CIBM translational MR neuroimaging & spectroscopy

This course's purpose is to provide students with a solid theoretical and practical knowledge in magnetic resonance imaging (MRI) and spectroscopy (MRS). This course will cover all of the core aspects that a PhD candidate or a post-doc  would require to design and carry out their own (neuro)imaging experiment in order to accomplish specific research goals. These include fundamentals of experimental design planning, data collecting, data (pre)processing, and data analytics on MRS, structural, and functional MRI in both humans and rodents. This course will provide extensive hands-on experience on both clinical 7T and preclinical 14.1T scanners, with a particular emphasis on the prospects for bench-to-bedside translation of these technologies for neuroscience.

Monday April 15

 

08:15 -10:00 - Introduction: MRI and MRS in neurological and psychiatric disorders; the importance of translational aspects; main requirements for planning a successful study (Speakers: Lijing Xin)
10:15 - 11:00 - Ethics for human study (Invited external speaker: E. Fornari)
11:15 - 12:00 - Ethics for animal study (Invited speaker: Stefan Mitrea)

 

Lunch Break

 

13:15-14:00 - Basics of nuclear magnetic resonance I: Hardware components (Magnets, Gradient coils, Shim coils, Transmit/receive chain); Radio frequency (RF) coils (Resonance circuits, Losses and decoupling, Surface coils, Phased arrays, Volume coils); High field MRI (High-field effects, Specific absorption rate, Electromagnetic field simulations, Parallel transmission, Advanced approaches in RF coil design for high field) (Speaker: Daniel Wenz)
14:15-15:00 - Basics of nuclear magnetic resonance II:The origin of magnetic resonance, nuclear spin and magnetic moment, basic terminology, interesting nuclei/isotopes; Energy levels, macroscopic magnetization, classical description and resonance frequency; Laboratory frame and rotating frame, magnetic excitation, RF pulses, precession; Relaxation(s), Bloch equations, basic pulse sequences (FID, spin-echo) (Speaker: Bernard Lanz)
15:15-16:00 - Basics of MRI : gradients, K-space (Speaker: Cristina Cudalbu)
16:15-17:00 - Basic of MR sequences (Invited external speak: Ruud B. van Heeswijk)

 

Tuesday April 16

 

8.15-9.30 - Brain structure & function I : an introduction to the MRI tools used to study whole-brain connectivity and brain-behavior interactions (Speaker: Valerio Zerbi)
9.45-10.45 - MRI sequences and applications of functional imaging, task and resting-state, introduction to large multi-site initiatives (EPI, GE, SE, www.humanconnectome.org/ and www.neurosynth.org) (Speaker: Valerio Zerbi)
11:00-12:00 - MRI sequences and applications of diffusion-weighted imaging (Invited external speaker: Ileana Jelescu)

 

Lunch Break

 

13.15 - 17:00 - RF coil design (1/2) The aim of this part of the course is to provide a theoretical and practical introduction to RF coil design for animal and human scanners. Participants should get an overview and hands-on experience on how to build basic RF coils for human (and animal) applications. The best design will be selected and used in MR phantom experiments.
13:15-14:00 - Theory: introduction & demonstration (Scattering parameter matrix, Impedance matching, tuning, decoupling, Vector network analyzer: calibration and demonstration, Lumped elements: capacitors, trimmers, inductors). Bench tools: soldering iron, pick-up loop, etc.
14:15-17:00 -€“ Practical teaching: RF coil construction and characterization at the bench (Surface coil for human (and/or animal) application, Construction of a single loop coil, Frequency tuning and impedance matching, Loading effect on the RF coil'€™s performance, Quality factor measurement). Optional: two surface coils in quadrature, Geometrical decoupling: overlapping
Teacher: Daniel Wenz

 

Wednesday April 17

08:15-09:00 - Introduction of MRS: J-coupling, chemical shift, basic localization methods (Speaker Lijing Xin)
09:15:10:00 - Outer volume suppression, water suppression, shimming,  spectral quality - (Speaker: Lijing Xin)
10:15-12:00 - Basics of Magnetic Resonance Spectroscopic Imaging, MRSI vs SVS (Speaker Cristina Cudalbu)

 

Lunch Break

 

13.15 - 17:00 - RF coil design (2/2) The aim of this part of the course is to provide a theoretical and practical introduction to RF coil design for animal and human scanners. Participants should get an overview and hands-on experience on how to build basic RF coils for human (and animal) applications. The best design will be selected and used in MR phantom experiments.
13:15-14:00 - Theory: introduction & demonstration (Scattering parameter matrix, Impedance matching, tuning, decoupling, Vector network analyzer: calibration and demonstration, Lumped elements: capacitors, trimmers, inductors). Bench tools: soldering iron, pick-up loop, etc.
14:15-17:00 - Practical teaching: RF coil construction and characterization at the bench (Surface coil for human (and/or animal) application, Construction of a single loop coil, Frequency tuning and impedance matching, Loading effect on the RF coil'€™s performance, Quality factor measurement). Optional: two surface coils in quadrature, Geometrical decoupling: overlapping
Teacher: Daniel Wenz

Thursday April 18

Morning
8.15-11:00 - 1H MRS quantification (Theory: 1h, Practical teaching: 2h) (Teachers: Cristina Cudalbu)
11:15-12:00 - Fast Magnetic Resonance Spectroscopic Imaging and reconstruction techniques (External invited speaker: Antoine Klauser)

