PT2 Chapter 1 & 2: Introduction and History | RF Pulse Sequences Spine Echo based

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PT2 Chapter 1 & 2: Introduction and History | RF Pulse Sequences Spine Echo based

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See for introduction in k-space trajectories the GRE RF sequences e-module.

And in repetition to the GRE based RF sequence e-module:

I will use a lot of abbreviations and acronyms:

Your task will be to perceive the acronyms/abbreviations of the different RF pulse sequences associated to your MRI system and to know which ones are implemented in your MRI system: be aware that several RF sequences are sold as an option.

Use the internet to find out more about the acronyms and abbreviations:  Glossary of MRTerms-ACR. The MRI Acronym pocket guide from Hitachi Medical covers 5 MRI manufacturers. . In my opinion, they really have a good overview and they are open for error corrections. But they only have the Siemens, GE and Philips ones. I also like to recommend the Radiology Science Dictionary: Keywords, names and definitions of David Dowsett.  This website also has the option to add terminology.

Or check your MRI manufacturer’s website. They often include acronym comparisons (like the Hitachi pocket guide comparing GE, Siemens, Philips, Toshiba (CANON Medical now) and Hitachi of course).

For medical abbreviations:

I could not find a website which covers all the RF sequences implemented on the different MRI systems. I will do my utmost best to stay up-to-date in this area. Please let me know if different terminology is implemented in your MRI system. I am always open for corrections and suggestions.

There are many great online resources available for lifelong MRI education. Find your way. Explore!

I am very well aware that I cannot cover all the RF sequences. Constantly new RF sequences are being developed and implemented. I hope to cover the most-important and most-used ones.

And there are always new technologies in development and scientific “energies” underway. Try to stay updated!

1.01 Introduction and history


We started with the SE RF pulse sequence, but I do not advise to use this one anymore: there are more than twenty T1w RF sequences available nowadays!

The image impression is often a little different, but at least the resolution is much higher and a shorter acquisition time can be reached. The number of RF pulse sequences per patient is increasing. We still do not use only one RF sequence per patient to visualize and get the optimum contrast between the different tissues like e.g. in MSK: optimal contrast between cartilage, bone-oedema, ligaments and menisci, lesion and tumors cannot be reach in one RF sequence. But at least we’re getting to 3D RF sequences from which we can reconstruct a T1 and T2w contrast. Regarding the T2w Spin echoes: they have not been made any more for dozens of years.

Although there are new methods avaialable like Synthetic Imaging: where just one RF sequence is made and with help of Artifical Intelligence and advanced postprocessing techniques several series of images can be calculated and reconstructed with different contrasts.

However, when starting to use those “newer” RF sequences you should be aware of the side effects.

1.02 History


L to R: Raymond Damadian, Larry Minkoff and Michael Goldsmith with “Indomitable” and its iced liquid helium and liquid nitrogen ports: the world’s first super-cooled, superconducting MR scanner and the world’s first MRI machine. Courtey:




Hinshaw 1977:  MRI Scanner Mark One (Fonar): the first MRI scanner to be built and used, sensitive point scan of  a human wrist Aberdeen Royal Infirmary in Scotland. Courtesy Wikipedia.



I had the fortune to work with some of them back in 1983.


The SE pulse sequence was devised in the early days of NMR by Carr and Purcell and exists now in many forms: the multi echo pulse sequence using single or multi slice acquisition, the Turbo (Fast) spin echo (FSE/TSE) pulse sequence, SE echo planar imaging (EPI) pulse sequence and the gradient and spin echo (GRASE-TGSE-GRACE) pulse sequence; all are based on the spin echo sequences.

Echoes were first detected in Nuclear Magnetic Resonance by Erwin Hahn in 1950, and spin echoes are sometimes still referred to as Hahn echoes. Hahn’s 1950 paper showed that another method for generating spin echoes is to apply three successive 90° pulses. After the first 90° pulse, the magnetization vector spreads out, forming what can be thought of as a “pancake” in the x-y plane. The spreading continues for a while, and then a second 90° pulse is applied so that the “pancake” is now in the x-z plane. A while later a third pulse is applied and a stimulated echo is observed after the last pulse.






Chapter 2 Chart overview and SE based RF sequences

2.01 RF Pulse Sequences Spine Echo based



2.02 The conventional SE RF sequences

2.02a SE

The SE RF pulse sequence diagram with simplified use of gradients

                                                                                                                 If a 256 matrix² is needed, 512 samples are made during the detection of the SE signal.


Spin Echo Sequence diagram

The simplest form of a Spin Echo RF sequence.


A diagram is mostly composed of several parallel lines if each parameter is diagrammed separately. At least 4 lines are required: one for the RF pulse, and one each for the x-, y-, and z-axis gradients. Often the signal is displayed. In addition, a line for the ADC sampling (analogue to digital convertor) is also shown in this diagram .

