Journal Papers

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Afacan, Onur, Burak Erem, Diona Roby, Noam Roth, Amir Roth, Sanjay Prabhu, and Simon Warfield. (2016) 2016. “Evaluation of Motion and Its Effect on Brain Magnetic Resonance Image Quality in Children”. Pediatr Radiol 46 (12): 1728-35. https://doi.org/10.1007/s00247-016-3677-9.
BACKGROUND: Motion artifacts pose significant problems for the acquisition of MR images in pediatric populations. OBJECTIVE: To evaluate temporal motion metrics in MRI scanners and their effect on image quality in pediatric populations in neuroimaging studies. MATERIALS AND METHODS: We report results from a large pediatric brain imaging study that shows the effect of motion on MRI quality. We measured motion metrics in 82 pediatric patients, mean age 13.4 years, in a T1-weighted brain MRI scan. As a result of technical difficulties, 5 scans were not included in the subsequent analyses. A radiologist graded the images using a 4-point scale ranging from clinically non-diagnostic because of motion artifacts to no motion artifacts. We used these grades to correlate motion parameters such as maximum motion, mean displacement from a reference point, and motion-free time with image quality. RESULTS: Our results show that both motion-free time (as a ratio of total scan time) and average displacement from a position at a fixed time (when the center of k-space was acquired) were highly correlated with image quality, whereas maximum displacement was not as good a predictor. Among the 77 patients whose motion was measured successfully, 17 had average displacements of greater than 0.5 mm, and 11 of those (14.3%) resulted in non-diagnostic images. Similarly, 14 patients (18.2%) had less than 90% motion-free time, which also resulted in non-diagnostic images. CONCLUSION: We report results from a large pediatric study to show how children and young adults move in the MRI scanner and the effect that this motion has on image quality. The results will help the motion-correction community in better understanding motion patterns in pediatric populations and how these patterns affect MR image quality.
Ortinau, Cynthia, Caitlin Rollins, Ali Gholipour, Hyuk Jin Yun, Mackenzie Marshall, Borjan Gagoski, Onur Afacan, et al. 2019. “Early-Emerging Sulcal Patterns Are Atypical in Fetuses With Congenital Heart Disease”. Cereb Cortex 29 (8): 3605-16. https://doi.org/10.1093/cercor/bhy235.
Fetuses with congenital heart disease (CHD) have third trimester alterations in cortical development on brain magnetic resonance imaging (MRI). However, the intersulcal relationships contributing to global sulcal pattern remain unknown. This study applied a novel method for examining the geometric and topological relationships between sulci to fetal brain MRIs from 21-30 gestational weeks in CHD fetuses (n = 19) and typically developing (TD) fetuses (n = 17). Sulcal pattern similarity index (SI) to template fetal brain MRIs was determined for the position, area, and depth for corresponding sulcal basins and intersulcal relationships for each subject. CHD fetuses demonstrated altered global sulcal patterns in the left hemisphere compared with TD fetuses (TD [SI, mean ± SD]: 0.822 ± 0.023, CHD: 0.795 ± 0.030, P = 0.002). These differences were present in the earliest emerging sulci and were driven by differences in the position of corresponding sulcal basins (TD: 0.897 ± 0.024, CHD: 0.878 ± 0.019, P = 0.006) and intersulcal relationships (TD: 0.876 ± 0.031, CHD: 0.857 ± 0.018, P = 0.033). No differences in cortical gyrification index, mean curvature, or surface area were present. These data suggest our methods may be more sensitive than traditional measures for evaluating cortical developmental alterations early in gestation.

D

Wallace, Tess, Jonathan Polimeni, Jason Stockmann, Scott Hoge, Tobias Kober, Simon Warfield, and Onur Afacan. 2021. “Dynamic Distortion Correction for Functional MRI Using FID Navigators”. Magn Reson Med 85 (3): 1294-1307. https://doi.org/10.1002/mrm.28505.
PURPOSE: To develop a method for slice-wise dynamic distortion correction for EPI using rapid spatiotemporal B0 field measurements from FID navigators (FIDnavs) and to evaluate the efficacy of this new approach relative to an established data-driven technique. METHODS: A low-resolution reference image was used to create a forward model of FIDnav signal changes to enable estimation of spatiotemporal B0 inhomogeneity variations up to second order from measured FIDnavs. Five volunteers were scanned at 3 T using a 64-channel coil with FID-navigated EPI. The accuracy of voxel shift measurements and geometric distortion correction was assessed for experimentally induced magnetic field perturbations. The temporal SNR was evaluated in EPI time-series acquired at rest and with a continuous nose-touching action, before and after image realignment. RESULTS: Field inhomogeneity coefficients and voxel shift maps measured using FIDnavs were in excellent agreement with multi-echo EPI measurements. The FID-navigated distortion correction accurately corrected image geometry in the presence of induced magnetic field perturbations, outperforming the data-driven approach in regions with large field offsets. In functional MRI scans with nose touching, FIDnav-based correction yielded temporal SNR gains of 30% in gray matter. Following image realignment, which accounted for global image shifts, temporal SNR gains of 3% were achieved. CONCLUSIONS: Our proposed application of FIDnavs enables slice-wise dynamic distortion correction with high temporal efficiency. We achieved improved signal stability by leveraging the encoding information from multichannel coils. This approach can be easily adapted to other EPI-based sequences to improve temporal SNR for a variety of clinical and research applications.

