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Postdoctoral Fellowships - PhD Theses

Please contact Prof. Matthias Stuber if you are interested in a non-advertised PhD thesis or postdoctoral project.

PhD position

Do you have an Masters degree in Physics, Engineering or SV? Would you like to use your engineering skills to help improve modern diagnostic technology, to make it more time efficient, easier to use, and more affordable? Would you like to be part of a team that changes the way magnetic resonance imaging (MRI) of the heart is done? Should the answer to the above questions be "yes", then please apply for a PhD position at CIBM-CHUV-MR that consists of 17 engineers and physicists and that is working in a direct interdisciplinary and translational collaboration with industry and medical professionals at the CHUV. Please contact Prof. Matthias Stuber (matthias.stuber@chuv.ch) or Dr. Ruud van Heeswijk (Ruud.Van-Heeswijk@chuv.ch), should you be interested.

Master Thesis Projects

Model-based water fat signal separation for simultaneous fat suppression and visualization in accelerated MRI

Distinguishing signals originating from different tissue compartments such as water and fat is challenging in MRI.  Imaging applications often require fat suppression, but there is an increased interest to quantify fat content. To overcome this problem, we are developing a technique that uses the frequency dependent signal behavior of different tissue compartments in an accelerated MRI sequence to separate water and fat signals, providing simultaneous fat suppression and fat imaging.
Project: In this project, the prospective student will characterize the frequency dependent signal behavior, both numerically and experimentally. The student will adapt the sequences for use in human volunteers, and will develop and implement signal models for the image reconstruction and to enable acceleration of the data acquisition. Experience with Matlab and C++ is helpful.
Who: Students with a background in physics, electrical engineering  or biomedical engineering who are interested in the development of novel applications in cardiac MRI that are directly translatable to the clinic.

Supervison and contact:     Dr. Jessica Bastiaansen

Submillisecond lipid suppression for robust whole heart MRI, breast MRI and peripheral angiography

Differentiating between different tissue types such as blood and muscle, myocardial lipid and scar, or malignant-benign tissues are challenging at high magnetic field strength in the presence of unsuppressed fat signals. These may complicate several MR applications such as angiography, whole heart cardiac imaging or breast MRI in patients. Our group has developed and patented a novel technique for fat suppression that is capable of manipulating the signals of both muscle, lipids and blood vessels in such a way that they become easily distinguishable on MRI.

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Project: The student will participate in an ongoing study that aims to develop new quantitative imaging methodology using ultrashort water excitation techniques. The work involves numerical simulations, MRI sequence adaptation, data analysis, and a thorough benchmarking against existing imaging techniques.
Who: The research projects are suited to motivated students with a background in physics, electrical or bio(medical) engineering.

Supervison and contact:     Dr. Jessica Bastiaansen

Precision measurements in cardiac MRI

Are you a student in Micro- or Electrical Engineering who wants to complete a Master’s Thesis at the intercept of engineering, medicine, and cutting-edge magnetic resonance imaging (MRI) research?

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Advanced, next generation magnetic resonance imaging technology is currently being developed by a team of almost 20 basic scientists and engineers located directly at the CHUV (University Hospital Lausanne). We are working on new technology that visualizes the heart, its structure, its blood vessels and its function with unprecedented detail. In that pursuit, we develop techniques to suppress adverse effects of respiratory and cardiac motion. However, these techniques remain to be characterized and validated not only to better understand - but also to maximize their performance. To meet that challenge, we have already built an MRI-compatible moving phantom whose motion can be programmed. However, the challenge is now to measure the “true” displacement of the phantom head as a function of time with sub-millimeter accuracy. We anticipate that the candidate will implement an optical measurement system that is powered by a laser and which will log phantom motion data during the MRI measurements. Skills in the domains of fiber optics, programming, signal processing, image processing and even experimental scanning on the MRI console will be acquired or further developed during the course of this interesting Masters thesis.

Supervision: Matthias Stuber

Improving quantitative 3D magnetic resonance imaging for the mapping of cartilage damage in knee osteoarthritis

Topic: Magnetic resonance imaging (MRI) numerical simulations, data acquisition, and image processing.
Who: Students with a background in physics or engineering who are interested in a project that will lead to a Master of Science (MSc) degree. Programming knowledge is essential, Matlab knowledge is an advantage.

Where: The project will take place in the Center for Biomedical Imaging at the Lausanne University Hospital (CHUV) and University of Lausanne (UNIL) in Switzerland (see www.unil.ch/cvmr). One of the main goals of the group is to develop new MRI techniques and to apply these in patients in a clinical setting.

