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Duan Xu

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14 papers
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14

YNIMG Journal 2024 Journal Article

Comparative evaluation of interpretation methods in surface-based age prediction for neonates

  • Xiaotong Wu
  • Chenxin Xie
  • Fangxiao Cheng
  • Zhuoshuo Li
  • Ruizhuo Li
  • Duan Xu
  • Hosung Kim
  • Jianjia Zhang

Significant changes in brain morphology occur during the third trimester of gestation. The capability of deep learning in leveraging these morphological features has enhanced the accuracy of brain age predictions for this critical period. Yet, the opaque nature of deep learning techniques, often described as "black box" approaches, limits their interpretability, posing challenges in clinical applications. Traditional interpretable methods developed for computer vision and natural language processing may not directly translate to the distinct demands of neuroimaging. In response, our research evaluates the effectiveness and adaptability of two interpretative methods-regional age prediction and the perturbation-based saliency map approach-for predicting the brain age of neonates. Analyzing 664 T1 MRI scans with the NEOCIVET pipeline to extract brain surface and cortical features, we assess how these methods illuminate key brain regions for age prediction, focusing on technical analysis with clinical insight. Through a comparative analysis of the saliency index (SI) with relative brain age (RBA) and the examination of structural covariance networks, we uncover the saliency index's enhanced ability to pinpoint regions vital for accurate indication of clinical factors. Our results highlight the advantages of perturbation techniques in addressing the complexities of medical data, steering clinical interventions for premature neonates towards more personalized and interpretable approaches. This study not only reveals the promise of these methods in complex medical scenarios but also offers a blueprint for implementing more interpretable and clinically relevant deep learning models in healthcare settings.

YNIMG Journal 2023 Journal Article

Hyperpolarized [2–13C]pyruvate MR molecular imaging with whole brain coverage

  • Brian T. Chung
  • Yaewon Kim
  • Jeremy W. Gordon
  • Hsin-Yu Chen
  • Adam W. Autry
  • Philip M. Lee
  • Jasmine Y. Hu
  • Chou T. Tan

Hyperpolarized (HP) 13C Magnetic Resonance Imaging (MRI) was applied for the first time to image and quantify the uptake and metabolism of [2–13C]pyruvate in the human brain to provide new metabolic information on cerebral energy metabolism. HP [2–13C]pyruvate was injected intravenously and imaged in 5 healthy human volunteer exams with whole brain coverage in a 1-minute acquisition using a specialized spectral-spatial multi-slice echoplanar imaging (EPI) pulse sequence to acquire 13C-labeled volumetric and dynamic images of [2–13C]pyruvate and downstream metabolites [5–13C]glutamate and [2–13C]lactate. Metabolic ratios and apparent conversion rates of pyruvate-to-lactate (k PL) and pyruvate-to-glutamate (k PG) were quantified to investigate simultaneously glycolytic and oxidative metabolism in a single injection.

YNICL Journal 2023 Journal Article

Multi-parametric hyperpolarized 13C/1H imaging reveals Warburg-related metabolic dysfunction and associated regional heterogeneity in high-grade human gliomas

  • Adam W. Autry
  • Sana Vaziri
  • Marisa LaFontaine
  • Jeremy W. Gordon
  • Hsin-Yu Chen
  • Yaewon Kim
  • Javier E. Villanueva-Meyer
  • Annette Molinaro

BACKGROUND: C imaging approach, we investigated dynamic and steady-state metabolism, together with physiological parameters, in high-grade gliomas to characterize active tumor. METHODS: and treatment effects. RESULTS: C]lactate and modified ratios relative to treatment effects. CONCLUSIONS: H imaging techniques.

YNICL Journal 2022 Journal Article

Assessment of higher-order singular value decomposition denoising methods on dynamic hyperpolarized [1-13C]pyruvate MRI data from patients with glioma

  • Sana Vaziri
  • Adam W. Autry
  • Marisa LaFontaine
  • Yaewon Kim
  • Jeremy W. Gordon
  • Hsin-Yu Chen
  • Jasmine Y. Hu
  • Janine M. Lupo

BACKGROUND: C]pyruvate MRI data acquired from patients with glioma. METHODS: ) conversion rates within regions of interest (ROIs) before and after denoising was then compared. RESULTS: modeling error increased from 0% to 15% (TRI) and 8% (GL-HOSVD). CONCLUSION: C data and thereby improve monitoring of metabolic changes in patients with glioma following treatment.

