary for accurate quantification of hepatic steatosis with MRI. J. Magn. Reson. Imaging 2009;29:1332–1339. © 2009 Wiley‐Liss, Inc.     

Fat‐water separated delayed hyperenhanced myocardial infarct imaging

Fat deposition associated with myocardial infarction (MI) has been reported as a commonly occurring phenomenon. Magnetic resonance imaging (MRI) has the ability to efficiently detect MI using T₁‐sensitive contrast‐enhanced sequences and fat via its resonant frequency shift. In this work, the feasibility of fat‐water separation applied to the conventional delayed hyperenhanced (DHE) MI imaging technique is demonstrated. A three‐point Dixon acquisition and reconstruction was combined with an inversion recovery gradient‐echo pulse sequence. This allowed fat‐water separation along with T₁ sensitive imaging after injection of a gadolinium contrast agent. The technique is demonstrated in phantom experiments and three subjects with chronic MI. Areas of infarction were well defined as conventional hyperenhancement in water images. In two cases, fatty deposition was detected in fat images and confirmed by precontrast opposed‐phase imaging. Magn Reson Med 60:503–509, 2008. © 2008 Wiley‐Liss, Inc.