MSBI Program Research Projects

UCSF’s Department of Radiology and Biomedical Imaging consistently ranks amongst the top departments in the nation in terms of funding from the National Institutes of Health. There is a wide breadth of research performed, ranging from basic science to applied clinical research.

The MSBI program encourages students to explore their own research interests and many research opportunities exist within the Department of Radiology and Biomedical Imaging, in other departments at UCSF, and even in local biotechnology and pharmaceutical companies.  A research elective course is introduced in the Spring quarter, which allows students time to explore potential research topics. Most MSBI students pursue the thesis option, which allows them to spend the summer quarter working full time on their research project.  The vast majority of MSBI thesis students receive a stipend during the summer quarter.  Summaries of the range of projects undertaken by MSBI students can be found at the links below.

Thesis & Abstracts

2023 - 2024

Radhika Bhalerao Predicting Meningioma Genetics from multi-sequence Magnetic Resonance Imaging using Machine Learning
Duc Huy Doan Application of Convolutional Neural Networks in Multiparametric MR Imaging to Predict Prostate Cancer Progression
Tangran Dong Optimizing Diffusion Weighted Imaging for Breast Cancer Treatment Evaluation: A Study on Correcting Echo Planar Imaging Distortions and Gradient Nonlinearity
Chase Fitch Dorsal Root Ganglia Diffusion Metrics in Patients with Lumbar Radiculopathy Undergoing Injection
Ellis Mayne Evaluating the Efficacy of Combination CD46-Targeted 225Ac Radioimmunotherapy and Antibody-Drug Conjugate Therapy in Multiple Myeloma
Siddharthasiva Anbu Rajan MRI - Based Measures of Metabolic Health in the Assessment of Patients with Chronic Inflammatory States
Nadezhda Urmanov Improved chemoenzymatic radiosynthesis of fluorine-18 labeled sakebiose for microPET-CT imaging of Staphylococcus aureus
Jo Veres The Impact of Proteoglycan Degradation and Fragmentation on T1rho Relaxation Times
Tianrun Xiao Optimization of the MR-guided Focused Ultrasound Induced Blood-Brain Barrier Opening in a rat model

2022 - 2023

Shixian Du Evaluation of the feasibility of in vivo Ac-225 imaging
Eric Park Improving Mouse Brain Hyperpolarized 13C MR data through User-Independent tMPPCA Denoising
Paramjot Singh Predicting Newly-Diagnosed Glioma Pathology with MRI
Katelyn Vu Evaluating target-specific pre-to-post DBS effects on brain function in Parkinson’s disease using fMRI
Ningjing Zhang Improving Quantification of Prostate-Specific Membrane Antigen (PSMA) - Positron Emission Tomography (PET) Clinical Data for Clinical Decision Making

2021 - 2022

Anna Bennett Improving Pyruvate Kinetic Measurements Using Variable Flip Angle Schemes in bSSFP Hyperpolarized Carbon-13 MR Imaging
Gabriella Ramil Using Time-Lapse HR-pQCT for Bone Turnover Classification in CKD-MBD Patients
Zachary Rossen White Matter Microstructure and Connectivity in mTBI Patients with Distinct Neuropsychiatric Phenotypes

2020 - 2021

Aryn Alanizi Targeting Peptidoglycan using Radiolabeled Click Chemistry for PET Infection Imaging
Umama Ali Development of 18F-labelled Tris(2-pyridylmethyl)amine-based Chelator to Image Zinc Distribution in Prostate Cancer Models Using Positron Emission Tomography
Maria Baida Comparative ROI analysis for Traumatic Brain Injury with TBSS and XTRACT masks using DTI and NODDI models
Bhanu Bucchireddigari Examining the efficacy of various novel radiotherapies on prostate cancer cell lines
Suchi Drona Development of PSMA Targeted Polymer Nanoparticles to Treat Prostate Cancer By Boron Neutron Capture Therapy Directed Against PSMA
Ryan Ellis Leveraging large scale data sets: a transfer learning approach for 7T super resolution
Cyril Fong Light-Induced One Pot Shot Synthesis as an Optimal Approach in the Development of 89Zr-radiolabeled Antibodies
Natalia Konovalova Dedicated breast positron emission tomography technology to characterize invasive lobular carcinoma
Sasank Sakhamuri Imaging granzyme biochemistry in CAR T cell immunotherapy with restricted interaction peptides and PET


