Optimization of 3D MP-RAGE for neonatal brain imaging at 3.0 T

Improved gray-white matter contrast using magnetization prepared fast imaging with steady-state free precession (MP-FISP) brain imaging at 0.55 T

PURPOSE

To improve the gray/white matter contrast of magnetization prepared rapid gradient echo (MP-RAGE) MRI at 0.55 T by optimizing the acquisition and sequence kernel parameters.

METHODS

A segmented magnetization prepared rapid gradient echo prototype sequence was implemented with (MP-RAGE*) and without (MP-FISP*) radiofrequency spoiling. Optimized parameters were derived with the assistance of an extended phase graph signal simulation as a function of the relaxation times, the flip angle, the delay times, and the effective inversion time using segmentation. The resulting protocols were compared to the MP-RAGE product sequence offered by the vendor in terms of signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). A tissue segmentation reproducibility study was performed on three volunteers for the product MP-RAGE and the MP-FISP*.

RESULTS

The MP-RAGE simulation reproduced the parameters already used in the product MP-RAGE on the scanner. An average CNR improvement of 15% for the custom MP-RAGE* over the product MP-RAGE and additional 22% for the MP-FISP* over the MP-RAGE* were observed, which is in accordance with the simulation results. The total improvement, averaged over all volunteers and regions, was 41%. The reproducibility study did not yield a significant difference between MP-RAGE and MP-FISP*.

CONCLUSION

We presented some easy-to-implement adjustments to the MP-RAGE sequence at 0.55 T, which can lead to an overall average improvement of 41% in CNR.

Highly accelerated 3D MPRAGE using deep neural network-based reconstruction for brain imaging in children and young adults

OBJECTIVES

This study aimed to accelerate the 3D magnetization-prepared rapid gradient-echo (MPRAGE) sequence for brain imaging through the deep neural network (DNN).

METHODS

This retrospective study used the k-space data of 240 scans (160 for the training set, mean ± standard deviation age, 93 ± 80 months, 94 males; 80 for the test set, 106 ± 83 months, 44 males) of conventional MPRAGE (C-MPRAGE) and 102 scans (77 ± 74 months, 52 males) of both C-MPRAGE and accelerated MPRAGE. All scans were acquired with 3T scanners. DNN was developed with simulated-acceleration data generated by under-sampling. Quantitative error metrics were compared between images reconstructed with DNN, GRAPPA, and E-SPIRIT using the paired t-test. Qualitative image quality was compared between C-MPRAGE and accelerated MPRAGE reconstructed with DNN (DNN-MPRAGE) by two readers. Lesions were segmented and the agreement between C-MPRAGE and DNN-MPRAGE was assessed using linear regression.

RESULTS

Accelerated MPRAGE reduced scan times by 38% compared to C-MPRAGE (142 s vs. 320 s). For quantitative error metrics, DNN showed better performance than GRAPPA and E-SPIRIT (p < 0.001). For qualitative evaluation, overall image quality of DNN-MPRAGE was comparable (p > 0.999) or better (p = 0.025) than C-MPRAGE, depending on the reader. Pixelation was reduced in DNN-MPRAGE (p < 0.001). Other qualitative parameters were comparable (p > 0.05). Lesions in C-MPRAGE and DNN-MPRAGE showed good agreement for the dice similarity coefficient (= 0.68) and linear regression (R² = 0.97; p < 0.001).

CONCLUSIONS

DNN-MPRAGE reduced acquisition time by 38% and revealed comparable image quality to C-MPRAGE.

KEY POINTS

• DNN-MPRAGE reduced acquisition times by 38%. • DNN-MPRAGE outperformed conventional reconstruction on accelerated scans (SSIM of DNN-MPRAGE = 0.96, GRAPPA = 0.43, E-SPIRIT = 0.88; p < 0.001). • Compared to C-MPRAGE scans, DNN-MPRAGE showed improved mean scores for overall image quality (2.46 vs. 2.52; p < 0.001) or comparable perceived SNR (2.56 vs. 2.58; p = 0.08).

