Patent Publication Number: US-2022236358-A1

Title: Model-Based Iterative Reconstruction for Magnetic Resonance Imaging with Echo Planar Readout

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of U.S. Provisional Patent Application Ser. No. 62/839,019 filed on Apr. 26, 2019, and entitled “Model-Based Iterative Reconstruction for Magnetic Resonance Imaging with Echo Planar Readout,” which is herein incorporated by reference in its entirety. 
    
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH 
     This invention was made with government support under EB024450 awarded by the National Institutes of Health. The government has certain rights in the invention. 
    
    
     BACKGROUND 
     Echo planar imaging (“EPI”) is widely used clinically for its speed, but is known to be sensitive to hardware non-idealities including B 0  field inhomogeneity, eddy-currents, and gradient nonlinearity (“GNL”). Such non-idealities are not typically managed during image reconstruction, resulting in geometrically distorted images. To correct these distortions, image-based post-processing methods (e.g., interpolation) are commonly applied, but these tend to degrade resolution and provide only partial corrections. Hybrid reconstruction models that leverage image-based corrections within an iterative framework have also been proposed, with some success. However, there remains a need for a comprehensive reconstruction framework that prospectively accounts for multiple non-idealities. 
     SUMMARY OF THE DISCLOSURE 
     The present disclosure addresses the aforementioned drawbacks by providing a method for reconstructing an image from data acquired with a magnetic resonance imaging (MRI) system. The method includes accessing k-space data with a computer system. The k-space data are acquired from a subject using an MRI system operating an echo planar imaging (EPI) pulse sequence. Signal model parameters are also accessed with the computer system. The signal model parameters are associated with non-idealities of the MRI system used to acquire the k-space data. An image is reconstructed from the k-space data using the computer system to construct a signal model based in part on the signal model parameters and to optimize an objective function that is based on the signal model. The signal model prospectively accounts for non-idealities of the MRI system. 
     In one configuration, a method is provided for reconstructing an image from data acquired with a magnetic resonance imaging (MRI) system. The steps of the method include accessing k-space data with a computer system. The k-space data are acquired from a subject using an MRI system operating an echo planar imaging (EPI) pulse sequence. The method also includes accessing signal model parameters with the computer system. The signal model parameters are associated with non-idealities of the MRI system used to acquire the k-space data. The method also includes reconstructing an image from the k-space data using the computer system to construct a signal model based in part on the signal model parameters and to optimize an objective function that is based on the signal model, which prospectively accounts for non-idealities of the MRI system. 
     In some configurations, the non-idealities of the MRI system are associated with off-resonance effects, gradient nonlinearities, and ramp-sampling. The k-space data may be undersampled k-space data, and the k-space data may be acquired using a partial Fourier encoding. 
     In some configurations, the signal model parameters include coil sensitivity profile data associated with a radio frequency (RF) coil array used when acquiring the k-space data. The coil sensitivity profile data may be accessed from a data storage of the MRI system. The signal model parameters may include ramp-sampling data, which may be accessed from a pulse sequence server of the MRI system. The signal model parameters may include gradient nonlinearity data, main magnetic field (B 0 ) map data, and/or phase reference data. The phase reference data may be generated by optimizing an objective function that is based on the signal model parameters without phase constraints, and reconstructing the image may include updating the signal model using the phase reference data. 
     In some configurations, the objective function is optimized using a nonlinear regularization. The nonlinear regularization may be a wavelet-based sparsity regularization for improved noise performance. The nonlinear regularization may include use of a set of convolutional linear transform functions for improved noise performance. 
     In some configurations, the k-space data includes multiple EPI k-space data sets and the method may include simultaneously reconstructing the multiple EPI k-space data sets using a model based iterative reconstruction procedure. 
     In some configurations, the objective function may be optimized using a nonlinear regularization that includes a regularization functional that considers each k-space data set separately. The objective function may be optimized using a nonlinear regularization that includes a regularization functional that considers two or more of the k-space data sets jointly. The nonlinear regularization may promote a set of reconstructed images to be low-rank. The nonlinear regularization may locally promote low-rankedness at one or more scales. 
     In some configurations, the pulse sequence implemented with the MRI system to acquire the k-space data is a single-shot EPI pulse sequence. In some configurations, the pulse sequence implemented with the MRI system to acquire the k-space data is a multi-shot EPI pulse sequence. 
     The foregoing and other aspects and advantages of the present disclosure will appear from the following description. In the description, reference is made to the accompanying drawings that form a part hereof, and in which there is shown by way of illustration a preferred embodiment. This embodiment does not necessarily represent the full scope of the invention, however, and reference is therefore made to the claims and herein for interpreting the scope of the invention. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a flowchart setting forth the steps of an example method for reconstructing images from k-space data acquired using an EPI acquisition and using a comprehensive model-based image reconstruction. 
         FIG. 2  is a block diagram of an example MRI system that can implement the systems and methods described in the present disclosure. 
         FIG. 3  is a block diagram of an example computer system that can implement the systems and methods described in the present disclosure. 
     
