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Available 'Travaux Pratiques IV' projects

Optimizing blood flow measurements of rodent brains.

TP IV project : reserved

Cerebral blood flow plays an essential role in supplying energy substrates for normal brain function. Magnetic resonance (MR) techniques allow us assessing cerebral blood flow in human non-invasively. Studies of rodent brains will help us understanding the underneath mechanisms of abnormal cerebral blood flow in human diseases, such as diabetes and stroke.

This project is suitable for students with a background in Medical Physics or Biophysics or Biomedical Engineering with an interest in studying MR instrumentations and MR applications of disease models. The aim of study is to acquire perfusion (blood flow) maps from rodent brains with satisfactory signal-to-noise ratios in a comparable time constraint using well-setup hardware in the CIBM. The work will include optimizing MR parameters, data acquisition and data processing. This project will allow us studying stroke models within limited time window in the near future.



Supervision :


Developing a post-processing tool to calculate motion-artifact free cerebral blood flow maps.

TP IV project : reserved

Cerebral blood flow is essential to sustain normal human brain function. Magnetic resonance imaging techniques allow us measuring cerebral blood flow non-invasively. In general, blood flow maps are calculated from the acquired paired images in an ultra-fast fashion to avoid any possible artifacts due to physiological motions, such as breathing rhythm and heart beats. However, all images devoid of any motions remain challenging to obtain. Alternatively, post-processing became attractive and necessary to minimize motion artifacts between the images, i.e. aligning all quality images before further calculating blood flow maps.

This project is suitable for students with a background in Physics or Medical Physics or Biomedical Electrical Engineer with an interest in studying magnetic resonance (MR) instrumentations or imaging processing or imaging reconstruction. The aim of study is, by adopting the existing imaging reconstruction methods in the Matlab (available in the CIBM) to deliver an efficient and elegant way to calculating blood flow maps shortly, which allows us on-line processing blood flow in the near future. The newly developed processing tools will be compared with the original results without any correction.

Supervision :


The effect of a neuroprotective reagent, c-Jun-N-terminal kinase inhibitor, on neurochemical changes following transient focal ischemia.

TP IV project : available

Stoke is one of the leading causes for disabilities in the world. Accurate diagnosis and early treatments will intrinsically help minimizing such risks. Studies in animal models shred insightful information to clinical. Recently, we established that early changes after ischemia in mice could be detected in vivo using 1H magnetic resonance spectroscopy. The aim of study is to investigate possible neuroprotective agents on ischemic mouse brain regions (striatum and cortex), such as c-Jun-N-terminal kinase inhibitor, using in vivo methods, including magnetic resonance (MR) imaging and MR spectroscopy.

This project is suitable for students with a background in Biophysics or Neuroscience with an interest in studying stroke model in vivo by means of in vivo MR techniques and in vitro studies. In addition, the person must be willing to work as a team because we collaborate with one strong stroke group from the CHUV for this project.

Supervision :


Determination of metabolic alterations during aging using in vivo 1H NMR spectroscopy.

TP IV project : available

The concentration of metabolites in different cerebral areas, so called neurochemical profile, can be taken as biomarker of regional development and differentiation. The decline in memory and cognitive function is a normal consequence of aging and is accentuated by neurodegenerative pathologies, such as Alzheimer's disease, which cause progressive deterioration of learning and memory, attention and concentration, use of language, and other mental functions. These aging-associated functional losses may be accompanied by neurochemical alterations that are unknown. The aim of this project is to evaluate the neurochemical alterations in the brain of aging mice. For that, high resolution in vivo 1H NMR spectroscopy will be used to determine concentration of metabolites composing the neurochemical profile in different cerebral structures.

This project would be suitable for a student interested in biophysics and neurochemistry.
For more informations, please contact João Duarte.

Supervision :


Evaluation and Optimization of Shim Protocols for High Field MRI and MRS.

TP IV project : available

Shimming in magnetic resonance imaging (MRI) and spectroscopy (MRS) refers to the process of removing small main magnetic field (B0) inhomogeneities using additional so-called shim coils. Due to increased field inhomogeneity at higher B0, shimming gains increased importance at these fields, e.g. at 7 Tesla (T), for obtaining high quality data.

The aim of the project is to evaluate and optimize shim protocols for their application in MRI/MRS. Parameters of an existing shim technique will be tested and adjusted to obtain "optimal" results from shimming. Phantom and in vivo experiments will be performed, mostly at 7T. Experimental testing can be complemented by magnetic field calculations using Matlab.

This project would be suitable for a physics or engineering student interested in biomedical imaging in general and performing experimental data acquisitions in particular.

Supervision :


Absolute Metabolite Quantification for MR Spectroscopy Data.

TP IV project : available

Data acquired using magnetic resonance imaging spectroscopy (MRS) techniques are usually processed to quantify metabolites, such as creatine (CR), choline (Cho) and several other substances that provide valuable information about pathology, function or metabolism. Unfortunately, often metabolite concentrations can only be obtained in institutional units or ratios, rather than as absolute values (in mmol/kg).

