D-Wave vs. MEP

Information box
The main purpose of this site is to extend the intraoperative monitoring to include the neurophysiologic parameters with intraoperative navigation guided with Skyra 3 tesla MRI and other radiologic facilities to merge the morphologic and histochemical data in concordance with the functional data.
CNS Clinic
Located in Jordan Amman near Al-Shmaisani hospital, where all ambulatory activity is going on.
Contact: Tel: +96265677695, +96265677694.

Skyra running
A magnetom Skyra 3 tesla MRI with all clinical applications started to run in our hospital in 28-October-2013.
Shmaisani hospital
The hospital where the project is located and running diagnostic and surgical activity.

Basic Principles of magnetism

The nuclei of many kinds of atoms, commonly hydrogen, are tiny magnets. In the earth’s magnetic field they line up to some extent just as you walk around. When you walk past a piece of iron they’ll flop around in different directions. Think of us as having microscopic compass needles precessing (spinning on their axes like gyroscopes) in an orderly direction. To make an MR image, this tendency of the nuclei to line up in the direction of a magnetic field can be manipulated and measured. Since the nuclei from different regions of the body can be made to precess at different frequencies (their magneto-resonance frequencies), the electromagnetic energy at these frequencies yields signals that are location dependent. Computer images can be calculated, enhanced, and displayed. MRI is safe because only a very tiny amount of energy is absorbed or emitted, corresponding to the amount of energy in radio waves, to which we are constantly exposed. MRI does not affect any chemical processes. It doesn’t change molecules at all. The atomic nuclei within the molecules just report what is happening.

In the presence of a static magnetic field (B0), the atomic nuclei possess energy which differs depending on their orientation( ΔE). ΔE determines the strength of the signal and is related to the resonance frequencies (ν), by Planck’s constant
(h). (Planck's constant h = 6.626x10-34 J.s ).

ΔE  = hv     (1)

The size of ΔE and v depend on the size of the static magnetic field, (B0), and the magnetogyric ratio, (ϒ), a characteristic of each kind of atomic nucleus, as shown in equation 2. This is the Larmor (Joseph Larmor, 1857 - 1942) relationship. The Larmor equation (2) is fundamental to all of nuclear magnetic resonance (NMR) and its subfield, MRI.

v = (ϒ/2π )
B0    (2) ( Larmor equation: Frequency rate of precession is proportional to the strength of magnetic field -  ϒ* B )

Together these two equations determine that

 ΔEhv = h (ϒ/2π )
B0    (3) ( This equation means that, the more the strength of the magnet, the higher the RF and the better the contrast and the resolution of the MRI data).


Basic Principles of MRI

The hydrogen (1^H) atom inside body possess “spin”
• In the absence of external magnetic field, the spin directions of all atoms are random and cancel each other.
• When placed in an external magnetic field, the spins align with the external field.
• By applying an rotating magnetic field in the direction orthogonal to the static field, the spins can be pulled away from the z-axis with an angle \alpha
• The bulk magnetization vector rotates around z at the Larmor frequency (precess)
• The precession relaxes gradually, with the xy-component reduces in time, z-component increases
• The xy component of the magnetization vector produces a voltage signal, which is the NMR signal we measure

What is spin?

• Spin is a fundamental property of nature like electrical charge or mass. Spin comes in multiples of 1/2 and can be + or -. Protons, electrons, and neutrons possess spin. Individual unpaired electrons, protons, and neutrons each possesses a spin of ½ or - ½.
• Two or more particles with spins having opposite signs can pair up to eliminate the observable manifestations of spin.
• In nuclear magnetic resonance, it is unpaired nuclear spins that are of importance.

Nuclear Spin
• A nucleus consists of protons and neutrons
• When the total number of protons and neutrons (=mass number A) is odd or the total number of protons is odd, a nucleus has an angular momentum (\phi) and hence spin – Ex. Hydrogen (1^H) (1 proton), 13^C
• The spin of a nucleus generates a magnetic filed, which has a magnetic moment (\mu)
• The spin causes the nucleus behave like a tiny magnet with a north and south pole

Angular momentum vs magnetic moment

Nuclear spin system

• Collection of identical nuclei in a given sample of material (also known as spin packet, a voxel in the imaged volume)
• In the absence of external magnetic field, the spin orientations of the nuclei are random and cancel each other
• When placed in a magnetic field, the microscopic spins tend to align with the external field, producing a net bulk magnetization aligned with the external field.