    
    
     DETAILED DESCRIPTION 
     Described here are systems and methods that implement a model-based reconstruction that prospectively and simultaneously accounts for multiple non-idealities in accelerated single-shot-EPI acquisitions. In some implementations, nonlinear regularization (e.g., sparsity regularization) is also incorporated to mitigate noise amplification. The methods described in the present disclosure provide for images with reduced distortions and noise amplification effects relative to those images that are processed post-reconstruction to correct for non-idealities. For instance, phantom and in vivo experiments have demonstrated that the systems and methods described in the present disclosure improve geometric accuracy and image SNR relative to both online standard reconstructions as well as widely used post-processing strategies. 
     As noted, the systems and methods described in the present disclosure implement an image reconstruction from data acquired using an EPI acquisition, such as a single-shot EPI acquisition. The signal model for this acquisition can be described as follows. 
     Let TE, Δt, and T denote the echo time, dwell time, and echo-spacing times of a single-shot EPI acquisition. Neglecting T 2 * and presuming pre-correction of eddy-current and gradient delay effects, the signal measured during readout m∈[0,M) of phase-encoding line n∈[0,N) can be modeled as: 
     
       
         
           
             
               
                 
                   
                     
                       
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     where f is the target signal, k x  and k y  are sampling maps, s c  is the sensitivity profile for coil c∈[0,C), ω 0  is the B 0 -field map, 
     
       
         
           
             
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     denotes sampling-time, n x (x, y) and η y (x, y) are gradient nonlinearity (“GNL”) maps, and ε is Gaussian noise. Note that Eqn. (1) accommodates ramp-sampling, parallel imaging, and partial Fourier acceleration. 
     Because EPI uses high readout-bandwidth, Δt  T, and off-resonances are primarily manifest along the phase encoded (i.e., blipped) direction, Δt≈0 can be assumed. Letting, 
         u ( x,y )= f ( x,y ) e   iΔω     0     (x,y)TE    
     and time-segmenting Eqn. (1) yields: 
     
       
         
           
             
               
                 
                   
                     
                       
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     Where Φ l  is a spectral window, γ l  denotes the center of segment l, and p∈[0,P) and q∈[0,Q) are pixel indices. Defining, 
     
       
         
           
             
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     Eqn. (2) abstracts to: 
     
       
         
           
             
               
                 
                   
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     where F is a Fourier transform. If a phase reference, θ, for u is available, the complex target reduces to, 
         u =diag{ e   jθ   }v=P (θ) v  
 
     where v∈   12 . 
     The target image in Eqn. (2) can be estimated, as one non-limiting example, via regularized least squares estimation: 
     
       
         
           
             
               
                 
                   
                     
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     where β&gt;0 is a regularization parameter. As one non-limiting example, a joint redundant wavelet sparsity regularization, such as the following, can be used: 
     
       
         
           
             
               
                 
                   
                     
