Outline of the module
The MR scanner interacts with and manipulates the status of the proton magnetisation in the biological tissue using a sequence of electromagnetic field. The specific MR pulse sequence makes the MR signal sensitive to different aspects of the tissue as the longitudinal and transversal magnetisations are determined by the local biochemical environment. For example, the water density of the tissue is different in tissue types and altered in various diseases (i.e. edema) and the MR signal can be made sensitive to proton density using specific MR pulse sequence parameters. In contrast to other imaging techniques (i.e. CT or PET), MRI allows to actively and non-invasively alter (the magnetisation of) the tissue and generate different tissue contrasts. The MR pulse sequences typically consist of three modules: a) excitation using radiofrequency (RF) pulses, b) evolution of the magnetisation potentially employing additional RF pulses and MR gradients and c) read-out module to detect the MR signal.
In this module, this general scheme of an MR sequence and the MR sequence diagram to represent the order of the electromagnetic fields employed will be introduced. The most important MR pulse sequences utilised in research and in the clinic will be intensely discussed. In addition, it will be taught how to programme an MR sequence and how to simulate an MR sequence using numerical simulation of the standard Bloch equations. Finally, students will learn how to implement MR sequences on-site at the MR scanner(s) and how to recognise on MR images which sequence was employed.
Learning objectives
At the end of the module, students will have expert knowledge about the following topics:
• MR sequence pulse diagram
• Radiofrequency (RF) pulse design
• Spatial encoding of MRI images using RF pulses and gradients (k-space)
• Different k-space trajectories
• What are the biological and physical determinants of longitudinal and transverse magnetisation times (proton density, T1, T2, T2*, MTR).
• Computer simulations of MRI sequences
• Implementation of MRI sequences on-site on MRI scanners
• Correlation of image contrasts with MRI sequences
• Interpretation of MR images from a clinical and basic research perspective
Content
MRI can display a lot of different contrasts in the tissue depending on the specific MRI parameters employed. This is a marked difference to other imaging technologies as they require additional contrast agents to assess additional properties of the tissue. Therefore, MRI is continuously developing and new ways of acquiring information of tissue status are discovered on a daily basis. The specific way electromagnetic fields are employed is called MR pulse sequence and function as follows:
When a radiofrequency (RF) pulse is applied, the RF excitation causes the net magnetisation vector to flip by a certain angle, and this produces two magnetisation vector components, longitudinal magnetisation and transverse magnetisation. When the RF energy source is turned off, the net magnetisation vector realigns with the axis of B0 through the process of T1 recovery, during which the longitudinal magnetisation increases in magnitude back to its initial, equilibrium value. At the same time, the transverse magnetisation decreases (decays) through additional mechanisms known as T2* decay and T2 decay. Importantly for the imaging of biological processes, different tissues have different T1, T2, and T2* values. Furthermore, T2* is dependent on the magnetic environment (the spatial uniformity of the external field). For example, fat has a shorter T1 (i.e., recovers faster) and a shorter T2 (i.e., decays faster) than water, which has a relatively long T1 and T2. T2* decay occurs very quickly in both fat and water. During T1 (spin-lattice) relaxation, the longitudinal magnetisation recovers as the spinning nuclei release energy into the environment.
During T2 (spin-spin) relaxation, the transverse magnetisation is dephased because of interaction between the spinning nuclei and their magnetic fields. In T2* signal decay, the transverse magnetisation is dephased because of magnetic field inhomogeneities. The weighting for T1 is achieved by the repetition time (TR) of subsequently acquired images; the weighting for T2 and T2* by the echo time (TE), which describes the acquisition time of the image. After the different contrasts are encoded in the MRI signal, a read-out module (combined with prior spatial preparation pulses) is employed collecting the data in a spatially specific manner. To summarise, an MRI pulse consists of three modules: a) an RF pulse to generate a transversal and longitudinal magnetisation far from thermodynamically equilibrium, b) manipulation of the magnetisation to generate MRI contrasts and c) a read-out module include spatial encoding.
The most popular and simple MRI pulse is free-induction decay and an echo-planar imaging read-out module, called gradient-recalled echo (GE) MRI sequence. IT is most sensitive to T2* and is used to detect magnetic inhomogeneities, e.g. change in iron concentration in Multiple Sclerosis (MS) or Parkinson’s disease or change in paramagnetic deoxygenated hemoglobin in functional MRI. If an additional 180° RF pulse is employed, the sequence is called spin-echo (SE) MRI sequence which measures T2. Typically, T2 is sensitive to similar processes as T2* with, however, more sensitivity to processes close to high susceptibility areas (i.e. tissue-air interfaces). If an inversion recovery (IR) pulse is applied prior to RF pulse excitation additional T1 weighting can be achieved. Grey and white matters have, for example, different T1 values and so these kinds of sequences are very useful for anatomical MRI. If a tagging pulse outside of the imaging area is employed, then the MRI signal becomes sensitive to flowing spins, i.e. to detect blood vessels in MR angiography. Additional bi-polar MR gradients make the signal sensitive to diffusion processes. Finally, the recently developed ultra-short echo time sequences (UTE and SWIFT) can detect hard tissue (i.e. bones) which previously were undetectable with MRI as bones and other solid states have very short T2* values.
In summary, MRI pulse sequences can involves many different MR pulses and gradients making the MR signal suitable different biological processes. This module will give an overview on these sequences and on how to programme and manipulate them. Finally, in the hands-on sessions, the students will identify on self-acquired MRI data which images belong to which MR sequences and how to use the information for clinical diagnosis and basic research.
Overview of tasks and lectures
There will be 10 lectures of 2 hours distributed over 5 days.
• Introduction into MR pulse sequences
• MRI sequences diagram
• RF pulse design
• Manipulation of magnetisation via Gradients and RF pulse
• MR signal read-out modules and schemes
• MR pulse sequences I (head)
• MR pulse sequences II (body)
• MR protocols
• Advanced, novel MRI Pulse sequences
• Summary and Introduction of post-module assignments
Position within the programme
This module is related to the modules on MRI physics, coils and sequences. To follow the content of the module, the MR physic modules are mandatory. This module will introduce scientist-practitioners to the complexities of an MR sequence to manipulate and obtain the signal and will be very useful for physicists and technicians to optimise MR protocols for specific clinical and basic research purposes.
Teaching format
Structure
The module is a one week-long residential module consisting of 10 lectures of 2 hours. Each day, the students will in addition perform data acquisition on the MRI scanners checking for performance of the system located at the UM (3, 7 and 9.4 Tesla), computer simulations of scanner performance and visual inspection of MR images. Furthermore, the residential part is combined with a preparatory reading phase and post-module marked assignments corresponding in total to 12 additional ECTS.
Grading
For passing the module, an 85% attendance to the lectures and practical sessions, and a satisfactory completion of the practical sessions and the module assignments are required. The module assignments will be summarised by the students in a written form which will be evaluated by the module coordinator(s).