Nuclear Magnetization

• Put sample in external magnetic field: B0=B0ž
• Spins align in one of two directions:

-540 of ž "up"  (Low energy state)
-180-540 off ž "down" (high energy state)
• Slight preference for "up" direction: N-/N+ = e-E/kT
• Sample becomes magnetized.
• Magnetization vector:


Spins PRECESS at a single frequency (w0), but incoherently − they are not in phase, so that the sum of x-y components is 0, with net magnetization vector in z direction W0=\gamma B_0: Larmor freq. Equilibrium value: M0 : same direction as B0 and depends on x=(x,y,z) only. Magnitude: M0

How to make spins in phase?

Irradiating with a rotating magnetic field B_1 of frequency w0, causes spins to precess coherently, or in phase, generating a xy-component
Process involved in MRI

• Put patient in a static field B_0 (much stronger than the earth’s field)
• (step 1) Wait until the nuclear magnetization reaches an equilibrium (align with B_0)
• Applying a rotating magnetic field B_1 (much weaker than B_0) to bring M to an initial angle \alpha with B_0 (rotating freq=Larmor freq.)
• M(t) precess around B_0 at Larmor frequency around B_0 axis (z direction) with angle \alpha
• The component in z increases in time (longitudinal relaxation) with time constant T1
• The component in x-y plane reduces in time (transverse relaxation) with time constant T2
• Measure the transverse component at a certain time after the excitation (NMR signal)
• Go back to step 1
• By using different excitation pulse sequences, the signal amplitude can reflect mainly the proton density, T1 or T2 at a given voxel


Evolution of magnetization when a time varying magnetic field is applied

  • M=M(x,t)
  • Relation to bulk angular momentum J : M=  J
  • Focus on small sample voxel
    - M=M(t)
    - Equations of motion = Bloch equations
  • M(t) experiences a torque when an external magnetic field B(t) is applied
    torque is   = MxB
  • Torque is related to angular momentum
  • Eliminate J to yield
    dM(t)/dt M(t) x B(t)
  • Valid for "short" times
    Using the right hand rule, M will rotate around z if M is not aligned with z
       i     j    k  
    MxB = Mx  My  Mz  
      Bx  By  Bz  
      = (MyBz-MzBy ) i + (MzBx-MxBz  ) j+ ( MxBy-MyBx )k  

Direction of MxB follows “right hand” rule


Solution under a Static Field with an Initial Angle

• B(t)=[0,0,B_0]
• MxB = M_y B_0 i - M_x B_0 j + 0 k
• dM_x/dt = M_y B_0
• dM_y/dt = - M_x B_0

Precession Due to a Static Field with an Initial Angle


Let B(t) = B0; M(0) angel α  with ź
Mx(t) = M0 sin
α cos (- B0t + Ψ )
My(t) = M0 sin α sin (- B0t + Ψ )
Mz(t) = M0 cos
M0 = |M(0)|
Ψ  arbitrary

Precession with Larmor frequency
0B0  or  v0B0
This is the frequency of the photon which would cause a transition between the two energy levels of the spin.
B0=1.5T, \gamma=42.58 MHz/T, v0=63.9 MHz

Longitudinal and Transverse Components

M(t) = (Mx(t), My(t), Mz(t))
Think of M(t) with two components:
Longitudinal magnetization - Mz(t) - No change
Transverse magnetization - Mxy(t) = Mx(t) + jMy(t) - Rapidly rotating


NMR Signal

• The rapidly rotating transverse magnetization (M_xy) creates a radio frequency excitation within the sample.
• If we put a coil of wire outside the sample, the RF excitation will induce a voltage signal.
• In MRI, we measure this voltage signal.
• Voltage produced is (Faraday’s Law of Induction)
  Br(r) is field produced at r by unit direct current in coil around sample.


