Contrast Manipulation

					Contrast Manipulation




               Contrast Manipulation

                 Manus J. Donahue
           manus.donahue@clneuro.ox.ac.uk
              FMRIB Physics Division
     Contrast Manipulation


                             Contrast Manipulation

•  Image contrast = signal difference between different tissues
   of interest
•  Image contrast is the combined effects of tissue differences in
   proton density (PD), T1 and T2
–  Many sequences can be either PD or T1 or T2 weighted,
   depending on details of timing
–  Typically aim to maximise the contrast due to one of these
   and minimise the contrast due to the others
   Contrast Manipulation


                           Contrast Manipulation

  PD-weighted                  T1-weighted         T2-weighted




MRI Signal ~ Water Density X Mz X Mx,y
      Contrast Manipulation


                              Excitation (90o RF pulse)

                                    z




                                                           x

                        y


Tip magnetization from z (along B0) into x-y plane
Wait some time and acquire an image
      Contrast Manipulation


                              Excitation (90o RF pulse)

                                    z



    Only magnetization in
    x-y plane is detectable


                                                           x

                        y


Tip magnetization from z (along B0) into x-y plane
Wait some time and acquire an image
       Contrast Manipulation


                               Excitation (90o RF pulse)


               z                                   z
                       x-y (transverse) plane            z direction




                                         x                                  x

 y                                      y
                                                Signal in z recovers to M0 (T1)

Signal in x-y plane dephases to zero (T2)
 Contrast Manipulation


                    Transverse Relaxation Time (T2)


                         - After excitation, signal decays
                         - Speed of signal loss is described by T2
                            (transverse relaxation time)
                         - T2 is different for each tissue
Mx,y




                                     Time
Contrast Manipulation


                  Echo Time (TE) and T2 Contrast



                    TE/2 = time from excitation to
                      180 RF refocusing pulse


                             Lower signal            Tissue 1

Mx,y





                             High contrast           (long T2)

                                                      Tissue 2

                                                     (short T2)

        High signal
        Low contrast


                                 TE

   Contrast Manipulation


                     Echo Time (TE) and T2 Contrast


T2 is the transverse relaxation time (time constant describing how fast
signal in x-y plane to decays)

T2 is different for different tissue types and at different field strengths
         Gray matter:       80 ms
         White matter: 70 ms
         CSF:               600 ms
         Arterial blood: 120 ms
         Venous blood: 40 ms                                   (3.0T)

By adjusting the TE (echo time), we achieve different T2-weighting
       Contrast Manipulation


                               Excitation (90o RF pulse)


              z                                    z
                       x-y (transverse) plane            z direction




                                        x                                   x


y                                       y
                                                Signal in z recovers to M0 (T1)

Signal in x-y plane dephases to zero (T2)
Contrast Manipulation


                          T1 Relaxation
               Tissue 1 (short T1)
 Mz


                                     Tissue 2 (long T1)



                        Excited magnetization returns to
                          alignment with main field
                        Speed of return is described by T1
                           (longitudinal relaxation time)
                        T1 varies with tissue and field strength

                                               time
  Contrast Manipulation


                          TR and T1 Contrast




Long TR: T1 recovers completely for
GM and WM - no contrast!

                                               12
   Contrast Manipulation


                           TR and T1 Contrast




Short TR: WM has shorter T1 and
recovers more than GM - this gives T1
contrast
                                                13
     Contrast Manipulation


                  Repetition Time (TR) and T1 Contrast


T1 is the longitudinal relaxation time (time constant describing how fast
signal in z “regrows” following RF)

T1 is different for different tissue types and at different field strengths
         Gray matter:       1200 ms
         White matter: 800 ms
         CSF:               4000 ms
         Arterial blood: 1700 ms
         Venous blood: 1500 ms                                 (3.0T)

By adjusting the TR (repetition time), we achieve different T1-weighting
Contrast Manipulation


                        T1 and T2 Contrast
Contrast Manipulation


                        T1 and T2 Contrast
Contrast Manipulation


                        T1 and T2 Contrast




                                             17
Contrast Manipulation


                        Contrast Possibilities



                          Short TE          Long TE

                                            T1 and T2
     Short TR            T1-weighted
                                            weighted


