Pulse Sequence Overview a

Pulse Sequence Overview

• An MRI sequence is a number of radiofrequency pulses and gradients that result in a set of images with particular appearance.
• This section presents a simplified approach to recognising and thinking about common MRI sequences, but does not concern itself with the particulars of each sequences.
• A more complete and accurate discussion about various MRI pulse sequences is provides in the next section.
• This leads to a broad categorisation as follows:
  T1
  

  • Gadolinium enhanced
    Fat suppressed

  T2
  
  • Fat suppressed
  • Fluid attenuated
  • Susceptibility sensitive
  Proton density
  
  • Fat suppressed
  Diffusion weighted
  Flow sensitive
  
  • MR angiography
  • MR venography
  • CSF flow studies
  Miscellaneous
  
  • MR cholangiopancreatography (MRCP)
                a special T2-weighted sequence
  
  • MR spectroscopy
  • MR perfusion
  • Functional MRI
  • Tractography
  
  
  

  Terminology

  Intensity

  When describing most MRI sequences we refer to the shade of grey of tissues or fluid with the word intensity, leading to the following absolute terms:
  
  • High signal intensity = white
  • Intermediate signal intensity = grey
  • Low signal intensity = black
  
  Often we refer to the appearance by relative terms:
  
  • Hyperintense = brighter than the thing we are comparing it to
  • Isointense = same brightness as the thing we are comparing it to
  • Hypointense = darker than the thing we are comparing it to
  
  
  • Annoyingly these relative terms are used without reference to the tissue being used as the comparison.
  • In some instances this does not lead to any problems; for example, a hyperintense lesion in the middle of the liver is clearly hyperintense compared to the surrounding liver parenchyma.
  • In many other situations however use of relative terms leads to potential confusion. Imagine a lesion within the ventricles of the brain described as "hypointense". Does this denote a lesion darker than CSF or than the adjacent brain?
  
  
  • As such it is preferable to either use absolute terminology or, if using relative terms, to acknowledge the comparison tissue e.g. "the lesion is hyperintense to the adjacent spleen".
  
  NB: the word density is for CT, and there are few better ways to show yourself as an MRI noob than by making this mistake.
  
  

  Diffusion

  • When describing diffusion weighted sequences, we also use the term intensity but additionally we use the words restricted diffusion and facilitated diffusion to denote whether water can move around less easily (restricted) or more easily (facilitated) than expected for that tissue.
  • Again many use these words as if they are absolute terms and this leads to confusion
  
  

  T1 weighted sequences

  • T1 weighted sequences are part of almost all MRI protocols and are best thought of as the most 'anatomical' of images, resulting in images that most closely approximate the appearances of tissues macroscopically, although even this is a gross simplification.
  The dominant signal intensities of different tissues are:
  
  • Fluid (e.g. urine, CSF): low signal intensity (black)
  • Muscle: intermediate signal intensity (grey)
  • Fat: high signal intensity (white)
  • Brain:
  •    Grey matter: intermediate signal intensity (grey)
  •    White matter: hyperintense compared to grey matter (white-ish).                            

    Contrast enhanced

    • The most commonly used contrast agents in MRI are gadolinium based.
    • At the concentrations used, these agents have the effect of causing T1 signal to be increased (this is sometimes confusingly referred to as T1 shortening).
    • The contrast is injected intravenously (typically 5-15 mL) and scans are obtained a few minutes after administration.
    • Pathological tissues (tumours, areas of inflammation / infection) will demonstrate accumulation of contrast (mostly due to leaky blood vessels) and therefore appear as brighter than surrounding tissue. Often post contrast T1 sequences are also fat suppressed (see below) to make this easier to appreciate.

    • Fat suppression

      • Fat suppression (or attenuation or saturated) is a tweak performed on many T1 weighted sequences, to suppress the bright signal from fat. This is performed most commonly in two scenarios:
      • Firstly, and most commonly, after the administration of gadolinium contrast. This has the advantage of making enhancing tissue easier to appreciate.
      • Secondly, if you think that some particular tissue is fatty and want to prove it, showing that it becomes dark on fat suppressed sequences is handy.                                                                                                             T2 weighted sequences
        
        • T2 weighted sequences are part of almost all MRI protocols.
        Without modification the dominant signal intensities of different tissues are:
        
        • Fluid (e.g. urine, CSF): high signal intensity (white)
        • Muscle: intermediate signal intensity (grey)
        • Fat: high signal intensity (white)
        • Brain
        •    Grey matter: intermediate signal intensity (grey)
        •    White matter: hypointense compared to grey matter (dark-ish). 
        •      

          Fat suppressed

          • In many instances one wants to detect oedema in soft tissues which often have significant components of fat.
          • As such suppressing the signal from fat allows fluid, which is of high signal, to stand out.
          • This can be achieved in a number of ways (e.g. chemical fat saturation or STIR) but the end result is the same.
          •  

            Fluid attenuated

            • Similarly in the brain, we often want to detect parenchymal oedema without the glaring high signal from CSF. To do this we suppress CSF. This sequence is called FLAIR.
            • Importantly, at first glance FLAIR images appear similar to T1 (CSF is dark).
            • The best way to tell the two apart is to look at the grey-white matter.
            • T1 sequences will have grey matter being darker than white matter.
            • T2 weighted sequences, whether fluid attenuated or not, will have white matter being darker than grey matter.

            • Susceptibility sensitive sequences

              • Being able to detect blood products or calcium is important in many pathological processes.
              • MRI offers a number of techniques that are sensitive to these sort of compounds.
              • Generally these sequences exploit what is referred to as T2* (T2 star) which is highly sensitive to small perturbations in the local magnetic field.
              • The most sensitive of these sequences is known as susceptibility weighted imaging (SWI) and is also able to distinguish calcium from blood.

              • PD weighted sequences

                • Given that nuclear magnetic resonance of protons (hydrogen ions) forms the major basis of MRI, it is not surprising that signal can be weighted to reflect the actual density of protons; an intermediate sequence sharing some features of both T1 and T2.
                • Proton density images were extensively used for brain imaging, however they have largely been replaced by FLAIR.
                • PD however continues to offer excellent signal distinction between fluid, hyaline cartilage and fibrocartilage makes this sequence ideal in the assessment of joints.
                
                The dominant signal intensities of different tissues are:
                
                • Fluid (e.g. joint fluid, CSF): high signal intensity (white)
                • Muscle: intermediate signal intensity (grey)
                • Fat: high signal intensity (white)
                • Hyaline cartilage: intermediate signal intensity (grey)
                • Fibrocartilage: low signal intensity