Course Identification

Imaging the Brain using MRI: From Physics to Applications

Lecturers and Teaching Assistants

Prof. Assaf Tal
Martins Otikovs

Course Schedule and Location

First Semester
Thursday, 14:15 - 16:00, FGS, Rm A

Tuesday, 11:15 - 13:00, FGS, Rm A

Field of Study, Course Type and Credit Points

Chemical Sciences: Lecture; Elective; Regular; 3.00 points
Life Sciences: Lecture; Elective; Regular; 2.00 points
Life Sciences (Molecular and Cellular Neuroscience Track): Lecture; Elective; Regular; 2.00 points
Life Sciences (Brain Sciences: Systems, Computational and Cognitive Neuroscience Track): Lecture; Elective; Regular; 2.00 points
Life Sciences (Computational and Systems Biology Track): Lecture; Elective; Regular; 2.00 points


The first lecture will be held on 24/10, 09:15-11:00 at FGS room B.


No prerequisites are required. 

A certain degree of maturity is expected from the students. Several mathematical constructs will be introduced throughout the course (such as discrete and continuous Fourier transforms), and while they will be taught from scratch they require the students be willing to tackle such quantitative concepts. 

In addition, the course will rely on writing some simple computer simulations to demonstrate basic ideas. Computer simulations are a wonderful way of getting a deep understanding of the physics of MRI. The students are free to use a programming language of their choice, although I will focus on MATLAB, with which I am most familiar. These simulations will be an integral part of the homework assignments.



Language of Instruction


Attendance and participation

Expected and Recommended

Grade Type

Numerical (out of 100)

Grade Breakdown (in %)

Students are required to submit at least 80% of the homework assignments

Evaluation Type


Scheduled date 1


Scheduled date 2

Perlman, Rm 404

Estimated Weekly Independent Workload (in hours)



Magnetic resonance imaging (MRI) is a powerful non-invasive imaging modality which can be used to examine the anatomy, physiology and microstructure of the human body. In this course we will cover the physical and biochemical principles which give rise to the rich palette of image contrasts obtainable with MRI, focusing mainly on imaging of the human brain.
Part 1: General Concepts
Basic Concepts In Imaging. Noise, resolution, signal to noise and contrast to noise. The point spread function.
MRI As A Black Box. An overview of the contrast types obtainable with MRI.
Part 2: Spin Physics
Spin Dynamics. How spins give off and are affected by magnetic fields. Bulk magnetism and its phenomenological description in an external magnetic field.  Basic Imaging. Excitation. The rotating frame. Resonance and excitation. Selective excitation. Response of spins to periodic pulse trains. Basic image formation mechanisms: phase and frequency encoding. The concept of reciporal space (k-space). The MRI cartesian point spread function. 
Part 3. T1, T2 and T2* Imaging - from Anatomy to Disease and Function
Modeling relaxation. Relaxation mechanisms in tissues. Generating T1 and T2 contrast. Gradient and spin-echo imaging. Spoiled steady state. The effects of B1 and B0 inhomogeneity. Unspoiled imaging (SSFP, FISP, trueFISP). Fast sequences. Echo planar imaging, turbo spin echo, multiplexing, multi-slice imaging. Signal to noise in MRI images. Using T1 and T2 contrast clinically in multiple sclerosis and cancer. Imaging blood flow and brain activity via the Blood-Oxygenation Level Dependent BOLD effect. Imaging cortical layers. Looking at iron deposition.
Part 4. Imaging Motion
Coherent motion. imaging constant flow via magnitude and phase encoding. Time-of-flight imaging. Imaging blood flow and the vascular system. Incoherent motion. A model for signal decay with Gaussian diffusion. Diffusion tensor imaging. Restricted diffusion. Imaging cellular microstructure.
Part 5. Molecular Imaging
Contrast agents. MR angiography and Gd-DTPA. Imaging with paramagnetic nano-particles. Designing target-specific contrast agents. Molceular imaging using chemical exchange (CEST).  Spectroscopy. The chemical shift effect. Scalar coupling and hyperfine splitting. Outer volume suppression: STEAM and PRESS. Spectroscopic imaging. Other interesting nuclei: carbon, phosphorous and sodium. Echo planar spectroscopic imaging.

Learning Outcomes

Upon successful completion of this course students should be able to understand the different types of contrasts obtainable in-vivo using magnetic resonance imaging, what they tell us about the brain, and how to generate them by shaping the magnetic fields inside the MRI scanner. 

Reading List