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Kurugol, Sila, Onur Afacan, Richard Lee, Catherine Seager, Michael Ferguson, Deborah Stein, Reid Nichols, et al. (2020) 2020. “Correction To: Prospective Pediatric Study Comparing Glomerular Filtration Rate Estimates Based on Motion-Robust Dynamic Contrast-Enhanced Magnetic Resonance Imaging and Serum Creatinine (eGFR) to Tc DTPA”. Pediatr Radiol 50 (5): 755-56. https://doi.org/10.1007/s00247-020-04654-9.
The originally published version of this article contained a typographical error. In the text under the subheading "Dynamic contrast-enhanced MRI method, post-processing, and MR-GFR calculation" and in Table 1 the intravenous injection rate of gadobutrol was incorrectly listed as 0.2 mL/s.

B

Coll-Font, Jaume, Onur Afacan, Jeanne Chow, Richard Lee, Alto Stemmer, Simon Warfield, and Sila Kurugol. 2020. “Bulk Motion-Compensated DCE-MRI for Functional Imaging of Kidneys in Newborns”. J Magn Reson Imaging 52 (1): 207-16. https://doi.org/10.1002/jmri.27021.
BACKGROUND: Evaluation of kidney function in newborns with hydronephrosis is important for clinical decisions. Dynamic contrast-enhanced (DCE) MRI can provide the necessary anatomical and functional information. Golden angle dynamic radial acquisition and compressed sensing reconstruction provides sufficient spatiotemporal resolution to achieve accurate parameter estimation for functional imaging of kidneys. However, bulk motion during imaging (rigid or nonrigid movement of the subject resulting in signal dropout) remains an unresolved challenge. PURPOSE: To evaluate a motion-compensated (MoCo) DCE-MRI technique for robust evaluation of kidney function in newborns. Our method includes: 1) motion detection, 2) motion-robust image reconstruction, 3) joint realignment of the volumes, and 4) tracer-kinetic (TK) model fitting to evaluate kidney function parameters. STUDY TYPE: Retrospective. SUBJECTS: Eleven newborn patients (ages <6 months, 6 female). FIELD STRENGTH/SEQUENCE: 3T; dynamic "stack-of-stars" 3D fast low-angle shot (FLASH) sequence using a multichannel body-matrix coil. ASSESSMENT: We evaluated the proposed technique in terms of the signal-to-noise ratio (SNR) of the reconstructed images, the presence of discontinuities in the contrast agent concentration time curves due to motion with a total variation (TV) metric and the goodness of fit of the TK model, and the standard variation of its parameters. STATISTICAL TESTS: We used a paired t-test to compare the MoCo and no-MoCo results. RESULTS: The proposed MoCo method successfully detected motion and improved the SNR by 3.3 (P = 0.012) and decreased TV by 0.374 (P = 0.017) across all subjects. Moreover, it decreased nRMSE of the TK model fit for the subjects with less than five isolated bulk motion events in 6 minutes (mean 1.53, P = 0.043), but not for the subjects with more frequent events or no motion (P = 0.745 and P = 0.683). DATA CONCLUSION: Our results indicate that the proposed MoCo technique improves the image quality and accuracy of the TK model fit for subjects who present isolated bulk motion events. LEVEL OF EVIDENCE: 3 Technical Efficacy Stage: 1 J. Magn. Reson. Imaging 2020;52:207-216.
Hesper, Tobias, Evgeny Bulat, Sarah Bixby, Alireza Akhondi-Asl, Onur Afacan, Patricia Miller, Garrett Bowen, Simon Warfield, and Young-Jo Kim. (2017) 2017. “Both 3-T DGEMRIC and Acetabular-Femoral T2 Difference May Detect Cartilage Damage at the Chondrolabral Junction”. Clin Orthop Relat Res 475 (4): 1058-65. https://doi.org/10.1007/s11999-016-5136-1.