Spin Echo:  the most common pulse sequence used in MR imaging is based on the detection of a spin or Hahn echo. It uses 90° RF pulses to excite the magnetization and one or more 180° pulses to refocus the spins to generate signal echoes called spin echoes (SE).

The 90° excitation pulse rotates the longitudinal magnetization (Mz) into the xy-plane and the de-phasing of the transverse magnetization (Mxy) starts.
The following application of a 180° refocusing pulse (rotates the magnetization in the x-plane) generates signal echoes. The purpose of the 180° pulse is to re-phase the spins, causing them to regain coherence and thereby to recover transverse magnetization, producing a spin echo.
The recovery of the z-magnetization occurs with the T1 relaxation time and typically at a much slower rate than the T2-decay, because in general T1 is greater than T2 for living tissues and is in the range of 100–2000/4000ms (dependent on the field strength).

Contrast values:
PD weighted: Short TE (~8-40ms) and long TR.
T1 weighted: Short TE (~4-20ms) and short TR (300-600ms / 700ms for 3T)
T2 weighted: Long TE (greater than 80ms) and long TR (greater than 2000ms)
With spin echo imaging no T2* occurs, caused by the 180° refocusing pulse. That is why spin echo sequences are more robust against e.g. susceptibility artefacts than gradient echo sequences.


Spin echo images of a patient with meningioma. A. PDw-image (TR/TE = 2000ms/10ms). B. T1w image (TR/TE = 600ms/10ms). C. T2w image (TR/TE 2000ms/100ms). Courtesy: Lothar R. Schad.

Spin Echo Basic Variations

  1. Dual Echo Sequence: Dual echo sequences include images with different weightings and echo times and are used to obtain both proton density and T2 weighted images. Dual echo also can be done in T(SE) RF sequences.
  2. Modified Spin Echo: a spin echo technique with a flip angle over 90° (see also below).
  3. Multi Echo Multi-planar: MEMP SE with a multi-slice and multi echo acquisition in one TR.
  4. Partial Saturation Spin Echo: PSSE (Partial Saturation SE): (PSSE) Partial saturation sequence in which the signal is detected as a spin echo. But there will not necessarily be a significant contribution of the T2 relaxation time to image contrast. Unless the TE is on the order of or longer than T2.
  5. Variable Echo Multi-planar VEMP: variable echo multi-planar: SE (also with T(F)SE with multiple variable echoes).


2.02b SE Multi Echo


The SE multi echo RF sequence was rather quickly developed starting to be used for a PDw and a T2w contrast in one acquisition: a second 180° RF pulse is applied de-phasing the signal from the first echo and once again being re-phased, generating a second (less strong) echo. Note: if you look to the diagram it is similar to the T(F)SE without looking to the gradients.






T2w contrast



TE 20ms



TE 40ms



TE 60ms


TE 80 ms


TE 100ms


Some MRI systems can produce up to 32 echoes!

Note: apart from the contrast parameters TR and TE, the flip angle (excitation RF pulse)can also be optimized to get a better contrast between the grey and white matter in the brain.


TR 550 ms flip 90°


TR 550 ms flip 70°


TR 582ms flip 90°


TR 582ms flip 69° (1.5T)



Courtesy Prof A. Stadlbauer



See below for a selection of TR and TE values, which can be used to produce the 3 image types with the SE method. The values shown are typical, but can be changed to some extent to accommodate specific imaging conditions. E.g. for a 3T the TR for a T1w image can be lengthened to 700ms.


2.02c MSE 


For a while, Modified Spin Echo was used where shorter TR’s could be used (<100-150ms) with larger flip angles (130-150 °) for abdominal imaging with multiple breath holds. But as far as I know it is not used anymore. Specifically, Philips has implemented this RF sequence.

So MSE is available for single echo scans. It will improve IQ in short-TR SE scans. A TR well below 100ms is possible.

When MSE is selected, the SE RF pulse is followed by an additional flip back pulse, thus realigning the longitudinal magnetization with the direction of the main magnetic field. The flip-back pulse is invoked automatically.

2.02d SR 


Saturation recovery (SR) RF sequences

Saturation recovery sequences consist of multiple 90° RF pulses at rather short TR’s. Residual longitudinal magnetization after the first 90° RF pulse is de-phased by a spoiling gradient (in this case with the slice select gradient). Longitudinal magnetization that develops during the TR period after the de-phasing gradient is rotated into the transverse plane by another 90° RF pulse. A GRE is acquired immediately after. The signal will reflect T1 differences in tissues, because of different amounts of longitudinal recovery during the TR period.

Courtesy P. Kellman


Although this RF sequence is rarely used for imaging, at the moment it is coming back as a Fast Imaging Technique in combination with parallel imaging techniques. Their primary use nowadays is as a technique to measure T1 times more quickly than an inversion recovery RF pulse sequence.