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     where δ and ⊗ are Kronecker&#39;s delta and product, Ψ is the Daubechies-4-wavelet, Γ k  is a shift operator over neighborhood ξ, and ∥⋅| 1,2  is the matrix-1,2 norm. Because Eqn. (4) is convex, it can be solved using techniques such as FISTA with composite splitting. For efficiency, the Fourier transform can be implemented as a type-III non-uniform fast Fourier transform (“NUFFT”). 
     Referring now to  FIG. 1 , a flowchart is illustrated as setting forth the steps of a non-limiting example of a method for reconstructing an image from magnetic resonance data (e.g., k-space data) using a comprehensive model-based image reconstruction, such as those described above in detail. The method begins by accessing k-space data for reconstruction, as indicated at step  102 . Accessing the k-space data can include retrieving previously acquired data from a memory or other data storage device or medium. Additionally or alternatively, accessing the k-space data can include acquiring such data with an MRI system and communicating that data to the computer system, which may be a part of the MRI system. As described above, the k-space data are generally acquired using an EPI pulse sequence, such as a single-shot EPI pulse sequence, whether or not undersampling is also implemented. As another example, data can be acquired using a multi-shot EPI pulse sequence. 
     As part of the model-based integrated reconstruction process, various parameters and data are provided to the computer system in order to implement or otherwise establish the model used for reconstruction, as generally depicted by process block  104 . As noted above, these parameters or data include coil sensitivity profiles, ramp-sampling data or information, GNL data or information, B 0  maps, and phase reference data or information. 
     In some implementations the coil sensitivity profiles can be vendor-provided coil sensitivity profiles. In some other implementations, the coil sensitivity profiles can be estimated or otherwise measured using any suitable technique known to those skilled in the magnetic resonance imaging arts. 
     As an example, ramp-sampling data can be provided from the pulse sequence server of the MRI system. The GNL information can be provided, as non-limiting examples, by retrieving the appropriate information from the MRI system data storage, by performing an appropriate electromagnetic simulation, or by using a calibration procedure based on phantom images acquired with the MRI system. 
     The B 0  field maps can be estimated using any suitable B 0  mapping techniques. As one non-limiting example, the B 0  maps can be estimated from a calibration scan (e.g., a dual-echo GRE calibration scan). For instance, the B 0  maps can be estimated from such a calibration scan using a graph cut-based procedure. As one non-limiting example, the phase reference, θ, can be obtained by minimizing Eqn. (4) without phase constraints. 
     Images are then reconstructed using a model-based image reconstruction, such as those described above, as indicated at step  106 . The model-based image reconstruction can be implemented by constructing a comprehensive signal model that incorporates the model parameters and data provided in step  104 , or otherwise accessing a previously constructed comprehensive signal model and incorporating the model parameters and data provided in step  104 . For instance, images are reconstructed using a model-based estimation process that provides correction for multiple different non-idealities during, rather than after, image reconstruction. In general, this process is based on a comprehensive signal model that incorporates the aforementioned model parameters and data, such as the signal models referenced in Eqns. (1), (2), or (3). 
     As an example, the image reconstruction can be implemented by solving the minimization problem in Eqn. (4). As described above, this reconstruction problem can be regularized using a nonlinear regularization, such as the sparsity regularization described with respect to Eqn. (5). In other implementations, the nonlinear regularization can include the use of a set of convolutional linear transform functions for improved noise performance. 
     In some instances, the acquired data include a plurality of k-space data sets that can be simultaneously reconstructed using the model-based image reconstruction. In these instances, the nonlinear regularization can include a regularization functional that considers each k-space data set separately. Alternatively, the regularization function can consider two or more of the k-space data sets jointly. The nonlinear regularization may also promote the reconstructed image set to be low-rank. In some instances, the low-rankedness can be promoted locally at one or more scales. 