BACKGROUND: In addition to case reports of gadolinium-related toxicities, there are increasing theoretical concerns about the use of gadolinium for MR imaging. As a result, there is increasing interest in noncontrast imaging techniques for biochemical cartilage assessment. Among them, T2 mapping holds promise because of its simplicity, but its biophysical interpretation has been controversial. QUESTIONS/PURPOSES: We sought to determine whether (1) 3-T delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) and T2 mapping are both capable of detecting cartilage damage at the chondrolabral junction in patients with femoroacetabular impingement (FAI); and (2) whether there is a correlation between these two techniques for acetabular and femoral head cartilage assessment. METHODS: Thirty-one patients with hip-related symptoms resulting from FAI underwent a preoperative 3-T MRI of their hip that included dGEMRIC and T2 mapping (symptomatic group, 16 women, 15 men; mean age, 27 ± 8 years). Ten volunteers with no symptoms according to the WOMAC served as a control (asymptomatic group, seven women, three men; mean age, 28 ± 3 years). After morphologic cartilage assessment, acetabular and femoral head cartilages were graded according to the modified Outerbridge grading criteria. In the midsagittal plane, single-observer analyses of precontrast T1 values (volunteers), the dGEMRIC index (T1Gd, patients), and T2 mapping values (everyone) were compared in acetabular and corresponding femoral head cartilage at the chondrolabral junction of each hip by region-of-interest analysis. RESULTS: In the symptomatic group, T1Gd and T2 values were lower in the acetabular cartilage compared with corresponding femoral head cartilage (T1Gd: 515 ± 165 ms versus 650 ± 191 ms, p < 0.001; T2: 39 ± 8 ms versus 46 ± 10 ms, p < 0.001). In contrast, the asymptomatic group demonstrated no differences in T1 and T2 values for the acetabular and femoral cartilages with the numbers available (T1: 861 ± 130 ms versus 860 ± 182 ms, p = 0.98; T2: 43 ± 7 ms versus 42 ± 6 ms, p = 0.73). No correlation with the numbers available was noted between the modified Outerbridge grade and T1, T1Gd, or T2 as well as between T2 and either T1 or T1Gd. CONCLUSIONS: Without the need for contrast media application, T2 mapping may be a viable alternative to dGEMRIC when assessing hip cartilage at the chondrolabral junction. However, acquisition-related phenomena as well as regional variations in the microstructure of hip cartilage necessitate an internal femoral head cartilage control when interpreting these results. LEVEL OF EVIDENCE: Level IV, diagnostic study.
Mitsouras, Dimitris, Robert Mulkern, Onur Afacan, Dana Brooks, and Frank Rybicki. (2007) 2007. “Basis Function Cross-Correlations for Robust K-Space Sample Density Compensation, With Application to the Design of Radiofrequency Excitations”. Magn Reson Med 57 (2): 338-52. https://doi.org/10.1002/mrm.21125.
The problem of k-space sample density compensation is restated as the normalization of the independent information that can be expressed by the ensemble of Fourier basis functions corresponding to the trajectory. Specifically, multiple samples (complex exponential functions) may be contributing to each independent information element (independent basis function). Normalization can be accomplished by solving a linear system based on the cross-correlation matrix of the underlying Fourier basis functions. The solution to this system is straightforward and can be obtained without resorting to discretization since the cross-correlations of Fourier basis functions are analytically known. Furthermore, no restrictions are placed on the k-space trajectory and its point-spread function. Additionally, the linear system can be used to elucidate key trade-offs involved in k-space trajectory design. The approach can be used to compensate samples acquired for image reconstruction or designed for low flip angle radiofrequency (RF) excitation. Here it is demonstrated for the latter application, using reversed spiral trajectories. In this case the linear system approach enables one to easily incorporate additional constraints such as smoothness to the solution. For typical RF excitation durations (<20 ms) it is shown that density compensation can even be achieved without numerical iteration.

