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Medical Imaging 101 pt 1
My circled friends keep asking me to post a tutorial about what each modality can and can't do. So today for +ScienceSunday , here is part 1 of what I plan to be a series of medical imaging tutorials. I'll start out by listing the main players and then follow up each week with a detailed post about each modality. Some of them require a contrast agent or exogenous component. A contrast agent is a compound that is given either orally or intravenously to enhance the image.

Here's the list: x-ray CT, MRI, PET, SPECT, Ultrasound, and optical. I'll throw in EPRI as a bonus even though it is experimental (relatively speaking).

X-ray computed tomography (CT) uses a series of 2D x-ray images. Computer algorithms (hence the computed part) reconstruct the 2D projections (as they are called) into 3D images. The method is called Filtered-back projection (FBP) reconstruction. CT is best for visualizing bone but can be used for soft-tissue imaging in humans, especially with a contrast agent. It can have high spatial resolution but suffers from poor sensitivity.

Magnetic Resonance Imaging (MRI) MRI is the imaging version of nuclear magnetic resonance (NMR). Although MRI can image different nuclei, most MRI are tuned for protons. Those protons are predominantly from water. A large magnetic field and magnetic gradients are used to generate frequency data, called k-space. Unlike CT a simple Fourier transform is used to reconstruct the image from the frequency data. MRI is great for soft-tissue imaging. Bone, having very little fluid, is dark, i.e., without signal, in MRI. There are functional images that can be generated from MRI with and without contrast agents. It has high relative spatial resolution and moderate sensitivity.

Positron Emission Tomography (PET) requires a radionuclide. It detects pairs of gamma rays. Most pre- and clinical PET scanners include a CT scanner for anatomic reference. Its main use is with 18-F labeled fludeoxy glucose, which is an analog of glucose. FDG gets trapped in highly metabolically active cells. Therefore, PET is good at detecting tumors as they are relatively more metabolically active relative to say muscle. The raw data is somewhat in between CT and MRI. Coincidence events, i.e., the two gamma rays, are detected. The reconstruction groups these coincidence events into projections similar to CT but unlike CT the project cannot be used alone to visualize anything. The projections are called sinograms and they are used to generate 3D images. It has high sensitivity but relatively low spatial resolution.

Single Photon Emission Computed Tomography (SPECT) is another technique that requires a radionuclide. For those familiar with autoradiography, it uses similar radioisotopes. Unlike PET, SPECT tracers are most often a radioisotope linked to a ligand. Like PET, SPECT scanners often have a CT on board, for the same reason mentioned. Like CT, SPECT acquires a series of 2D projections, that are reconstructed into a 3D image. PET images two gamma rays and infers the position of the radionuclide. SPECT images the radionuclides directly. SPECT has even lower resolution than PET but has equal and sometimes better sensitivity.

Ultrasound (US) is an imaging technique that uses sound waves with a frequency above the human audible range, hence ultra. Most are probably familiar with US due to its use during pregnancy. As you can image, it is good for imaging soft-tissue. It's real strengths are portability, relatively low cost, and no radiation. It does have relatively poor sensitivity, poor spatial resolution, and poor contrast. Gas bubbles can be used for enhanced contrast. Also, US can be used for therapy via thermal ablation.

Optical imaging in medical imaging is either fluorescence (FI) or bioluminescence imaging (BLI). A near-field image (think standard photograph) is used for anatomic reference. Some newer systems are starting to use CT with optical. BLI relies on light emitting organisms. The most common technique is to genetically engineer an organism/cell to be bioluminescent via introduction of luciferase (think firefly). FL requires tagging a ligand with a fluorophore. Optical imaging is typically 2D but there are some systems that are giving either 3D or "synthisized" 3D. Optical imaging has high sensitivity and relatively poor resolution. Its strength is relatively low cost, small size, and ability to visualize cell signaling.

Electron Paramagnetic Resonance Imaging (EPRI) is like NMR but detects unpaired electrons instead of nuclei (protons). It requires an exogenous contrast agent. It has a long history in spectroscopy like NMR but is relatively new as an imaging modality. It uses a relatively low magnetic field and gradients. Unlike MRI, it typically collects projections, 2D sinograms like PET, and FBP to reconstruct. It's strength is the quantitative physiological environments that it can image, e.g., oxygen, pH, etc. It has relatively low resolution (on the order of PET) and high sensitivity.

Images below
The first image is a visual example of the machines and images they can produce. The second image helps understand the scale of what medicine is interested in. The third image is a graphic for sensitivity vs. spatial resolution. The final image is a table comparing the techniques.

Edit Next week will be a detailed post on CT, followed by MRI, and so on. Please post questions and they will be answered either here or in the appropriate subsequent post.

Edit 2 I'm only interested in 3D imaging. If people are really interested in 2D techniques like fluoroscopy or x-ray, radiographs, let me know. I'll consider discussing them.

#CHMedicalImagingSeries

#ScienceSunday    #ScienceEveryday

+ScienceSunday curated by +Allison Sekuler +Rajini Rao and +Robby Bowles and guest curator (me, +Chad Haney )
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Medical Imaging SS pt 1
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Wrong Times Two
That mummy you thought was an Egyptian singer is actually a castrated priest. And the images that some journalists (ahem, forbes.com) are calling MRI is actually x-ray CT. The video that's attached in many of the news articles mistakenly says magnetic resonance tomography, which is technically a thing but most people say magnetic resonance imaging or MRI. If you want to get all technical, it should actually be called nuclear magnetic resonance but the nuclear part is confusing and scares some people. For x-ray based tomography, it's confusing because sometimes you hear computed aided tomography or CAT scan and you sometimes hear CT for computed tomography. The x-ray part is often omitted. I guess CAT scan sounds better than CT scan, so you probably hear CAT scan more often outside of radiolgy. I prefer dogs and am in radiology so I prefer CT scan but I digress.