A research group of the National Heart, Lung and Blood Institute USA (ref. P. Kellman) optimized a RF sequence for myocardial perfusion: a dual SR RF sequence with separate RF pulse sequences for AIF (Arterial Input Function) and myocardial tissue allowing separate parameters for blood and myocardium to show more clearly the amount of contrast agents in the myocardial tissue so the quantification between the measured signal and contrast agent concentration is improved.

It is a 2D multi-slice dual SR GRE single shot (EPI), using a parallel imaging technique. Low resolution blood pool images were made for estimating the AIF, the higher resolution myocardium images maybe either b-SSFP or GRE-EPI. The PDw images use a low flip angle without SR preparation to minimize artefacts due to the fat around the heart (fat suppression is used).

Interesting and useful developments are going on including sophisticated Compressed sensing (CS) methods to accelerate MRI acquisition by acquiring less data through undersampling the k-space trajectory.


2.02e IR




Nitrogen inversion. Courtesy Wikipedia.



And shortly after the SE RF sequence the IR was implemented, adding a 180° RF pulse in front of the SE RF pulses.







Inversion recovery is usually a variant of a SE RF sequence, that starts with a 180° inversion pulse. This inverts the longitudinal magnetization vector through 180°. When the inversion pulse is removed, the magnetization vector begins to relax back to B0.

A 90° excitation pulse is then applied after a while from the 180° inverting pulse known as the TI (time to inversion). The contrast of the resulting image depends primarily on the length of the TI as well as the TR and TE. The contrast in the image depends mostly on the magnitude of the longitudinal magnetization (as in SE) following the chosen delay time TI.

Note: lengthening the TE can produce a signal-swap as modifying the Ti!



Real and modulus / magnitude image type in combination with a Ti (inversion delay/time) suppressing the fat tissue. Modulus/ Magnitude image types with Ti 120 – 700 – 1900ms.

Phase-corrected IR Real image types preserves the information about Mz polarity, with more negative values rendered increasingly darker.



In the real image scalp fat is the brightest substance and CSF the darkest. Background air is rendered a mid-shade of grey.



Magnitude reconstructed IR is often represented on a “bounce point” diagram, showing values of Mz < 0 reflected and displayed as positive.

The contrast is based on T1 recovery curves following the 180° inversion pulse. Inversion recovery is used to produce heavily T1 weighted images to demonstrate anatomy. The 180° inversion pulse can produce a large contrast difference between fat and water because full saturation of the fat or water vectors can be achieved by utilizing the appropriate Inversion delay time (Ti) shown as FLAIR and STIR/TIRM RF sequences, which will be discussed in the Turbo(Fast) IR RF sequence.

Because we start with an inversion RF pulse, it is important in several cases to be aware which image type to look at: the real image type (second image), where we can get the whole palette of negative and positive contrast between the tissues. If we look to the magnitude or modulus image type, where we only see the positive part (swapping the negative part positive), depending on the Ti the contrast may be inversed: the image looks like a T2w image like above.

In the early days, we were playing a lot with the Inversion Time: suppressing the fat (STIR) which we still do, suppressing the liver tissue (all lesions were shown positive or negative on the real image type). This was more difficult, because there is up to 20% variation between the T1 of the liver of different persons.

Then Dr. Graeme Bydder invented the FLAIR (Fluid-attenuated inversion recovery) that can be used with both three-dimensional imaging (3D FLAIR) or two dimensional imaging (2D FLAIR). For a while I remember some groups were calling it the “FLAT-TIRE” RF sequence.

Nowadays, the fast IR sequences is only used in combination with the T(F)SE train!


See T(F)SE RF sequence

The STIR and FLAIR (Dark Fluid) RF sequences will be discussed in the Turbo(Fast) IR RF sequence.

2.02f SIR

SIR Saturation-inversion-recovery RF sequence

The SIR sequence is a 3-pulse RF sequence: 90° – 180° – 90° acquisition. It can be viewed as an additional 90° RF pulse added in front of the IR RF sequence or a 180° pulse inserted in the middle of the SR RF sequence. The SIR sequence combines saturation and inversion processes, hence the name saturation-inversion-recovery sequence (SIR).

Note: the SIR abbreviation is also used as Simultaneous Image Refocusing.

It is a newer multi-slice imaging technique which makes multiple slices in a single or dual echo train RF sequence. It differs from the conventional multi-slice in the excitation process timing and signal refocusing from different slices. SIR can be incorporated in an EPI RF sequence and is also called a Multi-Band Technique.



                                                                                                                                       After this introduction the basic SE RF sequences and at the end of the module you should be able:

To understand the principle, the basic SE RF sequences and the acronyms and abbreviations of the different SE based RF sequences

To have an in depth knowledge of the conventional basic SE RF sequences

To understand the indication and techniques of the basic SE RF sequences

To understand the importance of the basic SE RF sequences

To describe various applications for the basic SE RF sequences

At the end of this module to have the skills to design imaging protocols for MRI exams choosing the best method and contrast.




Answer the questions and statements so you can jump to the next part! 

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