A spectral approach to analyzing slice selection in planar imaging: optimization for through-plane interpolation

Fetal MRI by Robust Deep Generative Prior Reconstruction and Diffeomorphic Registration

Magnetic resonance imaging of whole fetal body and placenta is limited by different sources of motion affecting the womb. Usual scanning techniques employ single-shot multi-slice sequences where anatomical information in different slices may be subject to different deformations, contrast variations or artifacts. Volumetric reconstruction formulations have been proposed to correct for these factors, but they must accommodate a non-homogeneous and non-isotropic sampling, so regularization becomes necessary. Thus, in this paper we propose a deep generative prior for robust volumetric reconstructions integrated with a diffeomorphic volume to slice registration method. Experiments are performed to validate our contributions and compare with ifdefined tmiformat R2.5a state of the art method methods in the literature in a cohort of 72 fetal datasets in the range of 20-36 weeks gestational age. Results suggest improved image resolution Quantitative as well as radiological assessment suggest improved image quality and more accurate prediction of gestational age at scan is obtained when comparing to a state of the art reconstruction method methods. In addition, gestational age prediction results from our volumetric reconstructions compare favourably are competitive with existing brain-based approaches, with boosted accuracy when integrating information of organs other than the brain. Namely, a mean absolute error of 0.618 weeks ( R²=0.958 ) is achieved when combining fetal brain and trunk information.

Three-dimensional motion corrected sensitivity encoding reconstruction for multi-shot multi-slice MRI: Application to neonatal brain imaging

PURPOSE

To introduce a methodology for the reconstruction of multi-shot, multi-slice magnetic resonance imaging able to cope with both within-plane and through-plane rigid motion and to describe its application in structural brain imaging.

THEORY AND METHODS

The method alternates between motion estimation and reconstruction using a common objective function for both. Estimates of three-dimensional motion states for each shot and slice are gradually refined by improving on the fit of current reconstructions to the partial k-space information from multiple coils. Overlapped slices and super-resolution allow recovery of through-plane motion and outlier rejection discards artifacted shots. The method is applied to T₂ and T₁ brain scans acquired in different views.

RESULTS

The procedure has greatly diminished artifacts in a database of 1883 neonatal image volumes, as assessed by image quality metrics and visual inspection. Examples showing the ability to correct for motion and robustness against damaged shots are provided. Combination of motion corrected reconstructions for different views has shown further artifact suppression and resolution recovery.

CONCLUSION

The proposed method addresses the problem of rigid motion in multi-shot multi-slice anatomical brain scans. Tests on a large collection of potentially corrupted datasets have shown a remarkable image quality improvement. Magn Reson Med 79:1365-1376, 2018. © 2017 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.

Super-resolution reconstruction in frequency, image, and wavelet domains to reduce through-plane partial voluming in MRI

PURPOSE

To compare and evaluate the use of super-resolution reconstruction (SRR), in frequency, image, and wavelet domains, to reduce through-plane partial voluming effects in magnetic resonance imaging.

METHODS

The reconstruction of an isotropic high-resolution image from multiple thick-slice scans has been investigated through techniques in frequency, image, and wavelet domains. Experiments were carried out with thick-slice T2-weighted fast spin echo sequence on the Academic College of Radiology MRI phantom, where the reconstructed images were compared to a reference high-resolution scan using peak signal-to-noise ratio (PSNR), structural similarity image metric (SSIM), mutual information (MI), and the mean absolute error (MAE) of image intensity profiles. The application of super-resolution reconstruction was then examined in retrospective processing of clinical neuroimages of ten pediatric patients with tuberous sclerosis complex (TSC) to reduce through-plane partial voluming for improved 3D delineation and visualization of thin radial bands of white matter abnormalities.

RESULTS

Quantitative evaluation results show improvements in all evaluation metrics through super-resolution reconstruction in the frequency, image, and wavelet domains, with the highest values obtained from SRR in the image domain. The metric values for image-domain SRR versus the original axial, coronal, and sagittal images were PSNR = 32.26 vs 32.22, 32.16, 30.65; SSIM = 0.931 vs 0.922, 0.924, 0.918; MI = 0.871 vs 0.842, 0.844, 0.831; and MAE = 5.38 vs 7.34, 7.06, 6.19. All similarity metrics showed high correlations with expert ranking of image resolution with MI showing the highest correlation at 0.943. Qualitative assessment of the neuroimages of ten TSC patients through in-plane and out-of-plane visualization of structures showed the extent of partial voluming effect in a real clinical scenario and its reduction using SRR. Blinded expert evaluation of image resolution in resampled out-of-plane views consistently showed the superiority of SRR compared to original axial and coronal image acquisitions.