2019 - 2020

Casey Alcantar A Faster R-CNN Model for Detection of MR-Compatible Catheters
Souradeep Gogol Bhattacharya An imaging informatics-based risk assessment for early detection of depressive symptom onset
Jacob Ellison Improving the generalizability of convolutional neural networks for brain tumor segmentation in the post-treatment setting
Anil Kemisetti Comparing the Training Performance of a Deep Neural Network for Accelerated MRI Reconstruction Using Synthesized and Realistic k-Space Data
Chieh Te Jack Lin Synthesis of DFO with PSMA-targeted inhibitor labeled 89Zr to evaluate prostate cancer
Jacob Oeding Automatic Three-Dimensional Bone Shape Modeling Using Clinical MRI
Jonathan Renslo Distinguishing porosity and vasculature changes in Type 2 Diabetes (T2D) in distal tibia with MRI and HRqCT
Avantika Sinha Standardized, Open-Source Processing of Hyperpolarized 13C Data
Bishal Upadhyaya A Comparison of FDG and Amyloid PET for the Deep Learning Prediction of Alzheimer’s Disease in Low Income Communities


2018 - 2019

Ravi Chachad Temporal Impact of Sugar Metabolism on the Liver
Qing Dai Clear Cell Renal Cell Carcinoma: Deep Learning-Based Prediction of Tumor Grade from Contrast-Enhanced CT
Emilie Decavel-Bueff Drug capture efficacy using polystyrenesulfonate-coated chemofilter device
Virginia Hinostroza 4D Flow with Compressed Sensing for the Evaluation of Intracranial Aneurysmal Flow
Alison Myoraku Lifespan Changes of the Human Insula in Major Depression
Samuel Shu Understanding differences in quantification of conventional versus experimental contrast materials with different clinical dual-energy computed tomography systems, and development of universal contrast quantification “handshake”
Benjamin Sipes EEG Microstates in Neurofeedback Attention Training
Torie Tsuei Longitudinal Changes in Brain Structure and Integrity During Acute HIV
Jack Williams Evaluating EPflex MRline Guidewire for Endovascular Interventions Guided by MRI at 3T vs. X-ray Fluoroscopy
Fei Xiong Prediction of Abdominal Aortic Aneurysms (AAAs) Progression by Automatic Segmentation and Radiomics Feature Quantification
Jiamin Zhou Spectrome-AI: a Neural Network Framework for Inferring MEG Spectra

2017 - 2018

Sei Ahn Edge Density Imaging Characterization of White Matter Alterations and Overall Network Topology of 16p11.2 Deletion Carriers and Idiopathic ASD Individuals
David Baskin Advanced CEUS Techniques for MSK Imaging
Frank Chang Validatrion of an Augmented Reality System using MR Techniques
Xiao Gao Neuroimaging-based Artificial Neural Network Predicts Conversion of Cognitive Impairment Spectrum in Alzheimer’s Disease
Matthew Gibbons Identification of Blood Vessels in Cortical Bone Pores utilizing DCE-MRI and HR-pQCT
Mahima Goel Auditory Cortex Activity Modulation in Response to Sensory Feedback during Audiomotor Map Learning
Jeffrey Chieh Hsiao Measuring mTORC1 Signaling with Non-Invasive (89)Zr-Transferrin PET
Molly Kadlec Functional Magnetic Resonance Imaging Signature of Pain Anticipation and Clinical Depressive Symptomatology
I-Ju Eric Lee Cerebral vascular and hemodynamic imaging with two-photon microscopy
Jacob Mallott Diffusion Tensor Imaging Analysis of mTBI in Scholastic Athletes
Alex Nguyen Applying Deep Leaming Models on the Brain Connectome for Improving Cognitive Predictions of Parkinson's Disease
Guangzhong Su Incorporating Metabolic and Physiologic Imaging into Radiation Therapy Treatment Planning of Patients with Glioblastoma
Kai Qiao Tiong Exploration of Early Metabolic Changes in Alzheimer's Disease as a Biomarker using Hyperpolarized C-13
Guillaume Trusz Pharmacokinetics and Biodistribution of 89Zr-Df-PEG40 Nanoparticles in Xenograft Tumor Models using micro PET/CT
Dyana Vega Development of an anthropomorphic colon phantom to test the performance of dual energy computed tomography (DECT)