YNICL Journal 2021 Journal Article

Reduced anxiety and changes in amygdala network properties in adolescents with training for awareness, resilience, and action (TARA)

  • Olga Tymofiyeva
  • Eva Henje
  • Justin P. Yuan
  • Chiung-Yu Huang
  • Colm G. Connolly
  • Tiffany C. Ho
  • Sarina Bhandari
  • Kendall C. Parks

Mindfulness-based approaches show promise to improve emotional health in youth and may help treat and prevent adolescent depression and anxiety. However, there is a fundamental gap in understanding the neural reorganization that takes place as a result of such interventions. The Training for Awareness, Resilience, and Action (TARA) program, initially developed for depressed adolescents, uses a framework drawn from neuroscience, mindfulness, yoga, and modern psychotherapeutic techniques to promote emotional health. The goal of this study was to assess the effects of the TARA training on emotional health and structural white matter brain networks in healthy youth. We analyzed data from 23 adolescents who underwent the 12-week TARA training in a controlled within-subject study design and whose brain networks were assessed using diffusion MRI connectomics. Compared to the control time period, adolescents showed a significant decrease in anxiety symptoms with TARA (Cohen's d = -0.961, p = 0.006); moreover, the node strength of the Right Amygdala decreased significantly after TARA (Cohen's d = -1.026, p = 0.004). Post-hoc analyses indicated that anxiety at baseline before TARA was positively correlated with Right Amygdala node strength (r = 0.672, p = 0.001). While change in Right Amygdala node strength with TARA was not correlated with change in anxiety (r = 0.146, p = 0.51), it was associated with change in depression subscale of Anhedonia / Negative Affect (r = 0.575, p = 0.004, exploratory analysis), possibly due to overlapping constructs captured in our anxiety and depression scales. Our results suggest that increased structural connectivity of Right Amygdala may underlie increased anxiety in adolescents and be lowered through anxiety-reducing training such as TARA. The results of this study contribute to our understanding of the neural mechanisms of TARA and may facilitate neuroscience-based prevention and treatment of adolescent anxiety and depression.

YNICL Journal 2020 Journal Article

Characterization of serial hyperpolarized 13C metabolic imaging in patients with glioma

  • Adam W. Autry
  • Jeremy W. Gordon
  • Hsin-Yu Chen
  • Marisa LaFontaine
  • Robert Bok
  • Mark Van Criekinge
  • James B. Slater
  • Lucas Carvajal

BACKGROUND: C imaging in patients undergoing treatment for brain tumors and determine whether there is evidence of aberrant metabolism in the tumor lesion compared to normal-appearing tissue. METHODS: was measured in terms of the coefficient of variation (CV). RESULTS: . CONCLUSION: in gadolinium-enhancing and non-enhancing lesions. Larger prospective studies with homogeneous patient populations are planned to evaluate metabolic changes following treatment.

YNICL Journal 2019 Journal Article

Application of machine learning to structural connectome to predict symptom reduction in depressed adolescents with cognitive behavioral therapy (CBT)

  • Olga Tymofiyeva
  • Justin P. Yuan
  • Chiung-Yu Huang
  • Colm G. Connolly
  • Eva Henje Blom
  • Duan Xu
  • Tony T. Yang