     Long TR            Proton density    T2-weighted
     Contrast Manipulation


                        Inversion Recovery Spin Echo




                    180o            90xo         180yo


                             TI                TE

TI = inversion time (time from inversion to excitation)
Typically, TI >> TE (drawn as above for convenience)
Contrast Manipulation


                      Inversion Recovery Sequence

                              z




                                                 y

                  x
     Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz




                                                        time




 TI=delay before excitation
 Magnetization preparation =
 modify magnetization before excitation
     Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz   Image




                                                        time




 TI=delay before excitation
 Magnetization preparation =
 modify magnetization before excitation
     Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz       Image




                                                        time




 TI=delay before excitation
 Magnetization preparation =
 modify magnetization before excitation
       Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz           Image




0
                                                        time




    TI=delay before excitation
    Magnetization preparation =
    modify magnetization before excitation
     Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz              Image




                                                        time




 TI=delay before excitation
 Magnetization preparation =
 modify magnetization before excitation
     Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz                    Image




                                                        time




 TI=delay before excitation
 Magnetization preparation =
 modify magnetization before excitation
     Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz                           Image




                                                        time




 TI=delay before excitation
 Magnetization preparation =
 modify magnetization before excitation
     Contrast Manipulation



Magnetization preparation: T1 contrast with inversion recovery

Mz                                                       Image




                                                        time




 TI=delay before excitation
 Magnetization preparation =
 modify magnetization before excitation
Contrast Manipulation


                  Steady-state MRI and Flip Angle
                              z




                cos(θ) x Mz                          y
                                  θ



                                                     x
                                       sin(θ) x Mz
   Contrast Manipulation


                           TR and Flip Angle (FA)




Signal at each measurement = sin(θ) x Mz

For FA=90° pulse: sin(90°) x Mz = Mz.

But during the TR, Mz only recovers to 67%, (67% of signal)
      Contrast Manipulation


                         Changing the Flip Angle (FA)




FA = 70°. Signal is sin(70°) x Mz = 0.94 Mz

BUT leave cos(70°)=0.34 Mz which recovers to 75% of original Mz.

Steady-state signal is 0.94 x 0.75 = 71%. HIGHER than FA=90°!
      Contrast Manipulation


                         Changing the Flip Angle (FA)




FA = 40°. Signal is sin(40°) x Mz = 0.64 Mz

BUT leave cos(40°)=0.77 Mz which recovers to ~90% of Mz

Steady-state signal is 0.64 x 0.90 = 58%. Lower than FA= 70° or 90°
      Contrast Manipulation


                       Optimising the Flip Angle (FA)




For the specified TR and T1:
The optimal flip angle is ~70°.

More generally, we can use the Ernst Angle:
     Contrast Manipulation


                       ‘Dummy’ or Saturation Scans




It can take a few TRs for the signal to reach the steady-state.

First few volumes in a BOLD EPI are discarded for this reason.

More saturation scans are required when the TR is shorter or
when T1 is longer.
     Contrast Manipulation


                             Signal-to-noise Ratio (SNR)





‘Signal’ depends on tissue of interest
Here: SNR in white matter
     Contrast Manipulation


                        Contrast-to-noise Ratio (CNR)





‘Contrast’ depends on 2 tissues of interest
Here: SNR in WM, CNR GM vs WM
     Contrast Manipulation


                             Contrast Manipulation
•  Image contrast = signal difference between different tissues
   of interest
•  Image contrast is the combined effects of tissue differences in
   proton density (PD), T1 and T2
  Some different sequences that exploit T1 and T2 contrast:
    - FLAIR (multiple sclerosis lesion identification)
    - VASO (blood volume weighted functional imaging)
    - ASL (noninvasive blood flow weighted imaging)
    - DSC (invasive blood flow weighted imaging)
Contrast Manipulation



            FLuid Attenuated with IR-SE (FLAIR)