2016 - 2017

Sivakami Avadiappan Simultaneous Visualization of arteries, veins and cerebral microbleeds from 7T MRA-SWI images for assessing the effects of radiation therapy in brain
Jonathan Chan In-Vitro Flow Characteristics of Chemotherapy Filter Device
Kevin Chang Role of hyperpolarized Glutamate in Detecting Neuroendocrine Prostate Cancer
Hsu-Cheng Huang Optimizing bone marrow lesion detection using dual energy CT
Henry Li Detection of prostate cancer through molecular imaging of Zn using hyperpolarized 13C MRI
Cyrus Manuel Weakly supervised deep feature learning to predict amyloidosis from structural MR brain images
Michael Piel Predictive Modeling of Whole Body Dual Energy X-Ray Absorptiometry from 3D Optical Scans Using Shape and Appearance Modeling
Niecholle Roco Development and Imaging of Targeted Therapy Imaging Agents for BCBM
Benjamin Speidel Mapping EEG to Brain MRI for Epilepsy Localization
Radhika Tibrewala Strategies in MR-Guided Focused Ultrasound
Justin Yu  Optimization of pH imaging methodology for hyperpolarized 13C MRI

2015 - 2016

Joshua Fisher In vitro Binding of ChemoFilter with Cisplatin
Catherine Fu Translation of Zirconium -85 labeled antibodies for human imaging
Wesley Kuo Binding Kinetics of Cisplatin with Ion-exchange Resin
Joanne Lau Fetal Brain Measurements Predict Neonatal Brain Injury in Patients with CHD
Nathan Poulin Simulations of RF Probes for Endovascular MRI using the Finite Element Method
Vishal Samboju Evaluation of needle displacement errors in brachytherapy using electromagnetic (EM) tracking
Sizhe Wang Quantifying Bio-elimination of Oral Fumed Silica-based CT Contrast Agent
Jiajing Xu Exploring and Evaluation Novel Algorithm for interference rejection in MEG data
Joy Yeh Changes in Structural Networks After Radiation Therapy in Patients with Brain Tumors
Xinheng Zhang Comparison of CFD and 4D MRV in a flow model
Alan Zhu Evaluation of structural connectome models and network diffusion in predicting cortical atrophy in Alzheimer's disease spectrum

2014 - 2015

Samuel Huang Automatic Segmentation and Kinematic Quantification of ACL Injured Patients Knees
Nathaniel Jenkins NaF-18 PETMR Kinetic Analysis of Lower Back Pain
Gina Kirkish Cortical Recruitment of Motor Imagery in Timed Up and Go Task
Tiffany Kwak Evaluation of D-Amino Acids as a Probe for Molecular Imaging of Bacterial Infections
Tae Lee Does the trabecular bone score reflect the structure of trabecular bone?
Andrew Leynes Tissue Segmentation and Classification for PET/MR MR-based Attenuation Correction Using Zero-Echo Time (ZTE) MRI
Elizabeth Li ADC as an indicator of breast cancer response to Veliparib treatment
Elizabeth Phillips ROI Analysis of Brain Spectra from Patients with Traumatic Brain Injury
Hecong Qin In Vivo Hyperpolarized Carbon-13 Diffusion Weighted MRI Measures Lactate Metabolism and Transport in Prostate Cancer
Omar Rutledge Characterization of combat-induced post-traumatic stress disorder in OIF/OEF veterans using MEG-based imaging
Roksana Sadeghi Statistical Shape Analysis in MRI
Solomon Tang Metabolic characterization of slowly cycling melanoma cells
Jay Yu Development of filter device to limit systemic toxicity from doxorubicin chemotherapy: DNA ChemoFilter
Joseph Zhang Extending Glioma invasion of brain regions using tractography
Yukai Zhou Microstructural integrity of brain white matter in different substance using populations: Diffusion Tensor Imaging analysis of 4 Tesla MRI data