PURPOSE: Adolescent major depressive disorder (MDD) is a highly prevalent, incapacitating and costly illness. Many depressed teens do not improve with cognitive behavioral therapy (CBT), a first-line treatment for adolescent MDD, and face devastating consequences of increased risk of suicide and many negative health outcomes. "Who will improve with CBT?" is a crucial question that remains unanswered, and treatment planning for adolescent depression remains biologically unguided. The purpose of this study was to utilize machine learning applied to patients' brain imaging data in order to help predict depressive symptom reduction with CBT. METHODS: We applied supervised machine learning to diffusion MRI-based structural connectome data in order to predict symptom reduction in 30 depressed adolescents after three months of CBT. A set of 21 attributes was chosen, including the baseline depression score, age, gender, two global network properties, and node strengths of brain regions previously implicated in depression. The practical and robust J48 pruned tree classifier was utilized with a 10-fold cross-validation. RESULTS: The classification resulted in an 83% accuracy of predicting depressive symptom reduction. The resulting tree of size seven with only three attributes highlights the role of the right thalamus in predicting depressive symptom reduction with CBT. Additional analysis showed a significant negative correlation between the change in the depressive symptoms and the node strength of the right thalamus. CONCLUSIONS: Our results demonstrate that a machine learning algorithm that exclusively uses structural connectome data and the baseline depression score can predict with a high accuracy depressive symptom reduction in adolescent MDD with CBT. This knowledge can help improve treatment planning for adolescent depression.

YNIMG Journal 2019 Journal Article

Challenges in pediatric neuroimaging

  • Matthew J. Barkovich
  • Yi Li
  • Rahul S. Desikan
  • A. James Barkovich
  • Duan Xu

Pediatric neuroimaging is challenging due the rapid structural, metabolic, and functional changes that occur in the developing brain. A specially trained team is needed to produce high quality diagnostic images in children, due to their small physical size and immaturity. Patient motion, cooperation and medical condition dictate the methods and equipment used. A customized approach tailored to each child's age and functional status with the appropriate combination of dedicated staff, imaging hardware, and software is key; these range from low-tech techniques, such as feed and swaddle, to specialized small bore MRI scanners, MRI compatible incubators and neonatal head coils. New pre-and post-processing techniques can also compensate for the motion artifacts and low signal that often degrade neonatal scans.

YNIMG Journal 2018 Journal Article

Quantitative surface analysis of combined MRI and PET enhances detection of focal cortical dysplasias

  • Yee-Leng Tan
  • Hosung Kim
  • Seunghyun Lee
  • Tarik Tihan
  • Lawrence ver Hoef
  • Susanne G. Mueller
  • Anthony James Barkovich
  • Duan Xu

Objective Focal cortical dysplasias (FCDs) often cause pharmacoresistant epilepsy, and surgical resection can lead to seizure-freedom. Magnetic resonance imaging (MRI) and positron emission tomography (PET) play complementary roles in FCD identification/localization; nevertheless, many FCDs are small or subtle, and difficult to find on routine radiological inspection. We aimed to automatically detect subtle or visually-unidentifiable FCDs by building a classifier based on an optimized cortical surface sampling of combined MRI and PET features. Methods Cortical surfaces of 28 patients with histopathologically-proven FCDs were extracted. Morphology and intensity-based features characterizing FCD lesions were calculated vertex-wise on each cortical surface, and fed to a 2-step (Support Vector Machine and patch-based) classifier. Classifier performance was assessed compared to manual lesion labels. Results Our classifier using combined feature selections from MRI and PET outperformed both quantitative MRI and multimodal visual analysis in FCD detection (93% vs 82% vs 68%). No false positives were identified in the controls, whereas 3. 4% of the vertices outside FCD lesions were also classified to be lesional (“extralesional clusters”). Patients with type I or IIa FCDs displayed a higher prevalence of extralesional clusters at an intermediate distance to the FCD lesions compared to type IIb FCDs (p < 0. 05). The former had a correspondingly lower chance of positive surgical outcome (71% vs 91%). Conclusions Machine learning with multimodal feature sampling can improve FCD detection. The spread of extralesional clusters characterize different FCD subtypes, and may represent structurally or functionally abnormal tissue on a microscopic scale, with implications for surgical outcomes.