Infant study of hemispheric asymmetry after long-gap esophageal atresia repair

OBJECTIVES

Previous studies have demonstrated that infants are typically born with a left-greater-than-right forebrain asymmetry that reverses throughout the first year of life. We hypothesized that critically ill term-born and premature patients following surgical and critical care for long-gap esophageal atresia (LGEA) would exhibit alteration in expected forebrain asymmetry.

METHODS

Term-born (n = 13) and premature (n = 13) patients, and term-born controls (n = 23) <1 year corrected age underwent non-sedated research MRI following completion of LGEA treatment via Foker process. Structural T1- and T2-weighted images were collected, and ITK-SNAP was used for forebrain tissue segmentation and volume acquisition. Data were presented as absolute (cm³ ) and normalized (% total forebrain) volumes of the hemispheres. All measures were checked for normality, and group status was assessed using a general linear model with age at scan as a covariate.

RESULTS

Absolute volumes of both forebrain hemispheres were smaller in term-born and premature patients in comparison to controls (p < 0.001). Normalized hemispheric volume group differences were detected by T1-weighted analysis, with premature patients demonstrating right-greater-than-left hemisphere volumes in comparison to term-born patients and controls (p < 0.01). While normalized group differences were very subtle (a right hemispheric predominance of roughly 2% of forebrain volume), they represent a deviation from the expected pattern of hemispheric brain asymmetry.

INTERPRETATION

Our pilot quantitative MRI study of hemispheric volumes suggests that premature patients might be at risk of altered expected left-greater-than-right forebrain asymmetry following repair of LGEA. Future neurobehavioral studies in infants born with LGEA are needed to elucidate the functional significance of presented anatomical findings.

MRI of the Neonatal Brain: A Review of Methodological Challenges and Neuroscientific Advances

In recent years, exploration of the developing brain has become a major focus for researchers and clinicians in an attempt to understand what allows children to acquire amazing and unique abilities, as well as the impact of early disruptions (eg, prematurity, neonatal insults) that can lead to a wide range of neurodevelopmental disorders. Noninvasive neuroimaging methods such as MRI are essential to establish links between the brain and behavioral changes in newborns and infants. In this review article, we aim to highlight recent and representative studies using the various techniques available: anatomical MRI, quantitative MRI (relaxometry, diffusion MRI), multiparametric approaches, and functional MRI. Today, protocols use 1.5 or 3T MRI scanners, and specialized methodologies have been put in place for data acquisition and processing to address the methodological challenges specific to this population, such as sensitivity to motion. MR sequences must be adapted to the brains of newborns and infants to obtain relevant good soft-tissue contrast, given the small size of the cerebral structures and the incomplete maturation of tissues. The use of age-specific image postprocessing tools is also essential, as signal and contrast differ from the adult brain. Appropriate methodologies then make it possible to explore multiple neurodevelopmental mechanisms in a precise way, and assess changes with age or differences between groups of subjects, particularly through large-scale projects. Although MRI measurements only indirectly reflect the complex series of dynamic processes observed throughout development at the molecular and cellular levels, this technique can provide information on brain morphology, structural connectivity, microstructural properties of gray and white matter, and on the functional architecture. Finally, MRI measures related to clinical, behavioral, and electrophysiological markers have a key role to play from a diagnostic and prognostic perspective in the implementation of early interventions to avoid long-term disabilities in children. EVIDENCE LEVEL: 2 TECHNICAL EFFICACY STAGE: 1.