2013 - 2014

Nabeel Al-Aziz Synthesis of [18F]-MFBG analogs with in vitro characterization
Loi Do Quantitative MRI Measurements of Function Perfusion and Viability in Microembolized Severely Ischemic Hearts
Khaled Dostzada Radioiodination of MIBG for Neuroendocrine Tumor Imaging
Molly Gibson Impact of Fructose Restriction in Obese Children on Pancreatic Fat Fraction
Leon Hsueh The Reproducibility of PC-MRI for the Assessment of Intracranial Aneurysms
Natalie Korn Semi-Automatic Prostate Segmentation on an MR Fat Fraction Map
Ruby Kuang The Effects of Exercise on Bone Quality and Bone Strength in HIV-Positive Individuals Age 50 and Older
Collin Ma Quality Assessment of Investigational MR Sequence With Reference to the Clinical Standard
Sonam Machingal Sampling Strategies for Hyperpolarized Carbon-13 Imaging
Yuxin Sun Homogenization and Stabilization of Novel Enteric Dual Energy CT Contrast Material
Nicholas Tran Quantitative Analysis of Hypertrophic Myocardium using Diffusion Tensor Magnetic Resonance Imaging
Ruobin Wu Kinetic Modeling of Myocardial Perfusion Using SPECT Data
Alex Yeh Serial MRI/MRSI of Patients With Gliomas Being Treated With Novel Therapies
Jeffrey Hu Integrating Resonators to Catheters for MR-Guided Interventional Radiology

2012 - 2013

Madhav Agrawal 18f-FDG PET/CT to measure glucose metabolism of various breast cancer cell linesin vivo
Naeim Bahrami Modeling the 13-C Hyperpolarized Pyruvate and Urea Concentration Kinetics With Multiband RF Excitation MRI in Prostate Cancer
Rupinder Chandi In vivoImaging Assessment of Radionucliotide Therapy of Neuroblastoma Using Small Molecule PET Prove Targeting hNET
Dharshan Chandramoham Advanced Quantitative MR Imaging for Detecting Early Degeneration of Cartilage
YiShin Chang Differing Patterns of Brain Connectivity in Autism Spectrum Disorder vs Sensory Processing Disorder
Lindsay Conner The Association of Amyloid Count With a Decrease in the Complexity of the BOLD Signal Observed in Alzheimer's Disease
Marie LeDonne Reproducibility of Streamlines in Diffusion Fiber Tracking
Hsin-Wei Shen Optimization of the Design Parameter of MR Compatible HIFU Rodent System for Evaluating Hyperpolarized 13C as Hypothermia Probe
Charvi Shetty Developing Methods to Aid Edge Detection in a Micro-Computed Tomography Based Subcutaneous Versus Visceral Fat Segmentation Algorithm
Caleb Tam Quantitative Comparison of Bone Metabolism Using Fluorescence and X-Ray Microscopy Techniques
Shuyu Tang Development of a Novel 2D RF Pulse Sequence to Achieve An Improved Localization of Hyperpolarized 13-C Imaging
Alyssa Zhu Optimization of Brain Segmentation in Multiple Sclerosis Patients

2011 - 2012

Wei-Ching Lo Advanced Image Analysis and Finite Element Modeling for Knees with Acute Injury
Hendry Cahaya 68-Gallium (Ga-68) and 111-Indium (In-111) Labeled Plectin- 1 Targeting Peptides (PTP) as Novel Imaging Probes for the Detection of Human Pancreatic Cancer
Michelle Grabau Assessment of Porcine Intervertebral Disc Specimen pH via Chemical Exchange Saturation Transfer (CEST) MRI
Aditi Guha Rapid Magnetization Prepared Diffusion Weighted Imaging of Articular Cartilage in vivo
Tzu-Cheng Lee Tibia and Vertebra Bone Structure Changes in Old-Male Spontaneously Hypertensive Rats by Quantitative Micro-CT
Carmin Liang Predicting Disease Progression with Multiparametric Magnetic Resonance Imaging of Prostate Cancer Managed with Active Surveillance
Cheng-Liang Liu Comparison Between High-Resolution and Standard DTI in Apparent Diffusion Coefficient and Fractional Anisotropy in Patients with Locally Advanced Breast Cancer
Manutej Mulaveesala Quantitative Evaluation of Glioblastoma Multiforme Growth and Treatment with MRI in Murine Models: Tumor Volume, Diffusion Mapping, and T2 Relaxometry