MRI (Magnetic Resonance Imaging)

Estimated Time: 60 minutes


In 1977 for the first time the idea of Magnetic Resonance Imaging (MRI) had been brought to the publics attention. The first MRI took as long as five hours, whereas these days it could be done in seconds. Today patients have a choice of doing a much safer scan compare to X-ray or CT-Scan since MRI has no harm on the body, whereas X-ray or CT-Scan could be quite harmful. The original name of MRI used to be Nuclear Magnetic Resonance Imaging, but since people thought it is related to nuclear radiation the propaganda had to change. So the instrument ended up being known as MRI. You might have experienced having an MRI on some part of your body. Then you remember the cold room while doing the scan. And the reason is NMR & MRI are temperature dependant. Also viscosity of a sample plays a role on the quality of the results. In this experiment you are going to perceive an Earth Field Nuclear Magnetic Resonance (EFNMR), which is the same thing as an MRI with only one difference, and that being that EFNMR uses the earth magnetic field whereas MRI has a huge magnet 10,000 times stronger than the earths magnetic field.


Wikipedia, the free encyclopedia

EFNMR components

This instrument is made of a spectrometer and a probe that consists of three coils slot together: the polarizing coil, the gradient coil, and the B1 coil.

Image:probe.png Image:spectrometer.png

Image:coils.png Image:efnmr.png

Terranova manual


The theory of EFNMR

The nuclei of atoms are aligned with the Earth’s Magnetic Field because that is the only magnet we have by using this apparatus. Each time we send a pulse to the spectrometer, we are sending electricity to the probe. This causes the nuclei to position themselves perpendicular to the original status they had which was alignment with the magnetic field. So the nuclei originally are aligned parallel to the magnetic field and after a pulse they are positioned perpendicular to the earth’s magnetic field. When the electricity is shut off (as the term pulse applies, it only sends electricity for a few seconds), the nuclei realign themselves to the original status, which is parallel to the earth magnetic field. By doing so, a radio frequency in form of electricity is emitted by the nuclei, which is collected by the smallest coil of the probe that acts like an antenna picking up the radio that’s being emitted. So if we have a sample of water, it has lots of hydrogen in it, which is a good source of protons. The protons are first aligned with the earth’s magnetic field and then by receiving a pulse, they rotate 90 degrees, and by realigning they give off the energy they have gained in form of radio frequency, which is converted into electricity and collected by the B1 coil (the smallest coil). There is also the gradient coil (gradient=a varying magnetic field) that is the key to understanding how EFNMR or MRI work. The closer a patient to the magnet the stronger the magnetic field and the higher the frequency of absorption is going to be. Furthermore, the farther an object from a magnet, the weaker the magnetic field and the lower the frequency of absorption is going to be. Our body contains a lot of water except our bones. For example, if one does an MRI of his neck, let’s say the right part of the neck that is closer to the magnetic field feels a stronger magnetic field than the left part. So when a pulse is sent to the probe, the higher frequency is on the right side of the neck meaning on the right side the water will absorb at a higher frequency than the water on the left side of the neck. Therefore, we could do a map of water (a map of hydrogen=nucleus) at a certain distance away from the magnet that could be noticed by different frequency of absorption. Consequently, MRI has a magnet that is a coil that sets up a gradient, which is a varying magnetic field going from strong to weak and allows us to do the map, which is the higher the frequency the closer the object to the magnetic field.

Learning Objective

The goal of this experiment is to help you understand the basic structure and function of MRI and its application in the modern world.


This module will help you get started using the Terranova MRI and its software. You will begin by powering up the MRI machine by flipping the power switch located on the right hand side of the power supply.

Open the Prospa application by clicking the icon on the desktop or finding it through the start button. Once the main application window is open you will need to open four sub-windows: the CLI (command line interface) window, the 1D Plot window, the 2D Plot window, and the 3D Plot window. You can open all four windows by clicking on the Window menu.


It is convenient to position the four windows as follows.


Now that you have all four windows open, you are ready to begin the preliminary experiments (macros) required for an MRI scan.

First, open the macro called Analyze Coil found under the EFNMR menu.


Once open, the window looks like this and all you need to do is click on the run button. (The file name and directory is already entered for you, do not change it.)


Before the macro runs you will get this message, click yes.


The macro will run and you will see the results of the Analyze Coil preliminary experiment in the CLI (command line interface) window.


The second macro you will need to run is also located in the EFNMR menu and is called monitor noise.


The Monitor Noise window looks like this.


This window has several parameters that you can change. However, for now just click on run. The results will appear in the 1D Plot window and looks like this.


In order to get a good signal to noise ratio, the noise level must be below 3 micro volts. The image above shows 3.3 micro volts which is good. Noise above 10 is not good and causes trouble when running the actual experiment. You can try and decrease the noise by moving the MRI apparatus to the right, to the left, backwards and forwards. Be sure to move the apparatus only slightly. [By trial and error it appears the closer you get the apparatus pointed towards the earth’s magnetic field the lower the noise.]

Now that you have minimized the noise as best as possible, it is time to acquire an FID signal which stands for free induction decay. Go to the EFNMR menu and select the Pulse and Collect macro.