A

Stamm, Aymeric, Jolene Singh, Onur Afacan, and Simon Warfield. (2015) 2015. “Analytic Quantification of Bias and Variance of Coil Sensitivity Profile Estimators for Improved Image Reconstruction in MRI”. Med Image Comput Comput Assist Interv 9350: 684-91. https://doi.org/10.1007/978-3-319-24571-3_82.
Magnetic resonance (MR) imaging provides a unique in-vivo capability of visualizing tissue in the human brain non-invasively, which has tremendously improved patient care over the past decades. However, there are still prominent artifacts, such as intensity inhomogeneities due to the use of an array of receiving coils (RC) to measure the MR signal or noise amplification due to accelerated imaging strategies. It is critical to mitigate these artifacts for both visual inspection and quantitative analysis. The cornerstone to address this issue pertains to the knowledge of coil sensitivity profiles (CSP) of the RCs, which describe how the measured complex signal decays with the distance to the RC. Existing methods for CSP estimation share a number of limitations: (i) they primarily focus on CSP magnitude, while it is known that the solution to the MR image reconstruction problem involves complex CSPs and (ii) they only provide point estimates of the CSPs, which makes the task of optimizing the parameters and acquisition protocol for their estimation difficult. In this paper, we propose a novel statistical framework for estimating complex-valued CSPs. We define a CSP estimator that uses spatial smoothing and additional body coil data for phase normalization. The main contribution is to provide detailed information on the statistical distribution of the CSP estimator, which yields automatic determination of the optimal degree of smoothing for ensuring minimal bias and provides guidelines to the optimal acquisition strategy.
Scherrer, Benoit, Onur Afacan, Maxime Taquet, Sanjay Prabhu, Ali Gholipour, and Simon Warfield. (2015) 2015. “Accelerated High Spatial Resolution Diffusion-Weighted Imaging”. Inf Process Med Imaging 24: 69-81. https://doi.org/10.1007/978-3-319-19992-4_6.
Acquisition of a series of anisotropically oversampled acquisitions (so-called anisotropic "snapshots") and reconstruction in the image space has recently been proposed to increase the spatial resolution in diffusion weighted imaging (DWI), providing a theoretical 8x acceleration at equal signal-to-noise ratio (SNR) compared to conventional dense k-space sampling. However, in most works, each DW image is reconstructed separately and the fact that the DW images constitute different views of the same anatomy is ignored. In addition, current approaches are limited by their inability to reconstruct a high resolution (HR) acquisition from snapshots with different subsets of diffusion gradients: an isotropic HR gradient image cannot be reconstructed if one .of its anisotropic snapshots is missing, for example due to intra-scan motion, even if other snapshots for this gradient were successfully acquired. In this work, we propose a novel multi-snapshot DWI reconstruction technique that simultaneously achieves HR reconstruction and local tissue model estimation while enabling reconstruction from snapshots containing different subsets of diffusion gradients, providing increased robustness to patient motion and potential for acceleration. Our approach is formalized as a joint probabilistic model with missing observations, from which interactions between missing snapshots, HR reconstruction and a generic tissue model naturally emerge. We evaluate our approach with synthetic simulations, simulated multi-snapshot scenario and in vivo multi-snapshot imaging. We show that (1) our combined approach ultimately provides both better HR reconstruction and better tissue model estimation and (2) the error in the case of missing snapshots can be quantified. Our novel multi-snapshot technique will enable improved high spatial characterization of the brain connectivity and microstructure in vivo.

3

Pier, Danielle, Ali Gholipour, Onur Afacan, Clemente Velasco-Annis, Sean Clancy, Kush Kapur, Judy Estroff, and Simon Warfield. 2016. “3D Super-Resolution Motion-Corrected MRI: Validation of Fetal Posterior Fossa Measurements”. J Neuroimaging 26 (5): 539-44. https://doi.org/10.1111/jon.12342.
PURPOSE: Current diagnosis of fetal posterior fossa anomalies by sonography and conventional MRI is limited by fetal position, motion, and by two-dimensional (2D), rather than three-dimensional (3D), representation. In this study, we aimed to validate the use of a novel magnetic resonance imaging (MRI) technique, 3D super-resolution motion-corrected MRI, to image the fetal posterior fossa. METHODS: From a database of pregnant women who received fetal MRIs at our institution, images of 49 normal fetal brains were reconstructed. Six measurements of the cerebellum, vermis, and pons were obtained for all cases on 2D conventional and 3D reconstructed MRI, and the agreement between the two methods was determined using concordance correlation coefficients. Concordance of axial and coronal measurements of the transcerebellar diameter was also assessed within each method. RESULTS: Between the two methods, the concordance of measurements was high for all six structures (P < .001), and was highest for larger structures such as the transcerebellar diameter. Within each method, agreement of axial and coronal measurements of the transcerebellar diameter was superior in 3D reconstructed MRI compared to 2D conventional MRI (P < .001). CONCLUSIONS: This comparison study validates the use of 3D super-resolution motion-corrected MRI for imaging the fetal posterior fossa, as this technique results in linear measurements that have high concordance with 2D conventional MRI measurements. Lengths of the transcerebellar diameter measured within a 3D reconstruction are more concordant between imaging planes, as they correct for fetal motion and orthogonal slice acquisition. This technique will facilitate further study of fetal abnormalities of the posterior fossa.