Age-specific optimization of T1-weighted brain MRI throughout infancy

The infant brain undergoes drastic morphological and functional development during the first year of life. Three-dimensional T1-weighted Magnetic Resonance Imaging (3D T1w-MRI) is a major tool to characterize the brain anatomy, which however, manifests inherently low and rapidly changing contrast between white matter (WM) and gray matter (GM) in the infant brains (0-12 month-old). Despite the prior efforts made to maximize tissue contrast in the neonatal brains (≤1 months), optimization of imaging methods in the rest of the infancy (1-12 months) is not fully addressed, while brains in the latter period exhibit even more challenging contrast. Here, we performed a systematic investigation to improve the contrast between cortical GM and subcortical WM throughout the infancy. We first performed simultaneous T1 and proton density mapping in a normally developing infant cohort at 3T (n = 57). Based on the evolution of T1 relaxation times, we defined three age groups and simulated the relative tissue contrast between WM and GM in each group. Age-specific imaging strategies were proposed according to the Bloch simulation: inversion time (TI) around 800 ms for the 0-3 month-old group, dual TI at 500 ms and 700 ms for the 3-7 month-old group, and TI around 700 ms for 7-12 month-old group, using a centrically encoded 3D-MPRAGE sequence at 3T. Experimental results with varying TIs in each group confirmed improved contrast at the proposed optimal TIs, even in 3-7 month-old infants who had nearly isointense contrast. We further demonstrated the advantage of improved relative contrast in segmenting the neonatal brains using a multi-atlas segmentation method. The proposed age-specific optimization strategies can be easily adapted to routine clinical examinations, and the improved image contrast would facilitate quantitative analysis of the infant brain development.

Optimization of magnetization-prepared rapid gradient echo (MP-RAGE) sequence for neonatal brain MRI

BACKGROUND

Sequence optimization in neonates might improve detection sensitivity of abnormalities for a variety of conditions. However this has been historically challenging because tissue properties such as the longitudinal relaxation time and proton density differ significantly between neonates and adults.

OBJECTIVE

To optimize the magnetization-prepared rapid gradient echo (MP-RAGE) sequence to enhance both signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) efficiencies.

MATERIALS AND METHODS

We optimized neonatal MP-RAGE sequence through (1) reducing receive bandwidth to decrease noise, (2) shortening acquisition train length (acquisition number per repetition time or total number of read-out radiofrequency rephrasing pulses) using slice partial Fourier acquisition and (3) simulating the solution of Bloch's equation under optimal receive bandwidth and acquisition train length. Using the optimized sequence parameters, we scanned 12 healthy full-term infants within 2 weeks of birth and four preterm infants at 40 weeks' corrected age.

RESULTS

Compared with a previously published neonatal protocol, we were able to reduce the total scan time by reduce the total scan time by 60% and increase the average SNR efficiency by 160% (P<0.001) and the average CNR efficiency by 26% (P=0.029).

CONCLUSION

Our in vivo neonatal brain imaging experiments confirmed that both SNR and CNR efficiencies significantly increased with our proposed protocol. Our proposed optimization methodology could be readily extended to other populations (e.g., older children, adults), as well as different organ systems, field strengths and MR sequences.

Development and validation of a new MRI simulation technique that can reliably estimate optimal in vivo scanning parameters in a glioblastoma murine model

BACKGROUND

Magnetic Resonance Imaging (MRI) relies on optimal scanning parameters to achieve maximal signal-to-noise ratio (SNR) and high contrast-to-noise ratio (CNR) between tissues resulting in high quality images. The optimization of such parameters is often laborious, time consuming, and user-dependent, making harmonization of imaging parameters a difficult task. In this report, we aim to develop and validate a computer simulation technique that can reliably provide "optimal in vivo scanning parameters" ready to be used for in vivo evaluation of disease models.

METHODS

A glioblastoma murine model was investigated using several MRI imaging methods. Such MRI methods underwent a simulated and an in vivo scanning parameter optimization in pre- and post-contrast conditions that involved the investigation of tumor, brain parenchyma and cerebrospinal fluid (CSF) CNR values in addition to the time relaxation values of the related tissues. The CNR tissues information were analyzed and the derived scanning parameters compared in order to validate the simulated methodology as a reliable technique for "optimal in vivo scanning parameters" estimation.

RESULTS

The CNRs and the related scanning parameters were better correlated when spin-echo-based sequences were used rather than the gradient-echo-based sequences due to augmented inhomogeneity artifacts affecting the latter methods. "Optimal in vivo scanning parameters" were generated successfully by the simulations after initial scanning parameter adjustments that conformed to some of the parameters derived from the in vivo experiment.