Source of MR Contrast

• Different tissues vary in T1, T2 and PD (proton density)
• The pulse sequence parameters can be designed so that the captured signal magnitude is mainly influenced by one of these parameters
• Pulse sequence parameters
– Tip angle \alpha
– Echo time TE
– Pulse repetition time TR



  • B^r(r)=B^r
  • Longitudinal magnetization changes too slow
  • Transverse magnetization dominates
  • Final expression:
    |V| = 0VsM0 sin Br  
    Recall  0 = ϒB0, Mo = ( B0 ϒ2h2 /4kT ). PD
    Therefore |V| B02, PD


How to tilt M to an initial angle?


• Applying a circularly polarized (rotating) magnetic field B_1(t) in the x-y plane with the same Larmor frequency forces the magnetization vector to tilt down to the x-y plane
– B_1(t) has two orthogonal components, in x and y directions respectively, and is produced by using quadrature RF coil
– Simplest envelop B_1,e is a rectangular pulse
• Motion of M(t) is spiral

Circulatory Polarized Magnetic Field


Tip Angle

• If M is parallel to z-axis before the RF excitation pulse, the tip angle after the excitation (with duration \tau_p) is: 
• If B_1^e(t) is rectangular  = ϒB1p
• Pulse that leads to \alpha=\pi/2 is called “\pi over 2 pulse”, which
elicits the largest transverse component M_xy, and hence largest
NMR signal
• Pulse that leads to \alpha=\pi is called “\pi pulse” or inverse pulse,
which is used to induce spin echo (later)
• The excitation pulse (envelop of B_1(t)) is also called “an alpha


  • Magnetization cannot precess forever
  • Two independent relaxation processes
  • Transverse relaxation -  spin-spin relaxation
  • Longitudinal relaxation - spin-lattice relaxation
  • Detailed prosperities differ in tissues - Gives rise to tissue contrast.

Longitudinal Relaxation

• The magnetization vectors tend to return to equilibrium
state (parallel to B_0)
= M_0 cos\alpha

= 0 for \pi/2 pulse

In the laboratory frame, M takes a spiraling path back to its equilibrium orientation. But here in the rotating frame, it simply rotates in the y ׳-z ׳ plane. The z component of M, Mz, grows back into its equilibrium value, exponentially: Mz = |M|(1 - e-t/T1)


Transverse Relaxation
• The strength of the magnetic field in the immediate environment of a
1H nucleus is not homogeneous due to presence of other nucleus
(and their interactions)
• Hence the Larmor frequencies of nearby nuclides are slightly different
(some spins faster, some slower)
– Spin-spin interactions
• This causes dephasing of the xy components of the magnetization
vectors, leading to exponential decay of M_

• T_2 is called transverse relaxation time, which is the time for M_xy
to decrease by 1/e.
• Also called spin-spin relaxation time
• T2 is much smaller than T1
– For tissue in body, T2: 25-250ms, T1: 250-2500 ms

Free Induction Decay

• The voltage signal (NMR signal) produced by decaying M_xy also
• This is called free induction decay (FID), and is the signal we measure
in MRI

T2 Star Decay
• Received signal actually decays faster than T_2 (having a shorter relaxation
time T_2^*)
• Caused by fixed spatial variation of the static field B_0 due to imperfection
of the magnet
– Accelerates the dephasing of magnetization vectors
– Note that T2 is caused by spatial variation of the static field due to interactions of
nearby spins
• The initial decay rate is governed by T_2^* , but the later decay by T_2.

Formation of spin echo

• By applying a 180 degree pulse, the dephased spins can recover their coherence, and form an echo signal

RF Pulse Sequence and Corresponding NMR Signal



Spin echo sequence

• Multiple π pulses create “Carr-Purcell-Meiboom-Gill (CPMG)” sequence
• Echo Magnitude Decays with time constant T2


Bloch Equations

Typical Brain Tissue Parameters


  Proton Density T2 (ms) T1 (ms)
White matter 0.61 67 510
Gray matter 0.69 77 760
CSF 1.00 280 2650



T1 Short Short
T2 Long Long
PD Long  Short

• Signal at equilibrium proportional to PD  
• Long TR:
– Minimizes effects of different degrees of saturation (T1 contrast)
– Maximizes signal (all return to equilibrium)
• Short TE:
– Minimizes T2 contrast
– Maximizes signal