     In one non-limiting example study, two healthy volunteers were imaged using a compact 3T MRI system: (G=80 mT/m, SR=700 T/m/s), with C=32 or C=8 head-only receiver-only RF head coils. Following field map, coil sensitivity, and eddy current calibration, single-shot EPI acquisitions were performed with the following parameters: FOV=220×200 mm 2 , SENSE R=2, Partial Fourier=5/8, TR/TE=3700/50 ms, and BW=250 kHz. Prior to MBIR, eddy current correction was performed in k-space using vendor-provided tools. MBIR was performed in Matlab, using a 2X-oversampled NUFFT with width=5 Kaiser-Bessel kernel, L=N time segments, and a 7×7 shift window. FISTA was executed for 30 iterations. The regularization parameter was chosen manually (β=0.02). For comparison, vendor reconstructions were saved and post-processed using standard intensity corrected image interpolation for distortion correction. 
     The distortion correction performance of the proposed MBIR strategy was tested against the vendor reconstruction, with and without post-processing. Both conventional post-processing and MBIR effectively corrected coarse distortion, with the latter providing modest improvements; however, MBIR offered reduced noise amplification relative to both the original and post-processed vendor reconstructions. This advantage was particularly apparent in low-contrast structures like the caudate head. 
     Systems and methods for a comprehensive MBIR strategy for single-shot EPI that prospectively accounts for off-resonance, GNL, ramp-sampling, and parallel imaging and partial Fourier-type acceleration have been provided. In some implementations, the MBIR strategy leverages wavelet-based sparsity regularization for improved noise performance. The proposed framework could benefit any EPI-based application, such as diffusion or elastography. 
     Referring now to  FIG. 2 , a non-limiting example of an MRI system  200  that can implement the methods described herein is illustrated. The MRI system  200  includes an operator workstation  202  that may include a display  204 , one or more input devices  206  (e.g., a keyboard, a mouse), and a processor  208 . The processor  208  may include a commercially available programmable machine running a commercially available operating system. The operator workstation  202  provides an operator interface that facilitates entering scan parameters into the MRI system  200 . The operator workstation  202  may be coupled to different servers, including, for example, a pulse sequence server  210 , a data acquisition server  212 , a data processing server  214 , and a data store server  216 . The operator workstation  202  and the servers  210 ,  212 ,  214 , and  216  may be connected via a communication system  240 , which may include wired or wireless network connections. 
     The pulse sequence server  210  functions in response to instructions provided by the operator workstation  202  to operate a gradient system  218  and a radiofrequency (“RF”) system  220 . Gradient waveforms for performing a prescribed scan are produced and applied to the gradient system  218 , which then excites gradient coils in an assembly  222  to produce the magnetic field gradients G x , G y , and G z  that are used for spatially encoding magnetic resonance signals. The gradient coil assembly  222  forms part of a magnet assembly  224  that includes a polarizing magnet  226  and a whole-body RF coil  228 . 
     RF waveforms are applied by the RF system  220  to the RF coil  228 , or a separate local coil to perform the prescribed magnetic resonance pulse sequence. Responsive magnetic resonance signals detected by the RF coil  228 , or a separate local coil, are received by the RF system  220 . The responsive magnetic resonance signals may be amplified, demodulated, filtered, and digitized under direction of commands produced by the pulse sequence server  210 . The RF system  220  includes an RF transmitter for producing a wide variety of RF pulses used in MRI pulse sequences. The RF transmitter is responsive to the prescribed scan and direction from the pulse sequence server  210  to produce RF pulses of the desired frequency, phase, and pulse amplitude waveform. The generated RF pulses may be applied to the whole-body RF coil  228  or to one or more local coils or coil arrays. 
     The RF system  220  also includes one or more RF receiver channels. An RF receiver channel includes an RF preamplifier that amplifies the magnetic resonance signal received by the coil  228  to which it is connected, and a detector that detects and digitizes the I and Q quadrature components of the received magnetic resonance signal. The magnitude of the received magnetic resonance signal may, therefore, be determined at a sampled point by the square root of the sum of the squares of the I and Q components: 
         M =√{square root over ( I   2   +Q   2 )}  (6);
 
