MRI Practicals on CIBM preclinical imaging systems

PHYS-473 / 3 credits

Teacher(s): Cudalbu Cristina Ramona, Lanz Bernard

Language: English

Withdrawal: It is not allowed to withdraw from this subject after the registration deadline.

Summary

The goal of this course is to teach students how to perform basic MRI and MRS experiments in-vivo and ex-vivo directly on preclinical horizontal ultra-high field MRI systems.

Content

Main topics addressed in the course:

1. Introduction to MRI: Nuclear spin and magnetic moment, nmr-active nuclei/isotopes, macroscopic magnetization, classical description of magnetic resonance, FID, spin echo, gradient echo signal acquisition.

2. Basic anatomical imaging and contrast: T1, T2 and T2* weighted images, impact of acquisition parameters on image contrast

3. Introduction to advanced MRI and contrast : fast MRI, 3D imaging, volumetry, diffusion MRI, in vivo vs ex vivo imaging, volume vs surface RF coils properties

4. Introduction to Magnetic Resonance Spectroscopy (MRS), data acquisition and processing using MRS4Brain toolbox : 1H metabolites resonance patterns, chemical shift, J-coupling, shimming, MRS localization approaches, water signal suppression, outer volume signal suppression, metabolites quantification.

5. Introduction to Magnetic Resonance Spectroscopic Imaging (MRSI), reconstruction, data acquisition  and processing using MRS4Brain toolbox : Basics of spectroscopic imaging, signal encoding for localization, 2D and 3D MRSI, FID vs echo-based MRSI

6. Basic artifacts in MRS and MRI and how to avoid them

7. Data processing: volumetry, DTI, metabolic imaging

 

Keywords

Magnetic Resonance Imaging (MRI), Magnetic Resonance Spectroscopy (MRS), Brain, ultra high magnetic field, metabolic imaging, brain metabolites, spin physics, processing/quantification,

Learning Prerequisites

Recommended courses

Fundamentals of biomedical imaging - PHYS-438

 

Important concepts to start the course

NMR, MRI basics

Learning Outcomes

By the end of the course, the student must be able to:

  • Understand the physical principles of MRI and MRS during hands on exercises on MRI scanners
  • Perform basic MRI and MRS experiments
  • Establish MRI and MRS acquisition protocols and understand the impact of the acquisition parameters on image contrast or spectral pattern
  • Analyze the results for the acquired data
  • Explain the basics of organizing a successful MRS experiment, processing/quantification, image processing, using MRS4Brain toolbox
  • Read, analyze and discuss representative scientific papers
  • Discover the power of interdisciplinary interaction by working on questions and hands on exercises in groups

Transversal skills

  • Use both general and domain specific IT resources and tools
  • Communicate effectively with professionals from other disciplines.
  • Write a literature review which assesses the state of the art.
  • Write a scientific or technical report.

Teaching methods

The course will be held every week with alternated sessions of theory and practical teaching:

 

  • - odd sessions (2h): theoretical principles will be explained
  • - even sessions (4h): live demos on the scanner will be performed based on the previously explained theoretical principles.

Expected student activities

Active participation in the theoretical courses with questions

Discussions/questions during the live demos

Supervised experimental manipulation of the MRI scanner

Processing of the acquired data

Work in teams for a joint project

Assessment methods

Report/mini project

Supervision

Office hours Yes
Assistants Yes

Resources

Bibliography

In Vivo NMR Spectroscopy: Principles and Techniques (Robin de Graaf); Principles of Magnetic

Resonance Imaging: A Signal Processing Perspective (Zhi-Pei Liang & Paul C. Lauterbur)

1. Nuclear Magnetization (youtube.com)

magritek - YouTube

Ressources en bibliothèque

Websites

Moodle Link

Videos

In the programs

  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional
  • Semester: Fall
  • Number of places: 10
  • Exam form: During the semester (winter session)
  • Subject examined: MRI Practicals on CIBM preclinical imaging systems
  • Courses: 2 Hour(s) per week x 14 weeks
  • Project: 1 Hour(s) per week x 14 weeks
  • Type: optional

Reference week

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