YNICL Journal 2017 Journal Article

Early changes in brain structure correlate with language outcomes in children with neonatal encephalopathy

  • Kevin A. Shapiro
  • Hosung Kim
  • Maria Luisa Mandelli
  • Elizabeth E. Rogers
  • Dawn Gano
  • Donna M. Ferriero
  • A. James Barkovich
  • Maria Luisa Gorno-Tempini

Global patterns of brain injury correlate with motor, cognitive, and language outcomes in survivors of neonatal encephalopathy (NE). However, it is still unclear whether local changes in brain structure predict specific deficits. We therefore examined whether differences in brain structure at 6 months of age are associated with neurodevelopmental outcomes in this population. We enrolled 32 children with NE, performed structural brain MR imaging at 6 months, and assessed neurodevelopmental outcomes at 30 months. All subjects underwent T1-weighted imaging at 3 T using a 3D IR-SPGR sequence. Images were normalized in intensity and nonlinearly registered to a template constructed specifically for this population, creating a deformation field map. We then used deformation based morphometry (DBM) to correlate variation in the local volume of gray and white matter with composite scores on the Bayley Scales of Infant and Toddler Development (Bayley-III) at 30 months. Our general linear model included gestational age, sex, birth weight, and treatment with hypothermia as covariates. Regional brain volume was significantly associated with language scores, particularly in perisylvian cortical regions including the left supramarginal gyrus, posterior superior and middle temporal gyri, and right insula, as well as inferior frontoparietal subcortical white matter. We did not find significant correlations between regional brain volume and motor or cognitive scale scores. We conclude that, in children with a history of NE, local changes in the volume of perisylvian gray and white matter at 6 months are correlated with language outcome at 30 months. Quantitative measures of brain volume on early MRI may help identify infants at risk for poor language outcomes.

YNIMG Journal 2016 Journal Article

NEOCIVET: Towards accurate morphometry of neonatal gyrification and clinical applications in preterm newborns

  • Hosung Kim
  • Claude Lepage
  • Romir Maheshwary
  • Seun Jeon
  • Alan C. Evans
  • Christopher P. Hess
  • A. James Barkovich
  • Duan Xu

Cerebral cortical folding becomes dramatically more complex in the fetal brain during the 3rd trimester of gestation; the process continues in a similar fashion in children who are born prematurely. To quantify this morphological development, it is necessary to extract the interface between gray matter and white matter, which is particularly challenging due to changing tissue contrast during brain maturation. We employed the well-established CIVET pipeline to extract this cortical surface, with point correspondence across subjects, using a surface-based spherical registration. We then developed a variant of the pipeline, called NEOCIVET, that quantified cortical folding using mean curvature and sulcal depth while addressing the well-known problems of poor and temporally-varying gray/white contrast as well as motion artifact in neonatal MRI. NEOCIVET includes: i) a tissue classification technique that analyzed multi-atlas texture patches using the nonlocal mean estimator and subsequently applied a label fusion approach based on a joint probability between templates, ii) neonatal template construction based on age-specific sub-groups, and iii) masking of non-interesting structures using label-fusion approaches. These techniques replaced modules that might be suboptimal for regional analysis of poor-contrast neonatal cortex. The proposed segmentation method showed more accurate results in subjects with various ages and with various degrees of motion compared to state-of-the-art methods. In the analysis of 158 preterm-born neonates, many with multiple scans (n =231; 26–40weeks postmenstrual age at scan), NEOCIVET identified increases in cortical folding over time in numerous cortical regions (mean curvature: +0. 003/week; sulcal depth: +0. 04mm/week) while folding did not change in major sulci that are known to develop early (corrected p <0. 05). The proposed pipeline successfully mapped cortical structural development, supporting current models of cerebral morphogenesis, and furthermore, revealed impairment of cortical folding in extremely preterm newborns relative to relatively late preterm newborns, demonstrating its potential to provide biomarkers of prematurity-related developmental outcome.