           SE (T2-weighted)     IR-SE (T2-weighted)
     Contrast Manipulation


 Magnetization preparation: T1 contrast with inversion recovery


Mz                    Image




                                                         time




  TI=delay before excitation
  Magnetization preparation =
  modify magnetization before excitation
Contrast Manipulation



           Multiple Sclerosis Imaging and FLAIR
        Fluid Attenuated Inversion Recovery (FLAIR): Null CSF
    Contrast Manipulation


Measuring CBV with Vascular-space-occupancy (VASO) MRI

Image




  Invert
                    Contrast Manipulation


                                    Measuring CBV Changes with VASO



                                                    Voxel size=780µm x 780µm
                                                    Slice thickness 3 mm
                                                    TR/TI/TE=3000/889/32 ms

                                                    fMRI:
Fractional Signal




                                                    Visual stimulus (6 Repetitions of
                                                    30s off/on flashing checkerboard)



                                                    Non-BOLD method for measuring
                                                    brain activity (CBV adjustments)
                              60        120   180
                                   Time (s)
     Contrast Manipulation


 Cerebral Blood Flow (CBF): Rate of Blood Delivery to Tissue
                  Arterioles            Capillaries    Veins




   Blood
H2O, Glucose




                                              CO2

                               (Restricted)
                                Exchange                       CBF:
                                        O2, Glucose   mL water/100g tissue/min
      Contrast Manipulation


         Measuring CBF with Arterial Spin Labeling (ASL)




 Control Preparation             Label Preparation               Difference Image
 (no labeling of blood)          (labeling of blood)             (Control – Label)
                                                                 Proportional to CBF

CBF (rate blood is delivered to tissue) quantified from difference image:
mL blood / 100 g tissue / minute
Contrast Manipulation


          Measuring CBF Changes with ASL fMRI




                              3.0T ASL fMRI
                              Left hand joystick task
                              Spatial resolution=3.8x3.8x3.8 mm3
                              CBF change =60-70%
                              TR/TI=2500/1600 ms
      Contrast Manipulation


                                  Changing the TI in ASL MRI



              Difference Signal




                                               TI

Graph shows expected ASL signal as TI is increased
Curve reveals information about the arterial blood transit time and the
  cerebral blood flow (CBF).
May be useful in: stroke, tumor imaging, functional studies.
        Contrast Manipulation


      Dynamic Susceptibility Contrast (DSC) Perfusion Imaging


•  Use injection of gadolinium to measure blood flow
    –  Gadolinium (Gd-DTPA) is injected into vein in arm
    –  Gd-DTPA enhances BOLD-like T2* dephasing
    –  Draw ROI in artery to define
       “Arterial Input Function”




 DSC data courtesy of Atle Bjørnerud, Oslo
         Contrast Manipulation


                                 DSC Perfusion Imaging

                    Ct(t) = CBF × ( Ca(t)  R(t) )
         concentration of         concentration of tracer in artery   residue function - corresponds to
          tracer in tissue         - equivalent to Arterial Input         tissue curve if AIF were an
                                          Function (AIF)                       impulse function


tracer                                                                 CBF
conc


                                  deconvolution


                                                                 AREA = CBV


                                       time                                                   time
     Contrast Manipulation


                             DSC Imaging

             Arrival            CBF                 CBV
              time




                                           Ibaraki et al, JCBFM 2005


•  DSC is invasive and suffers from quantification issues

•  Industry standard for acute stroke (perfusion)
      Contrast Manipulation


        Tumour Segmentation Using Multiple MRI Contrasts
              FLAIR           T1w   VASO   Tumour Segmentation Gd-T1w


GBM




AO




LG


 GBM: Glioblastoma multiforme; AO: Anaplastic oligodendroglioma; LG: Low-grade
     Contrast Manipulation


                             Contrast Manipulation

•  Image contrast = signal difference between different tissues
   of interest
•  Image contrast is the combined effects of tissue differences in
   proton density (PD), T1 and T2
–  Many sequences can be either PD or T1 or T2 weighted,
   depending on details of timing
–  Typically aim to maximise the contrast due to one of these
   and minimise the contrast due to the others

				
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