Project: MRI is a non-invasive and non-harmful medical imaging technique. The contrast in its images relies on the difference in so-called relaxation times between tissues. In the context of knee cartilage, the T2 relaxation time correlates with the water and collagen content of the extracellular matrix, as well as the structure of the collagen network. The T2 relaxation time can thus be used as imaging biomarker of early-stage osteoarthritis (OA), during which the breakdown of the cartilage matrix and cartilage loss start occurring. In T2 mapping, the acquisition of multiple images with different T2 weights enables the calculation of the T2 value for each pixel. Unlike the qualitative evaluation of (arbitrary) grayscale intensity images, T2 mapping can potentially help in more accurately, precisely and quantitatively identifying early-stage OA cartilage changes.

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Our group recently developed a new 3D technique for knee cartilage T2 mapping with a very high spatial resolution (Colotti et al., J Magn Reson 2017). The Master thesis project will aim to improve this technique in several ways, among others by refining and accelerating the modeling and calculation of the T2 relaxation time. In practice, this means that the student will: 1) familiarize her- or himself with MRI theory and the MRI scanner; 2) expand and improve the numerical simulations of the technique; 3) develop a dictionary T2 fitting framework in Matlab. This improved fitting framework will be then compared with the method that is currently used in terms of precision/accuracy of T2 quantification in phantoms and volunteers. A collaboration with the clinical muskoskeletal radiology service is also foreseen.

Duration: The project duration can be adapted to the student’s requirements, but is expected to take 5 to 9 months.

Supervision:
Dr. Ruud van Heeswijk
 

Accelerated 3D cardiac T2 mapping

Who: We are looking for a highly motivated physics or engineering Master student for a project that will lead to a Master of Science (MSc) degree.

Where: The project will be on the subject of magnetic resonance imaging (MRI), and will take place in the CardioVascular Magnetic Resonance center (CVMR, see www.unil.ch/cvmr) of the University Hospital of Lausanne (CHUV) and the University of Lausanne (UNIL) in Switzerland.

What: The goal of the project will be to expand a two-dimensional (2D) T2 mapping technique to 3D.

Background: Magnetic resonance imaging (MRI) is a non-invasive medical imaging technique without ionizing radiation. MRI contrast between tissues is mostly determined by the T1 and T2 relaxation times, which depend on the composition of the tissue that is being imaged (water, fat, muscle, etc.). The T2 relaxation time has the unique property that it changes if the tissue becomes swollen (edema), which is the case in myocardial infarction for instance. In so-called T2 mapping, multiple images with different T2 weights are used to calculate the T2 value for each pixel. This quantitative technique with values instead of arbitrary grayscale intensities can therefore potentially help in more accurately and precisely identifying edema and thus to distinguish treatable heart muscle from dead tissue.

T2 mapping of the heart from 3 T2-weighted input images.

The CVMR recently developed a technique that combines T2 mapping with a KWIC filter that shares part of the data between different T2-weighted input images in order to accelerate the acquisition time. This new technique called SKRATCH was developed as a 2D acquisition (i.e. a single slice). The objective of this project is thus to convert the existing technique to 3D acquisition.

The work itself: The project will consist of first familiarizing oneself with MRI theory and the MRI scanner, establishing and optimizing the combination of the  different T2-weighted images via Matlab, defining a 3D T2 mapping protocol in vitro (bottles of water with predetermined T2 values) that is processed in MATLAB, followed by MRI scans in healthy volunteers. Collaboration with the clinical cardiology service is also foreseen.

Duration: The project duration can be adapted to the student’s requirements.

Supervision:
Emeline Darçot, CHUV/UNIL
Dr. Ruud van Heeswijk, CHUV/UNIL
Prof. Matthias Stuber, CIBM – CHUV/UNIL

Lipid-insensitive magnetization preparation for clinical MR angiography

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Topic: Experimental work (lab + MRI), numerical simulations of MRI, analysis of different MRI techniques, data acquisition and processing, clinical translation of established techniques. 
Who: Students with a background in physics, electrical or bio(medical) engineering who are interested in the development of novel applications in cardiac MRI that are directly translatable to the clinic.
Introduction: At high magnetic field it is challenging to differentiate blood vessels from muscle tissue, which complicates angiography in patients using MRI at 3T. To overcome this problem, MRI preparation modules are used that manipulate the magnetizations of both muscle tissue and blood in such a way that they become distinguishable on MRI images.  However, fat signal that surrounds vessels represent an issue in angiography, and it results in MRI images that do not display the vessels correctly.  In the CHUV we have developed state-of-the-art of the art free-breathing methods that are not sensitive to MRI signals from fat and thus eliminate these disturbing signals from the final MRI images. This novel method is currently being used in patients, and we aim to extend this method to a 100% lipid insensitive MRI acquisition by incorporating the method in the preparation modules.
Project: In this project, the prospective student will quantitatively compare several magnetization preparation modules for lipid-insensitive in MRI, both numerically, and experimentally. Once the MRI sequences are quantitatively evaluated in phantoms, we will perform the study in human volunteers.