The aim of the project is to attempt to achieve reliable metabolite quantification in absolute values for MRS data acquired in a specific set-up (scanner, radiofrequency coil, acquisition technique). Phantom experiments will initially be used to calibrate the measurements and data processing using solutions containing metabolites of known concentrations. Transferring this established methodology to in vivo metabolite quantification will comprise the second part of the project.

This project would be suitable for a physics, engineering or neuroscience student interested in biomedical imaging in general and performing precise data analysis of experimentally acquired data in particular.

Supervision :


Calculation of magnetic susceptibility maps based on MRI phase imaging

TP IV project : available

Magnetic resonance phase imaging has been providing some of the most interesting anatomical contrast obtainable in vivo. The main drawback of this contrast is its non-locality. The phase image observed is a result of the convolution of the magnetic susceptibility and the field generated by a magnetic dipole. Ideally the useful anatomical information would be that encoded on the susceptibility maps, sadly the de-convolution is ill-defined.

Different approaches have been suggested to tackle this issue: (a) acquire the field maps (phase images) at different object positions to make the problem invertible; (b) make prior assumptions regarding the shape and range of values of the object to constrain the inversion/deconvoluiton of the problem;

The first part of the project will involve the creation of a phantom with a magnetic susceptibility distribution comparable to that found in brain tissue (such as grey and white matter). This phantom will be used to test different approaches to calculate the susceptibility maps. Once reliable results are obtained with this model, the methodologies developed will be applied to whole brain images.

Supervision :


Optimizing design of spoke rfpulses

TP IV project : available

The short wavelength used in RF pulses to excite protons at high magnetic fields (such as our 7T MR system), which are smaller than the imaged object (in our case, a human head), generate artifacts in the images due to constructive and destructive interference of these RF waves (as can be seen in the images on the right side). Parallel transmission together with the design of spatial frequency pulses offers a very promising approach to correct for this radiofrequency inhomogeneities. The focus of this project will be on the optimization of the 2D k-space positioning of the slice selective excitations (often referred as spokes) given the measured B1 maps of the different coils.

The accuracy of the optimization will be tested experimentally in phantoms and volunteers.

Supervision :


In vivo 1H and 15N MRS in the rat brain

TP IV project : available

Glutamine synthetase is a critical step in the glutamate-glutamine cycle, the major mechanism of glutamate neurotransmission and is implicated in the mechanism of ammonia toxicity. 15N MRS is an alternative approach to 13C MRS in studying glutamate-glutamine metabolism during infusion of 15N labeled ammonia. Ammonia is metabolized to glutamine by glutamine synthetase (GS) in astrocytes.

All the in vivo data will be acquired using a 9.4T animal MR scanner. In vivo localized 15N MRS will be used interleaved with in vivo 1H MRS to measure the net glutamine synthesis rate and the glutamine synthesis rate under 15N labeled ammonia infusion in the rat brain.

Supervision :


1H MRS of the mouse lacking prion protein

TP IV project : available

The prion diseases form a group of fatal neurodegenerative diseases, also described as transmissible spongiform encephalopathies (TSEs), which are caused by abnormal conformational isomers (PrPSc) of the host-encoded prion proteins (PrPc). The nature of the prion has been a longstanding enigma. The mechanism by which prions elicit brain damage and the relative contributions of PrPSc accumulation and PrPc depletion to the prion replication remains unclear. Consequently, different animal models were created in order to study the role of the PrPc. Among these models, knockout mouse models were crucial in elucidating the precursor-product relationship between PrPc and PrPSc. In vivo 1H MRS (proton magnetic resonance spectroscopy) allows non invasive characterization of brain metabolism and it has been used to study brain metabolites changes in a wide range of neurodegenerative diseases. From our knowledge, no in vivo MRS study was performed until now in mice lacking prion protein.

The purpose of this study is to use in vivo high-resolution 1H MRS at 14.1T to measure the neurochemical profile (also called brain metabolites) in mice lacking prion protein with ultimate goal of a rapid and precise determination of the neurochemical changes. The project will involve data acquisition (imaging and localized spectroscopy) at 14.1T and data processing (determination of brain metabolite concentrations).

Supervision :


Creatine kinase reaction rates in rat brain measured by localized phosphorus saturation transfer spectroscopy

TP IV project : available

This project is suitable for students of biochemistry, bio- or biomedical physics or physics, who wish to apply physical principles and methods for studying metabolic processes in living animals.
In vivo phosphorus (31P) magnetic resonance spectroscopy is capable of determining concentrations of phosphorus-containing metabolites in tissues. In addition, the technique of magnetization (saturation) transfer MR spectroscopy can provide information about rates of interconversion between phosphocreatine and ATP (the creatine kinase reaction). The rate of this reaction can be seriously affected in various pathological conditions such as ischemia, degenerative disease etc., and these changes can be used for research, drug development or even for clinical diagnostics. In this project, a series of localized saturation transfer spectra will be measured in healthy rat brain on a 9.4 Tesla animal MR scanner. The reaction rates of the creatine kinase reaction will be calculated and compare with previously reported data obtained with unlocalized protocols (using surface coils only).

Supervision :


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