 

Afternoon:
13h15:17:00 - Introduction to in vivo MRS @14T
Teachers: Cristina Cudalbu and Bernard Lanz

Week 2

 

Monday April 22

 

Practical teaching: MRI/MRS (Group 1 & Group 2)

 

Group 1: 7T MRI & MRS - Phantom/fruit/human experiment (Theory: 1h, Practical teaching: 3h)
The participants will get practical training on a human 7T MRI scanner and perform experiments with a phantom and a fruit (or a human if there is volunteer). This part includes: basic safety aspects, operation of an MRI system, preparation of an experimental setup (RF coil loaded with a phantom/human), demonstration and optimization of common MRI and MRS protocols to get different imaging contrast and spectra.
Teacher: Lijing Xin, Antonia Kaiser and Daniel Wenz

 

Group 2: 14T MRI & MRS - Phantom, ex-vivo, in vivo (Theory: 1h, Practical teaching: 3h)
The participants will get practical training on the 14.1T preclinical MRI system. The basic parameters, tips and tricks to obtain high-quality scans and we will look together at the meaning of several scan parameters. We will also present the environment for in vivo scanning at 14.1T with the animal holding equipment, anesthesia units and physiology monitoring capabilities to perform metabolic experiments in best conditions. We will show how to prepare and place the rat in a stabilized position in the magnet holder, with physiology monitoring setups and how to position an RF coil for best signal induction and reception. We will show how to run localizer images, perform coil and B0 shim optimizations, run anatomical images with acquisition parameters. For 1H MRS, we will show how to position an acquisition voxel in the area of interest, optimize the shim and water suppression to get a reliable 1H spectrum, and how to evaluate its quality.
Teachers: Valerio Zerbi, Cristina Cudalbu and Bernard Lanz

 

Afternoon:

 

Group 2: 7T MRI & MRS - Phantom/fruit/human experiment (Theory: 1h, Practical teaching: 3h)
The participants will get practical training on a human 7T MRI scanner and perform experiments with a phantom and a fruit (or a human if there is volunteer). This part includes: basic safety aspects, operation of an MRI system, preparation of an experimental setup (RF coil loaded with a phantom/human), demonstration and optimization of common MRI and MRS protocols to get different imaging contrast and spectra.
Teacher: Lijing Xin, Antonia Kaiser and Daniel Wenz

 

Group 1: 14T MRI & MRS - Phantom, ex-vivo, in vivo (Theory: 1h, Practical teaching: 3h)
The participants will get practical training on the 14.1T preclinical MRI system. The basic parameters, tips and tricks to obtain high-quality scans and we will look together at the meaning of several scan parameters. We will also present the environment for in vivo scanning at 14.1T with the animal holding equipment, anesthesia units and physiology monitoring capabilities to perform metabolic experiments in best conditions. We will show how to prepare and place the rat in a stabilized position in the magnet holder, with physiology monitoring setups and how to position an RF coil for best signal induction and reception. We will show how to run localizer images, perform coil and B0 shim optimizations, run anatomical images with acquisition parameters. For 1H MRS, we will show how to position an acquisition voxel in the area of interest, optimize the shim and water suppression to get a reliable 1H spectrum, and how to evaluate its quality.
Teachers: Valerio Zerbi, Cristina Cudalbu and Bernard Lanz

 

Tuesday April 23

 

8:15-9:00 - X nuclei MRS (13C, 31P, 15N, 2H). Physical specificities, applications as in vivo tracers of metabolic pathways, specific acquisition schemes (Speaker Lijing Xin)
9:15-10:00 - Quantification: 1H, 13C MRS, 31P MRS, 15N MRS and 2H MRS (Speaker Cristina Cudalbu)
10:15-12:00 - Interpretation of dynamic X-nuclei experiments with metabolic modelling: biochemical network, infusion protocol, accessible metabolic pools, mathematical aspects of quantitative metabolic modelling (Speaker: Bernard Lanz)

 

Lunch Break

 

13:15-17 :00 - X-nuclei data modelling (Theory: 1h, Practical teaching: 3h) (Teacher: Bernard Lanz)

Wednesday April 24

 

8:15 - 12:00 - Theory of clinical MRI segmentation and registration for MP2RAGE. Introduction to surface and voxel based morphometry (VBM and SBM) and fMRI processing. (Invited external speakers: M B Cuadra, E. Fornari, A. Kaiser)

 

Lunch Break

 

13:15 - 17:00 -€“ practical teaching for structure MRI processing (VBM and SBM) and fMRI. (Invited external speakers: M B Cuadra, E. Fornari, A. Kaiser)

Thursday April 25

 

8:15-9:00 - Brain structure & function II: an introduction to rodent MRI; history, potentials, caveats & hardware (Speaker Valerio Zerbi)
9:15-10:00 - Rodent multimodal fMRI. Tools for manipulating neural activity (electrical stimulation, chemogenetics, optogenetics) & fMRI applications (Speaker Valerio Zerbi)
10:15-12:00 - Translational fMRI. Assessing (dys)similarities across species using fMRI and brain connectivity (Speaker Valerio Zerbi)

NB: the course is for now opened to only 12 participants due to the limitations related to the practical teaching sessions. If requested 6 additional participants can be added, however additional practical teaching sessions will be organized for these 6 participants in the week after the course. Or/and an additional session can be organised in the autumn if the demand is strong.