• Long TR:
– Minimizes influence of different T1
• Long TE:
– Maximizes T2 contrast
– Relatively poor SNR

• Short TR:
– Maximizes T1 contrast due to different degrees of saturation
– If TR too long, tissues with different T1 all return equilibrium already
• Short TE:
– Minimizes T2 influence, maximizes signal


Summary: Process Involved in MRI

• Put patient in a static field B_0 in z-direction
• (step 1) Wait until the bulk magnetization reaches an equilibrium (align with B_0)
• Apply a rotating field (alpha pulse) in the xy plane to bring M to an initial angle \alpha with B_0. Typically \alpha=\pi/2
• M(t) precesses around B_0 (z direction) at Larmor freq. with angle \alpha
• The component in z increases in time (longitudinal relaxation) with time constant T1
• The component in x-y plane reduces in time (transverse relaxation) with time constant T2
• Apply \pi pulse to induce echo to bring transverse components in phase to increase signal strength
• Measure the transverse component at different times (NMR signal), to deduce T1 or T2
• Go back to step 1
• By using different excitation pulse sequences (differing in TE, TR, \alpha), the signal amplitude can reflect mainly the proton density, T1 or T2 at a given voxel


Transforming the acquired MRI data to images

MRI task is to acquire k-space image then transform to a spatial-domain image. kx is sampled (read out) in real time to give N samples.
ky is adjusted before each readout. MRI image is the magnitude of the Fourier transform of the k-space image.


Gradient Echo Imaging
•Signal is generated by magnetic field refocusing mechanism only (the use of negative and positive gradient)
•Signal intensity is governed by

                      S = So e-TE/T2*

•Can be used to measure T2* value of the tissue
•R2* = R2 + R2ih +R2ph  (R2=1/T2)
•Used in 3D and BOLD fMRI




  1. The Larmor frequency f0 ( Center frequency is the frequency rate at which protons spin (precess) with just static magnetic field) for a 1.5 T magnet is 1.5(T)*42.56(MHz T-1) = 63.8 MHz, for 3T= 128 MHz, for 7T = 300 MHz and for 11.7T = 500 MHz. The gyromagnetic ratio here is for 1H
  2. One gauss is defined as one maxwell per square centimeter; it equals 1Χ10−4 tesla.
  3. Typical values
    10−9–10−8 gauss: the human brain magnetic field
    0.31–0.58 gauss: the Earth's magnetic field on its surface
    25 gauss: the Earth's magnetic field in its core
    50 gauss: a typical refrigerator magnet
    100 gauss: a small iron magnet
    2000 gauss: a small neodymium-iron-boron (NIB) magnet
    15,000-30,000 gauss: a medical magnetic resonance imaging electromagnet
    1012–1013 gauss: the surface of a neutron star
    4Χ1013 gauss: the quantum electrodynamic threshold
    1015 gauss: the magnetic field of some newly created magnetars
    1017 gauss: the upper limit to neutron star magnetism, no known object in the universe can generate a stronger magnetic field
  4. The relation between FOV and gradient direction: FOV is defined as bandwidth divided by the gradient times and gyromagnetic ration
  5. Bandwidth is defined as follows: BW = 1/ ΔT,
  6.  Δk = 1/FOV where  k is the spatial frequency of k-space and Δk are cycles per distance


The gyromagnetic ratio is dependent upon the atoms:


γ / 106 rad s−1 T−1

γ/2π / MHz T−1






































This is a neurosurgical site dedicated to intraoperative monitoring to catch in time the early signs of possible functional complications before they evolve to morphologic ones.

Complications in neurosurgery

So as to have a digital data, the best ever made Inomed Highline ISIS system was put in service to provide documented information about the complications.

Directed by Prof. Munir Elias

Team in action.

Starting from July-2007 all the surgical activities of Prof. Munir Elias will be guided under the electrophysiologic control of ISIS- IOM

ISIS-IOM Inomed Highline



Copyright [2017] [CNS Clinic - Jordan - Munir Elias]. All rights reserved