CONCLUSIONS

Thick-slice 2D T2-weighted MRI scans are part of many routine clinical protocols due to their high signal-to-noise ratio, but are often severely affected by through-plane partial voluming effects. This study shows that while radiologic assessment is performed in 2D on thick-slice scans, super-resolution MRI reconstruction techniques can be used to fuse those scans to generate a high-resolution image with reduced partial voluming for improved postacquisition processing. Qualitative and quantitative evaluation showed the efficacy of all SRR techniques with the best results obtained from SRR in the image domain. The limitations of SRR techniques are uncertainties in modeling the slice profile, density compensation, quantization in resampling, and uncompensated motion between scans.

Super-resolution reconstruction to increase the spatial resolution of diffusion weighted images from orthogonal anisotropic acquisitions

Diffusion-weighted imaging (DWI) enables non-invasive investigation and characterization of the white matter but suffers from a relatively poor spatial resolution. Increasing the spatial resolution in DWI is challenging with a single-shot EPI acquisition due to the decreased signal-to-noise ratio and T2(∗) relaxation effect amplified with increased echo time. In this work we propose a super-resolution reconstruction (SRR) technique based on the acquisition of multiple anisotropic orthogonal DWI scans. DWI scans acquired in different planes are not typically closely aligned due to the geometric distortion introduced by magnetic susceptibility differences in each phase-encoding direction. We compensate each scan for geometric distortion by acquisition of a dual echo gradient echo field map, providing an estimate of the field inhomogeneity. We address the problem of patient motion by aligning the volumes in both space and q-space. The SRR is formulated as a maximum a posteriori problem. It relies on a volume acquisition model which describes how the acquired scans are observations of an unknown high-resolution image which we aim to recover. Our model enables the introduction of image priors that exploit spatial homogeneity and enables regularized solutions. We detail our SRR optimization procedure and report experiments including numerical simulations, synthetic SRR and real world SRR. In particular, we demonstrate that combining distortion compensation and SRR provides better results than acquisition of a single isotropic scan for the same acquisition duration time. Importantly, SRR enables DWI with resolution beyond the scanner hardware limitations. This work provides the first evidence that SRR, which employs conventional single shot EPI techniques, enables resolution enhancement in DWI, and may dramatically impact the role of DWI in both neuroscience and clinical applications.

Robust super-resolution volume reconstruction from slice acquisitions: application to fetal brain MRI

Fast magnetic resonance imaging slice acquisition techniques such as single shot fast spin echo are routinely used in the presence of uncontrollable motion. These techniques are widely used for fetal magnetic resonance imaging (MRI) and MRI of moving subjects and organs. Although high-quality slices are frequently acquired by these techniques, inter-slice motion leads to severe motion artifacts that are apparent in out-of-plane views. Slice sequential acquisitions do not enable 3-D volume representation. In this study, we have developed a novel technique based on a slice acquisition model, which enables the reconstruction of a volumetric image from multiple-scan slice acquisitions. The super-resolution volume reconstruction is formulated as an inverse problem of finding the underlying structure generating the acquired slices. We have developed a robust M-estimation solution which minimizes a robust error norm function between the model-generated slices and the acquired slices. The accuracy and robustness of this novel technique has been quantitatively assessed through simulations with digital brain phantom images as well as high-resolution newborn images. We also report here successful application of our new technique for the reconstruction of volumetric fetal brain MRI from clinically acquired data.

Diffusion tensor imaging (DTI) of the brain in moving subjects: application to in-utero fetal and ex-utero studies

We present a methodology to achieve 3D high-resolution diffusion tensor image reconstruction of the brain in moving subjects. The source data is diffusion-sensitized single-shot echo-planar images. After continuous scanning to acquire a repeated series of parallel slices with 15 diffusion directions, image registration is used to realign the images to correct for subject motion. Once aligned, the diffusion images are treated as irregularly-sampled data where each voxel is associated with an appropriately rotated diffusion direction. This data is used to estimate the diffusion tensor on a regular grid. The method has been tested on data acquired at 1.5T from adults who deliberately moved and from eight fetuses imaged in utero. Maps of apparent diffusion coefficient (ADC) were reliably produced in all cases and promising performance was achieved for fractional anisotropy maps. Results from normal fetal brains were found to be consistent with published data from premature infants of similar gestational age.