Supervison and contact:  
Dr. Jessica Bastiaansen, Department of Radiology, CHUV
Prof. Matthias Stuber, CIBM, CHUV

Chemical exchange saturation transfer (CEST) MRI for the quantification of heart function at a molecular level

Topic: Experimental work (lab + MRI), design of a protocol for test measurements, data analysis methods for CEST-MRI, clinical translation of developed techniques, data acquisition and processing. 
Who: Students with a background in physics, (bio)chemistry, electrical or bio(medical) engineering who are interested in the development of novel applications in cardiac MRI that are clinically translatable.
Introduction: MRI typically measures the proton signals of water. Specific biomolecules containing protons can be indirectly visualized by measuring the fraction of protons that are in exchange with water. The obtained images therefore reflect the biomolecular content, and allow for example the visualization of glucose and creatine, biomolecules which are associated with myocardial energetic processes. Therefore, imaging these biomolecules can give an indication myocardial tissue function. In the CHUV we aim to develop CEST-MRI in humans, and we wish to extend this method for cardiac applications related to the investigation of heart failure at a molecular level.
Project:  The prospective student will participate in the development of a CEST-MRI method in the heart. This involves the design of tools for the experimental characterization of the method, as well as optimization of the MRI data acquisition.  Once established in phantoms, human volunteer studies will be performed to establish a method that can be translated to patients to measure cardiac tissue function.

Supervison and contact:
Dr. Jessica Bastiaansen, Department of Radiology, CHUV
Prof. Matthias Stuber, CIBM, CHUV

Imaging of super paramagnetic iron-oxide based nanoparticles (SPIONs) with off-resonance ultra short echo time (UTE) MRI

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Topic: Experimental work (lab+MRI), MRI contrast comparison, pre-clinical evaluation of MRI methods, data acquisition and processing. 
Who: Students with a background in (bio)physics, chemistry, or bio(medical) engineering who are interested in the development of novel imaging applications of nanoparticles.
Introduction:  Functionalized iron-oxide based contrast agents are used in the clinic for cancer detection and treatment. The detection of such particles is necessary to locate diseases, but it is extremely challenging since they appear as dark regions in the MRI image, which could lead to misinterpretation.  In the CHUV we have developed a novel MRI method that results in regions that give a bright signal on MRI images, and this will help in detecting the location of SPIONs. Our aim is to quantify the sensitivity of the novel MRI method in phantoms and pre-clinical models. 
Project:  The prospective student will quantify the sensitivity of existing MRI methods and compare them with a novel MRI method developed in the CHUV. The student will establish the relation of the concentration of SPIONs with the level of contrast, both in home-built agarose gels, as in pre-clinical models.

Supervision and contact: 
Dr. Jessica Bastiaansen, Department of Radiology, CHUV
Prof. Matthias Stuber, CIBM, CHUV

We are looking for volunteers!

We are always looking for people that are interested in being scanned as part of an MRI study with a scanner operating at 3 Tesla. MRI studies are non-invasive and not dangerous for your health, painless and aim to improve the diagnostic tools used in clinical research.

For the volunteer it involves lying in the scanner for roughly an hour and perhaps holding your breath for 15 seconds a few times.
The used scanner is located in the CHUV in Lausanne. The study is not remunerated with money but volunteers are usually given several images of their heart as well as a movie of their beating heart (as seen below this text).

You can participate in a study if:
• You are 18 years old or older
• You are in good health
• You are not pregnant
• You are not claustrophobic (since the scanner is a narrow enclosed space)
• You do not have a cardiac pacemaker or any other metallic implant

Should you be interested please send an e-mail with your contact information to wwwcvmr@unil.ch. You will then be contacted by our staff, which will give you further information. 
 

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CIBM-CVMR - CHUV BH 8.84 - Rue du Bugnon 46 - CH-1011 Lausanne
Switzerland
Tel. +41 21 314 75 35
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