Medical Imaging 101 pt 3: MRI

OK, it’s been a while since the last medical imaging post. If you missed part 1 and part 2, they are here http://goo.gl/LTWUf and here http://goo.gl/IHaFw. The prelude to this post, was about quenching an MRI magnet (http://goo.gl/mePgt). Most of you have heard of MRI, magnetic resonance imaging. Hopefully you haven’t had to have one, unless as a volunteer. You’ve probably also heard the word fMRI tossed around G+ too. It stands for functional MRI. MRI and fMRI use the same equipment. fMRI is just a special type of MRI. The importance of MRI as a research tool cannot be overstated. In 2003 Paul Lauterbur and Sir Peter Mansfield shared the Nobel Prize in Physiology or Medicine for their contribution in developing MRI, i.e., taking NMR spectroscopy to imaging. http://www.nobelprize.org/nobel_prizes/medicine/laureates/2003/ 

Physics for raw data acquisition

So how does it work. Typically, MRI magnets are super-conducting, which I’ve talked about in the quenching post. In nuclear magnetic resonance, NMR, a strong magnetic field is used with the natural spin of isotopes with an odd number of protons and/or neutrons. They have an intrinsic magnetic moment that we can take advantage of. Hydrogen, H-1, is the most common, considering how much is present in organic compounds and the fact that there is so much water in living organisms. MRI is just an extension of NMR. Lauterbur and Mansfield had the idea that if you added a gradient to the main magnetic field, it could be possible to encode spatial position and therefore get an image.

At its basic level, for MRI, you need a strong magnet, gradient coils, and radio frequency (RF) coils. Unlike, CT, PET, and SPECT, which I talked about briefly in pt 1, MRI does not use projection data, i.e., a set of 2D pictures. MRI collects data in the frequency domain. That’s where the RF comes in. You use the gradients to get the molecules to spin in a certain direction and then transmit an RF pulse. The received RF signal can be transformed, using a Fourier Transform, to get the spatial information back. There is a lot to explain in a short post. There’s Java tool that can show you how the magnetic field and RF pulse work together here: –http://www.magnet.fsu.edu/education/tutorials/java/mri/index.html-

https://nationalmaglab.org/education/magnet-academy/learn-the-basics/stories/mri-a-guided-tour

The math and more can be found here: http://www.cis.rit.edu/htbooks/mri/inside.htm 

Contrast

There are three types of relaxation times that reflect the physical properties of the sample. Spin lattice or longitudinal relaxation times (T1) is a measure of the time it takes a proton to realign with the main magnetic field. Water and fat have different T1s so a T1-weighted image is good for brain imaging, for example. Spin-spin or transverse relaxation times (T2) is another physical property relating to dephasing of spins following application of a transverse energy pulse. The interaction between spins of the nearby nuclei is what gives contrast in T2-weighted images. The third type is T2* or T2 Star. It is spin-spin relaxation that takes into account field inhomogeneities. You use different pulse sequences, i.e., different combinations of gradient currents and RF pulses to get different types of images (contrast). Each image type takes advantage of the T1 and T2 differences in the sample to get contrast.

An example of k-space data is shown in the first picture. It has 3 slices, i.e., 3 locations within the sample that I prescribed a slice to be imaged. Although the whole sample could be imaged, it is much faster to image just 3 slices. The image has multiple echoes, i.e., 180 deg RF rephasing pulses. As the echo times get longer, there is more noise in the data, but that’s a long story. The next images is the result of the of reconstructing the k-space data. There are 3 sagittal slices of a mouse leg with the foot at the top. 

Strengths

MRI’s strength is the ability to get high resolution, anatomical images with great contrast, without having to inject a contrast agent. 

Weakness

MRI’s weakness is the cost of the equipment and limitations of using a magnet, e.g., patients with a pace maker are excluded.

Something unique: functional and anatomic

Unlike the other imaging modalities, MRI can provided high resolution, anatomic images with good contrast and multiple types of functional images. The types of functional images possible are:

Diffusion Weighted Imaging (DWI). Pulse sequences are set up to image the diffusion of fluid in the sample.

Diffusion Tensor Imaging (DTI). This is like DWI except the direction of diffusion is recorded.

Arterial Spin Labeling (ASL). ASL saturates a section of the sample, outside of the field of view, such that you can image the saturated blood flowing into the field of view. This can be enhanced with an injected contrast agent.

Chemical Shift Imaging (CSI). CSI takes advantage of the T2* effect, i.e., the local susceptibility differences. It can be a spectroscopic method as well. This can be enhanced with an injected contrast agent.

Dynamic Contrast Enhanced MRI. (DCE-MRI). DCE-MRI requires a contrast agent to be injected, typically gadolinium based. The kinetics of the contrast agent uptake can be modeled to gain more information about the underlying physiology.

Dynamic Susceptibility Enhanced MRI (DSE-MRI). DSE takes advantage of the T2* effect of an injected contrast agent, typically iron oxide particles.

Blood Oxygen Level Dependent MRI (BOLD-MRI). Some people use BOLD-MRI and fMRI interchangeably, forgetting that there are other functional images.  BOLD takes advantage of the T2* effect of deoxy vs. oxygenated hemoglobin in blood.

I’m probably forgetting some but the list is already fairly long.

Example:

The video and last two images are of a mouse leg DCE-MRI. In the video you can see the contrast agent uptake. This is a transaxial slice with the tumor at the top and muscle and femur at the bottom. The contrast agent uptake is plotted in the next image. It can be modeled to generate a parametric image, shown in the last image. The last example is a parametric image of the contrast agent transfer rate, denoted Ktrans. It gives an indication of the perfusion or vascularity of the sample. The red areas have high perfusion with the dark blue is very low.

#ScienceSunday  curated by Allison Sekuler Rajini Rao Robby Bowles and me. Don’t forget to circle ScienceSunday it makes it easier to tag you when we re-share. Also tag #ScienceEveryday  the rest of the week because science is beautiful and science is everywhere.

#CHMedicalImagingSeries

Hopefully now you don’t think MRI is strange magic.

http://www.youtube.com/watch?v=11A8JZ-RDDo