MRI of moving subjects using multislice snapshot images with volume reconstruction (SVR): application to fetal, neonatal, and adult brain studies

Motion degrades magnetic resonance (MR) images and prevents acquisition of self-consistent and high-quality volume images. A novel methodology, Snapshot magnetic resonance imaging (MRI) with Volume Reconstruction (SVR) has been developed for imaging moving subjects at high resolution and high signal-to-noise ratio (SNR). The method combines registered 2-D slices from sequential dynamic single-shot scans. The SVR approach requires that the anatomy in question is not changing shape or size and is moving at a rate that allows snapshot images to be acquired. After imaging the target volume repeatedly to guarantee sufficient sampling every where, a robust slice-to-volume registration method has been implemented that achieves alignment of each slice within 0.3 mm in the examples tested. Multilevel scattered interpolation has been used to obtain high-fidelity reconstruction with root-mean-square (rms) error that is less than the noise level in the images. The SVR method has been performed successfully for brain studies on subjects that cannot stay still, and in some cases were moving substantially during scanning. For example, awake neonates, deliberately moved adults and, especially, on fetuses, for which no conventional high-resolution 3-D method is currently available. Fine structure of the in-utero fetal brain is clearly revealed for the first time and substantial SNR improvement is realized by having many individually acquired slices contribute to each voxel in the reconstructed image.

Magnetic resonance image registration and subtraction in the assessment of minor changes in low grade glioma volume

The purpose of this study was to apply image registration and subtraction to standard T2-weighted (T2-W) and FLAIR magnetic resonance imaging (MRI) protocols in an attempt to improve the detection of minor changes in low grade glioma volume. Thirteen patients with low grade glial tumours and minimal or no apparent change on serial MRI scans were prospectively recruited for the study. Forty-two pairs of images were compared (T2-W sequences in 27/27 and FLAIR sequences in 15/27). The image pairs were registered, subtracted and randomised. Three independent raters assigned non-parametric ratings according to the dominant volume change for unregistered, registered and subtracted image sets. There was a statistically significant improvement in the detection of tumour volume change using T2-W registration and T2-W and FLAIR registration/subtraction relative to unregistered images. The reproducibility and increased sensitivity of FLAIR images relative to T2-W images were most apparent when registration was applied. Smaller degrees of low grade glioma tumour volume change are detectable using image registration and subtraction techniques that can be applied successfully to images acquired with standard clinical protocols.

Subvoxel image registration of multislice (2D) magnetic resonance images in patients with high-grade gliomas of the brain

AIMS

To implement a multislice two-dimensional (2D) T2-weighted sequence suitable for subvoxel image registration and to assess its usefulness in detecting change in high-grade intracranial gliomas.

MATERIALS AND METHODS

Twenty patients with high-grade gliomas were studied on two or more occasions. T2-weighted multislice pulse sequences with a Gaussian slice profile, 50% overlapping slices and nearly isotropic voxels were acquired. The images were registered and subtraction images were produced. The images were compared with three-dimensional (3D) T1-weighted registered images and conventional unregistered T2-weighted images. All images were scored for changes in the lesions and ventricular system.

RESULTS

The 2D and 3D registered subtraction images were the most sensitive for detecting changes in both the lesions and other regions in the brain. The mean rank scores were significantly higher for the lesions (chi2=86.742; df=5, n=38, P<0.0001) and for the ventricles (chi2=63.837; df=5, n=35, P<0.0001) compared with the unregistered and registered anatomical images. The subtraction images were also most sensitive for detecting signal intensity changes irrespective of the direction of change.

CONCLUSION

Rigid body subvoxel registration can be successfully performed with both multislice 2D and 3D imaging. In principle, virtually all forms of clinical MR images of the brain can be accurately registered and subtracted.

Generalized SMASH imaging

A generalized parallel imaging method has been developed that uses coil profiles to generate missing k-space lines. The proposed method is an extension of SMASH, which uses linear combinations of coil sensitivity profiles to synthesize spatial harmonics. In the generalized SMASH approach described here, coil sensitivity profiles are represented directly in the Fourier domain to provide a general description of the spatial properties of the coils. This removes restrictions imposed by conventional SMASH, so that the choice and position of the receiver coils can be made on the basis of sensitivity to the volume of interest rather than suitability for constructing spatial harmonics. Generalized SMASH also intrinsically allows the freedom to accommodate acquisitions with uniform or nonuniform k-space sampling. The proposed method places SMASH on an equal footing with other parallel imaging techniques (SENSE and SPACE-RIP), while combining strengths from each. The method was tested on phantom and human data and provides a robust method of data recovery.

Prospective multiaxial motion correction for fMRI

Corruption of the image time series due to interimage head motion limits the clinical utility of functional MRI. This paper presents a method for real-time prospective correction of rotation and translation in all six degrees of rigid body motion. By incorporating an orbital navigator (ONAV) echo for each of the sagittal, axial, and coronal planes into the fMRI pulse sequence, rotation and translation can be measured and the spatial orientation of the image acquisition sequence that follows can be corrected prospectively in as little as 160 msec. Testing of the method using a computerized motion phantom capable of performing complex multiaxial motion showed subdegree rotational and submillimeter translational accuracy over a range of +/-8 degrees and +/-8 mm of motion. In vivo images demonstrate correction of simultaneous through-plane and in-plane motion and improved detection of fMRI activation in the presence of head motion.