     and the phase of the received magnetic resonance signal may also be determined according to the following relationship: 
     
       
         
           
             
               
                 
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     The pulse sequence server  210  may receive patient data from a physiological acquisition controller  230 . By way of example, the physiological acquisition controller  230  may receive signals from a number of different sensors connected to the patient, including electrocardiograph (“ECG”) signals from electrodes, or respiratory signals from a respiratory bellows or other respiratory monitoring devices. These signals may be used by the pulse sequence server  210  to synchronize, or “gate,” the performance of the scan with the subject&#39;s heart beat or respiration. 
     The pulse sequence server  210  may also connect to a scan room interface circuit  232  that receives signals from various sensors associated with the condition of the patient and the magnet system. Through the scan room interface circuit  232 , a patient positioning system  234  can receive commands to move the patient to desired positions during the scan. 
     The digitized magnetic resonance signal samples produced by the RF system  220  are received by the data acquisition server  212 . The data acquisition server  212  operates in response to instructions downloaded from the operator workstation  202  to receive the real-time magnetic resonance data and provide buffer storage, so that data is not lost by data overrun. In some scans, the data acquisition server  212  passes the acquired magnetic resonance data to the data processor server  214 . In scans that require information derived from acquired magnetic resonance data to control the further performance of the scan, the data acquisition server  212  may be programmed to produce such information and convey it to the pulse sequence server  210 . For example, during pre-scans, magnetic resonance data may be acquired and used to calibrate the pulse sequence performed by the pulse sequence server  210 . As another example, navigator signals may be acquired and used to adjust the operating parameters of the RF system  220  or the gradient system  218 , or to control the view order in which k-space is sampled. In still another example, the data acquisition server  212  may also process magnetic resonance signals used to detect the arrival of a contrast agent in a magnetic resonance angiography (“MRA”) scan. For example, the data acquisition server  212  may acquire magnetic resonance data and processes it in real-time to produce information that is used to control the scan. 
     The data processing server  214  receives magnetic resonance data from the data acquisition server  212  and processes the magnetic resonance data in accordance with instructions provided by the operator workstation  202 . Such processing may include, for example, reconstructing two-dimensional or three-dimensional images by performing a Fourier transformation of raw k-space data, performing other image reconstruction algorithms (e.g., iterative or backprojection reconstruction algorithms), applying filters to raw k-space data or to reconstructed images, generating functional magnetic resonance images, or calculating motion or flow images. 
     Images reconstructed by the data processing server  214  are conveyed back to the operator workstation  202  for storage. Real-time images may be stored in a data base memory cache, from which they may be output to operator display  202  or a display  236 . Batch mode images or selected real time images may be stored in a host database on disc storage  238 . When such images have been reconstructed and transferred to storage, the data processing server  214  may notify the data store server  216  on the operator workstation  202 . The operator workstation  202  may be used by an operator to archive the images, produce films, or send the images via a network to other facilities. 
     The MRI system  200  may also include one or more networked workstations  242 . For example, a networked workstation  242  may include a display  244 , one or more input devices  246  (e.g., a keyboard, a mouse), and a processor  248 . The networked workstation  242  may be located within the same facility as the operator workstation  202 , or in a different facility, such as a different healthcare institution or clinic. 
     The networked workstation  242  may gain remote access to the data processing server  214  or data store server  216  via the communication system  240 . Accordingly, multiple networked workstations  242  may have access to the data processing server  214  and the data store server  216 . In this manner, magnetic resonance data, reconstructed images, or other data may be exchanged between the data processing server  214  or the data store server  216  and the networked workstations  242 , such that the data or images may be remotely processed by a networked workstation  242 . 
     Referring now to  FIG. 3 , a block diagram of a non-limiting example of a computer system  300  that can perform the methods described in the present disclosure is shown. The computer system  300  generally includes an input  302 , at least one hardware processor  304 , a memory  306 , and an output  308 . Thus, the computer system  300  is generally implemented with a hardware processor  304  and a memory  306 . 
     In some embodiments, the computer system  300  can be a workstation, a notebook computer, a tablet device, a mobile device, a multimedia device, a network server, a mainframe, one or more controllers, one or more microcontrollers, or any other general-purpose or application-specific computing device. 
     The computer system  300  may operate autonomously or semi-autonomously, or may read executable software instructions from the memory  306  or a computer-readable medium (e.g., a hard drive, a CD-ROM, flash memory), or may receive instructions via the input  302  from a user, or any another source logically connected to a computer or device, such as another networked computer or server. Thus, in some embodiments, the computer system  300  can also include any suitable device for reading computer-readable storage media. 
     In general, the computer system  300  is programmed or otherwise configured to implement the methods and algorithms described in the present disclosure. For instance, the computer system  300  can be programmed to implement image reconstruction algorithms, such as those described in the present disclosure. 
     The input  302  may take any suitable shape or form, as desired, for operation of the computer system  300 , including the ability for selecting, entering, or otherwise specifying parameters consistent with performing tasks, processing data, or operating the computer system  300 . In some aspects, the input  302  may be configured to receive data, such as data acquired with an MRI system. Such data may be processed as described above to reconstruct images. In addition, the input  302  may also be configured to receive any other data or information considered useful for reconstructing images using the methods described above. 
     Among the processing tasks for operating the computer system  300 , the one or more hardware processors  304  may also be configured to carry out any number of post-processing steps on data received by way of the input  302 . 
     The memory  306  may contain software  310  and data  312 , such as data acquired with an MRI system, and may be configured for storage and retrieval of processed information, instructions, and data to be processed by the one or more hardware processors  304 . In some aspects, the software  310  may contain instructions directed to implementing image reconstruction algorithms, such as those described in the present disclosure. 
     In addition, the output  308  may take any shape or form, as desired, and may be configured for displaying reconstructed images, in addition to other desired information. 
     In some embodiments, any suitable computer readable media can be used for storing instructions for performing the functions and/or processes described herein. For example, in some embodiments, computer readable media can be transitory or non-transitory. For example, non-transitory computer readable media can include media such as magnetic media (e.g., hard disks, floppy disks), optical media (e.g., compact discs, digital video discs, Blu-ray discs), semiconductor media (e.g., random access memory (“RAM”), flash memory, electrically programmable read only memory (“EPROM”), electrically erasable programmable read only memory (“EEPROM”)), any suitable media that is not fleeting or devoid of any semblance of permanence during transmission, and/or any suitable tangible media. As another example, transitory computer readable media can include signals on networks, in wires, conductors, optical fibers, circuits, or any suitable media that is fleeting and devoid of any semblance of permanence during transmission, and/or any suitable intangible media. 
     The present disclosure has described one or more preferred embodiments, and it should be appreciated that many equivalents, alternatives, variations, and modifications, aside from those expressly stated, are possible and within the scope of the invention.