YNICL Journal 2015 Journal Article

Clinically feasible NODDI characterization of glioma using multiband EPI at 7 T

  • Qiuting Wen
  • Douglas A.C. Kelley
  • Suchandrima Banerjee
  • Janine M. Lupo
  • Susan M. Chang
  • Duan Xu
  • Christopher P. Hess
  • Sarah J. Nelson

Recent technological progress in the multiband echo planer imaging (MB EPI) technique enables accelerated MR diffusion weighted imaging (DWI) and allows whole brain, multi-b-value diffusion imaging to be acquired within a clinically feasible time. However, its applications at 7 T have been limited due to B1 field inhomogeneity and increased susceptibility artifact. It is an ongoing debate whether DWI at 7 T can be performed properly in patients, and a systematic SNR comparison for multiband spin-echo EPI between 3 T and 7 T has not been methodically studied. The goal of this study was to use MB EPI at 7 T in order to obtain 90-directional multi-shell DWI within a clinically feasible acquisition time for patients with glioma. This study included an SNR comparison between 3 T and 7 T, and the application of B1 mapping and distortion correction procedures for reducing the impact of variations in B0 and B1. The optimized multiband sequence was applied in 20 patients with glioma to generate both DTI and NODDI maps for comparison of values in tumor and normal appearing white matter (NAWM). Our SNR analysis showed that MB EPI at 7 T was comparable to that at 3 T, and the data quality acquired in patients was clinically acceptable. NODDI maps provided unique contrast within the T2 lesion that was not seen in anatomical images or DTI maps. Such contrast may reflect the complexity of tissue compositions associated with disease progression and treatment effects. The ability to consistently obtain high quality diffusion data at 7 T will contribute towards the implementation of a comprehensive brain MRI examination at ultra-high field.

YNIMG Journal 2015 Journal Article

Effects of rejecting diffusion directions on tensor-derived parameters

  • Yiran Chen
  • Olga Tymofiyeva
  • Christopher P. Hess
  • Duan Xu

Diffusion Tensor Imaging (DTI) is adversely affected by subject motion. It is necessary to discard the corrupted images before diffusion parameter estimation. However, the consequences of rejecting those images are not well understood. In this study, we investigated the effects of excluding one or more volumes of diffusion weighted images by analyzing the changes in fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), radial diffusivity (RD) and the primary eigenvector (V1). Based on the full set of diffusion images acquired by the Jones30 diffusion scheme, we generated incomplete sets of at least six in three different ways: random, uniform and clustered rejections. The results showed that MD was not significantly affected by rejecting diffusion directions. In the cases of random rejections, FA, AD, RD and V1 were overestimated more greatly with increasing number of rejections and the overestimations were worse in low FA regions than high FA regions. For uniform rejections, at which the remaining diffusion directions are evenly distributed on a sphere, little change was observed in FA and in V1. Clustered rejections, on the other hand, displayed the most significant overestimation of the parameters, and the resulting accuracy depended on the relative orientation of the underlying fibers with respect to the excluded directions. In practice, if diffusion direction data is excluded, it is important to note the number and location of directions rejected, in order to make a more precise analysis of the data.

YNIMG Journal 2008 Journal Article

Development of a robust method for generating 7.0 T multichannel phase images of the brain with application to normal volunteers and patients with neurological diseases

  • Kathryn E. Hammond
  • Janine M. Lupo
  • Duan Xu
  • Meredith Metcalf
  • Douglas A.C. Kelley
  • Daniel Pelletier
  • Susan M. Chang
  • Pratik Mukherjee

The increased susceptibility effects and high signal-to-noise ratio at 7. 0 T enable imaging of the brain using the phase of the magnetic resonance signal. This study describes and evaluates a robust method for calculating phase images from gradient-recalled echo (GRE) scans. The GRE scans were acquired at 7. 0 T using an eight-channel receive coil at spatial resolutions up to 0. 195×0. 260×2. 00 mm. The entire 7. 0 T protocol took less than 10 min. Data were acquired from forty-seven subjects including clinical patients with multiple sclerosis (MS) or brain tumors. The phase images were post-processed using a fully automated phase unwrapping algorithm that combined the data from the different channels. The technique was used to create the first phase images of MS patients at any field strength and the first phase images of brain tumor patients above 1. 5 T. The clinical images showed novel contrast in MS plaques and depicted microhemorrhages and abnormal vasculature in brain tumors with unsurpassed resolution and contrast.

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