CONCLUSION

Scanning parameter optimization using the computer simulation was shown to be a valid surrogate to the in vivo approach in a glioblastoma murine model yielding in a better delineation and differentiation of the tumor from the contralateral hemisphere. In addition to drastically reducing the time invested in choosing optimal scanning parameters when compared to an in vivo approach, this simulation program could also be used to harmonize MRI acquisition parameters across scanners from different vendors.

Magnetization-prepared shells trajectory with automated gradient waveform design

PURPOSE

To develop a fully automated trajectory and gradient waveform design for the non-Cartesian shells acquisition, and to develop a magnetization-prepared (MP) shells acquisition to achieve an efficient three-dimensional acquisition with improved gray-to-white brain matter contrast.

METHODS

After reviewing the shells k-space trajectory, a novel, fully automated trajectory design is developed that allows for gradient waveforms to be automatically generated for specified acquisition parameters. Designs for two types of shells are introduced, including fully sampled and undersampled/accelerated shells. Using those designs, an MP-Shells acquisition is developed by adjusting the acquisition order of shells interleaves to synchronize the center of k-space sampling with the peak of desired gray-to-white matter contrast. The feasibility of the proposed design and MP-Shells is demonstrated using simulation, phantom, and volunteer subject experiments, and the performance of MP-Shells is compared with a clinical Cartesian magnetization-prepared rapid gradient echo acquisition.

RESULTS

Initial experiments show that MP-Shells produces excellent image quality with higher data acquisition efficiency and improved gray-to-white matter contrast-to-noise ratio (by 36%) compared with the conventional Cartesian magnetization-prepared rapid gradient echo acquisition.

CONCLUSION

We demonstrated the feasibility of a three-dimensional MP-Shells acquisition and an automated trajectory design to achieve an efficient acquisition with improved gray-to-white matter contrast. Magn Reson Med 79:2024-2035, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Optimizing the magnetization-prepared rapid gradient-echo (MP-RAGE) sequence

The three-dimension (3D) magnetization-prepared rapid gradient-echo (MP-RAGE) sequence is one of the most popular sequences for structural brain imaging in clinical and research settings. The sequence captures high tissue contrast and provides high spatial resolution with whole brain coverage in a short scan time. In this paper, we first computed the optimal k-space sampling by optimizing the contrast of simulated images acquired with the MP-RAGE sequence at 3.0 Tesla using computer simulations. Because the software of our scanner has only limited settings for k-space sampling, we then determined the optimal k-space sampling for settings that can be realized on our scanner. Subsequently we optimized several major imaging parameters to maximize normal brain tissue contrasts under the optimal k-space sampling. The optimal parameters are flip angle of 12°, effective inversion time within 900 to 1100 ms, and delay time of 0 ms. In vivo experiments showed that the quality of images acquired with our optimal protocol was significantly higher than that of images obtained using recommended protocols in prior publications. The optimization of k-spacing sampling and imaging parameters significantly improved the quality and detection sensitivity of brain images acquired with MP-RAGE.

Optimizing hippocampal segmentation in infants utilizing MRI post-acquisition processing

This study aims to determine the most reliable method for infant hippocampal segmentation by comparing magnetic resonance (MR) imaging post-acquisition processing techniques: contrast to noise ratio (CNR) enhancement, or reformatting to standard orientation. MR scans were performed with a 1.5 T GE scanner to obtain dual echo T2 and proton density (PD) images at term equivalent (38-42 weeks' gestational age). 15 hippocampi were manually traced four times on ten infant images by 2 independent raters on the original T2 image, as well as images processed by: a) combining T2 and PD images (T2-PD) to enhance CNR; then b) reformatting T2-PD images perpendicular to the long axis of the left hippocampus. CNRs and intraclass correlation coefficients (ICC) were calculated. T2-PD images had 17% higher CNR (15.2) than T2 images (12.6). Original T2 volumes' ICC was 0.87 for rater 1 and 0.84 for rater 2, whereas T2-PD images' ICC was 0.95 for rater 1 and 0.87 for rater 2. Reliability of hippocampal segmentation on T2-PD images was not improved by reformatting images (rater 1 ICC = 0.88, rater 2 ICC = 0.66). Post-acquisition processing can improve CNR and hence reliability of hippocampal segmentation in neonate MR scans when tissue contrast is poor. These findings may be applied to enhance boundary definition in infant segmentation for various brain structures or in any volumetric study where image contrast is sub-optimal, enabling hippocampal structure-function relationships to be explored.