Characterization and correction of interpolation effects in the realignment of fMRI time series

Subject motion in functional magnetic resonance imaging (fMRI) studies can be accurately estimated using realignment algorithms. However, residual changes in signal intensity arising from motion have been identified in the data even after realignment of the image time series. The nature of these artifacts is characterized using simulated displacements of an fMRI image and is attributed to interpolation errors introduced by the resampling inherent within realignment. A correction scheme that uses a periodic function of the estimated displacements to remove interpolation errors from the image time series on a voxel-by-voxel basis is proposed. The artifacts are investigated using a brain phantom to avoid physiological confounds. Small- and large-scale systematic displacements show that the artifacts have the same form as revealed by the simulated displacements. A randomly displaced phantom and a human subject are used to demonstrate that interpolation errors are minimized using the correction.

Overt verbal responding during fMRI scanning: empirical investigations of problems and potential solutions

This paper presents a pair of studies designed to empirically explore the severity of potential artifacts associated with overt verbal responding during fMRI scanning and to examine several different solutions to these artifacts. In Study One, we compared susceptibility artifacts, signal-to-noise ratios, and activation patterns when overt versus covert verbal responses were elicited during fMRI scanning, using both individual and group analyses. The results indicated that different patterns of brain activation were elicited during covert as compared to overt verbal responses. This suggests that covert responses cannot be used as a simple substitute for overt verbal responses. Further, the results suggested that the use of overt verbal responses during fMRI scanning can produce interpretable results if: (1) the primary comparison is between two conditions that both use overt verbal responses, and (2) analyses are conducted on pooled group data rather than individual participant data. In Study Two, we evaluated the feasibility and validity of a method for acquiring participants' overt responses during fMRI scanning. The results indicated that our method was very accurate in acquiring the content of participant's responses. Further, inspection of the responses demonstrated that participants do not always comply with task instructions and highlighted the importance of obtaining behavioral performance measures during fMRI scanning.

High-resolution three-dimensional in vivo imaging of atherosclerotic plaque

The internal structure of atherosclerotic-plaque lesions may be a useful predictor of which lesions will rupture and cause sudden events such as heart attack or stroke. With lipid and flow suppression, we obtained high-resolution, three-dimensional (3D) images of atherosclerotic plaque in vivo that show the cap thickness and core size of the lesions. 3D GRASE was used because it provides flexible T(2) contrast and good resistance to off-resonance artifacts. While 2D RARE has similar properties, its resolution in the slice-select direction, which is important because of the irregular geometry of atherosclerotic lesions, is limited by achievable slice-excitation profiles. Also, 2D imaging generally achieves lower SNR than 3D imaging because, for SNR purposes, 3D image data is averaged over all the slices of a corresponding multislice 2D dataset. Although 3D RARE has many of the advantages of 3D GRASE, it requires a longer scan time because it uses more refocusing pulses to acquire the same amount of data. Finally, cardiac gating is an important part of our imaging sequence, but can make the imaging time quite long. To obtain reasonable scan times, a 2D excitation pulse was used to restrict the field of view. Magn Reson Med 42:762-771, 1999.

Evaluation of respiratory artifact correction techniques in multishot spiral functional MRI using receiver operator characteristic analyses

Navigator corrections and low-spatial frequency (LSF) oversampling are investigated as methods for reducing respiration-related effects in multishot functional MRI. Both techniques take advantage of the smoothly varying or nearly constant phase variations linked to the respiration cycle. These techniques were tested in functional MRI studies with spiral k-space acquisitions. Receiver operator characteristic (ROC) analyses and the temporal variance averaged across the brain were used to evaluate their effectiveness. Both methods were found to increase the area under the ROC curve and to reduce the standard deviation, with the LSF oversampling method being more effective.

Asymmetric sampling along k(slice-select) in two-dimensional multislice MRI

Reduction of the slice-select refocusing gradient in two-dimensional multislice imaging results in asymmetry of the k-space representation of collected data along the slice-select direction. Standard methods of partial Fourier reconstruction developed for other methods of asymmetric k-space sampling can be used to reconstruct these data with final through-plane resolution smaller than the collected slice thickness. This method can be used for reducing scan time in the same manner as asymmetric sampling in the phase-encoded direction. In addition, the reduced refocusing gradient reduces minimum TE and motion artifacts in the same manner as for asymmetric sampling in the frequency-encoded direction (fractional echoes). Results using a resolution phantom and a flow phantom illustrate these concepts.