Once selected, the GUI looks like this.


Again there are many parameters you can change; usually we could alter the capacitance to make a change, but for now just click on the run button. You will see the experiment in progress and the results of the experiment in the CLI window. It will look like this.


Notice the max signal for the orange that I placed in the center of the MRI machine is 16.3 at a frequency of 1810. Now that we know the frequency we can enter it into the B1 frequency field of the Pulse and Collect interface.


When we do this and click on the run button again, you should see an increase in signal by adjusting the B1 frequency. The results of the test with the new frequency are shown below.


Notice that the signal increased from 16.3 to 18.4.

Now that you have acquired an FID signal, you can adjust the capacitance of the MRI apparatus. This is done by changing the Acquisition delay field from 25 ms to 2 ms in the Pulse and Collect GUI. Once the change has been made, click on the run button. You will see that the FID signal (located in the 1D Plot window) and the Magnitude spectrum will change. You will see something like this.


We will concentrate only on the second image to the right, the Magnitude spectrum. Notice there is now an upside down peak located somewhat in the center of the spectrum. To properly adjust the capacitance, we must increase or decrease the capacitance to ensure the upside down peak is in the center of the spectrum. Increasing the capacitance moves the upside down peak to the right, and decreasing the capacitance moves the upside down peak to the left. Therefore, we must increase the capacitance to center the upside down peak in our example. Thus, I will change the capacitance from 17.09 to the max at 17.15. The following image shows the results.


Perhaps not much difference is evident in this example (with other samples it is possible to center the upside down peak). However, keep in mind for an optimal signal; get the upside down peak in the center of the spectrum.

Once you have adjusted the capacitance accordingly, change the Acquisition time back to 25 milliseconds and run the Pulse and Collect experiment again and notice an increase in signal.

Now it is time to shim the apparatus. This is done by clicking on the EFNMR menu and selecting Auto Shim.


The GUI looks like this


Make sure the B1 frequency and capacitance is correct. It is best to click on reset to clear the shim parameters of the previous sample. Once you have reset the values, click on run. The autoshim process takes anywhere from 10 to 20 minutes. When the auto shim experiment is over it will ask you if you want to save the new values, click yes. Now run the Pulse and Collect experiment again and you should get an even better signal.

The B1 Duration experiment is the next macro you should run. It is found in EFNMR.


The B1 Duration GUI looks like this.


Click on run. This experiment is required to run 3D experiments. Normally the results for this test will vary only slightly based on differing samples so its results are not needed.

The T1 experiment is now ready to be run. Click on the EFNMR menu and select T1Bp. Its’ GUI looks like this.


Without changing any parameters, click on run. The results of the experiment will be seen in the CLI window and will look similar to this.


The T1 value is what we need. In this example the value is 1400 + or – 200 milliseconds. Multiply this value by 2 and write it down, you will need it later. For this example, multiplying by 2 will give us a T1 value of 2800. Don’t worry about the std deviation, however, keep in mind the smaller the std deviation the better the T1 value.

Now we need to calculate the T2 time. Click on the EFNMR menu and select T2. The T2 GUI looks like this.


Without changing parameters click on run. The results of the experiment can be seen in the CLI window. It will look similar to this.


The T2 value for this example is 700. Divide this number by 3. In this case the T2 value we would use is 233. Write this number down, you will need it later.

Now you are ready to take your MRI image. Click on the MRI menu and select GradEchoImaging.


The GUI looks like this. . .


From here you can select the type of image you want, 1D, 2D, or 3D image. You can also select which image orientation you want by clicking on the drop down menu next to Image orientation. Measure your sample in the X, Y, and Z directions in millimeters and enter your measurements in the Field of View field respectively. You may want to add about 30 mm to your findings to avoid overlap of the image. If you find you still have overlap, add 50 mm to your measurements.

The Matrix size will determine the resolution of the sample. A high resolution will provide more detail of the sample, however, it will also take longer to complete.

In the Polarizing duration field, enter your T1 time. In the Echo time field, enter your T2 time. Change the experiment name accordingly and click on run. The MRI apparatus is now processing and no electrical devices (cell phones, cameras, etc) should be used while it is in progress for this will stop the machine and potentially harm it and or the electrical device.

You will notice the 1D Plot and the 2D plot windows displaying data.


2D images will also appear in the 2D plot window.


This is where you will be able to tell if overlap is evident. If it is, then you should stop the experiment and change the Field of View values accordingly.

When the experiment is complete, there will be a pop up window stating this. Now you can activate the 3D plot window by clicking on it. Right click in the blue area of the 3D plot window and select Display 3D surface plot. You will see the name of your experiment. Select it and you will bring up a GUI that looks like this.


Click on plot and you should see something in the 3D plot window. Now here is where it gets a little tricky. If nothing is showing, you must enter values into the surface level field until something is seen. Normally you want to enter values that are lower than the original, perhaps all the way down to 10. Then proceed to enter values in higher increments until you see your image. Sometimes you will have more than one image; it is up to you to distinguish the actual image from the noise.


1. Explain how MRI works as it correlates with NMR

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