Optimized inversion-prepared gradient echo imaging

PURPOSE

To implement a method using an extended phase graph (EPG)-based simulation to optimize inversion-prepared gradient echo sequences with respect to signal and contrast within the shortest acquisition time.

MATERIALS AND METHODS

A critical issue in rapid gradient-echo imaging is the effect of residual transverse magnetization between consecutive data acquisition windows. Various spoiling schemes have been proposed to mitigate this problem, and while spoiling is often considered to be perfect, imaging can be more truthfully described using the EPG. An EPG-based simulation is used to analyze and predict the image signal and contrast to serve as a basis for sequence optimization.

RESULTS

Fourteen biological phantom experiments and five brain imaging experiments on each of five healthy volunteers was performed to validate and verify the accuracy of the EPG-based simulation. In addition, two experiments on an in-cranial cadaver brain were performed to show the ability of the proposed method for improving overall image quality.

CONCLUSION

From the experiment results, it is demonstrated that optimization of 3D magnetization-prepared rapid gradient-echo imaging sequences can be performed with an EPG-based simulation to manipulate the sequence parameters for generating images with highly specific signal and contrast characteristics for quantitative T1-weighted human brain imaging.

Optimized T1- and T2-weighted volumetric brain imaging as a diagnostic tool in very preterm neonates

BACKGROUND

T1- and T2-W MR sequences used for obtaining diagnostic information and morphometric measurements in the neonatal brain are frequently acquired using different imaging protocols. Optimizing one protocol for obtaining both kinds of information is valuable.

OBJECTIVE

To determine whether high-resolution T1- and T2-W volumetric sequences optimized for preterm brain imaging could provide both diagnostic and morphometric value.

MATERIALS AND METHODS

Thirty preterm neonates born between 24 and 32 weeks' gestational age were scanned during the first 2 weeks after birth. T1- and T2-W high-resolution sequences were optimized in terms of signal-to-noise ratio, contrast-to-noise ratio and scan time and compared to conventional spin-echo-based sequences.

RESULTS

No differences were found between conventional and high-resolution T1-W sequences for diagnostic confidence, image quality and motion artifacts. A preference for conventional over high-resolution T2-W sequences for image quality was observed. High-resolution T1 images provided better delineation of thalamic myelination and the superior temporal sulcus. No differences were found for detection of myelination and sulcation using conventional and high-resolution T2-W images.

CONCLUSION

High-resolution T1- and T2-W volumetric sequences can be used in clinical MRI in the very preterm brain to provide both diagnostic and morphometric information.

Safety first: Recognizing and managing the risks to child participants in magnetic resonance imaging research

Specialized and up-to-date knowledge is required to identify and manage the risks associated with advanced biomedical research. Additional complexities need to be considered when the research involves infants or young children. In this article, we focus on recent information about the physical risks of pediatric magnetic resonance imaging research and highlight information gaps. With an eye to assisting institutional review boards and researchers, we consider strategies for the management of these risks and formulate key questions aimed at exposing hidden hazards. Institutional review boards should ask these questions, and researchers should bear them in mind as they develop research protocols.

Females follow a more "compact" early human brain development model than males. A case-control study of preterm neonates

The pattern of sexual differentiation of the human brain is not well understood, particularly at the early stages of development when intense growth and multiple maturational phenomena overlap and interrelate. A case-control study of 20 preterm males and females matched for age was conducted. Three-dimensional images were acquired with 3 T MRI. The cerebral volume and the cortical folding area (FA), defined as the surface area of the interface between cortical gray and white matter, were compared between males and females. Females had smaller cerebra than males even after removing the influence of overall size differences between the subjects. The cortical FA increased in relation to volume by a power of 4/3 in both groups. Females had larger cortical FA compared with males with similar cerebral volumes. The study provides in vivo evidence of sexually dimorphic early human brain development. The relatively more "compact" female model may well relate to sex differences in neural circuitry and cognitive domains.