Either way, magnetic resonance requires protons, which typically means water. You can imagine that a mummy doesn't have much water. There are other techniques with magnetic resonance that can be employed but it won't produce the spectacular (detailed) images you often see with x-ray CT. Here's one example with MRI (note the emphasis of a hydrated mummy).

Magnetic resonance imaging performed on a hydrated mummy of medieval Korea
J Anat. 2010 Mar; 216(3): 329–334.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829391/

Anyway, it's a neat story about using x-ray CT to identify a mummy that's been in the Russian Hermitage Museum for a long time. It was thought to be the mummy of a famous Egyptian singer called Babat. It turns out that it's a castrated priest named Pa-kesh. The attached news article does a better job than Forbes. At least the Daily Fail version didn't say MRI.

Here's a direct link to the video if you're interested.
https://youtu.be/eR0wJrKd0VQ

If you need a refresher on how x-ray CT and MRI works:

Medical Imaging 101 pt 2: CT
http://goo.gl/IHaFw

Medical Imaging 101 pt 3: MRI
http://goo.gl/UVbiU

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Posting this for +Kee Hinckley. I'll explain later but you are welcome to guess what this is and what it is used for.
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Open Exploration of Vertebrate Diversity in 3D
Here's an interesting project funded by the National Science Foundation (NSF),
where they plan to use x-ray CT to image 20,000 vertebrate specimens. It reminds me of a small NSF project I was involved with. We borrowed 50 specimen from +The Field Museum and had 48 hours to image them all. You can read about that here:

Evolutionary forces - Working Together
https://plus.google.com/u/0/+ChadHaney/posts/Fsardnw7gBD

Here's two related posts:

Joy and Luck of Fixing a Leech
https://plus.google.com/u/0/+ChadHaney/posts/d16RZKfGWF7

BaSO4, X-ray Contrast
https://plus.google.com/u/0/+ChadHaney/posts/jLJWteP74TD

If you need a refresher on how x-ray CT works:

Medical Imaging 101 pt 2: CT
http://goo.gl/IHaFw

Have a great #ScienceSunday

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Technology is good, right?
You probably have heard a lot about artificial intelligence (AI) and self-driving cars. You probably think new technology and automation are good things; they make life better. If we look at politics and economics, one thing related to automation that's missing in the conversation is that automation takes jobs away. I'm not going to discuss if that's good or bad.

This article focuses on a more social aspect and how that relates to medical care. The article describes how the change from film based x-rays to digital x-rays. The file format is called DICOMM and I wrote about the before.
https://plus.google.com/u/0/+ChadHaney/posts/5XxbKYFix5q
I agree that technology has made it easier for non-experts, e.g., non-radiologists in this context. However, I also agree that we still need those experts. Even though I'm in radiology, I can say that there are times when I look at an MRI that's not related to my area of expertise and I struggle with the diagnosis.

I haven't been active with my medical imaging posts so I hope you enjoy this article as much as I did.

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Stat, there's a problem with my fMRI.
There are multiple versions of this news article floating around G+. I'm not sure if the popularity is due to schadenfreude or people applauding scientists for ever refining/correcting their work. Nevertheless, there are many things to correct and clarify in news about the "fMRI bug".

It's important to note that this is only for BOLD MRI, often called fMRI (functional MRI, which is a misused label) and this is nothing really new. Let me explain. I've written a lot about fMRI and it's drawbacks before (see links below). If you aren't familiar with what MRI is, you'll also want to see the Medical Imaging 101 on MRI (below).

There are two main imaging tools for imaging brain activity. BOLD MR and PET imaging.
BOLD-MRI stands for Blood Oxygen Level Dependent Magnetic Resonace Imaging. 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.e., the iron in hemoglobin has different magnetic properties depending on whether oxygen is bound or not. Positron emission tomography (PET) with F-18 labeled fluorodeoxyglucose (FDG), measures changes in metabolic activity. Putting the bug in statistical software aside for the moment, it's important to note that neither BOLD-MRI or FDG-PET measure brain activity directly. They measure oxygenation and metabolism, respectively. Also, note that PET directly measures metabolism, which we infer brain activity. BOLD-MRI indirectly measures blood oxygenation, which we then infer brain activity. You add on top of that issues with post processing and you can see where I have little faith in BOLD-MRI.

Here are to older post that demonstrate that the errors in BOLD-MRI post processing software are not new. In the first link, a graduate student made a mistake and noticed that the resulting image looked like any previous image she acquired. The second link talks about how the size of the smoothing kernel can effect the data and it's worth discussing because image resolution has improved and the kernel size has an effect.

When a blob is just a blob
http://goo.gl/Fx74F

Not functional fMRI
https://plus.google.com/u/0/+ChadHaney/posts/CP3dEwRWg7X

The discussion on voxels in many version of this news is misleading. A voxel is simply a volumetric pixel. Most people know what a pixel is and it's 2D. For example, your cell phone camera might have 8 megapixel resolution, i.e., 8 million pixels from 8 million sensor elements. A voxel is an element in a 3D image (don't be confused by 3D vision, i.e., 3D movies). Nearly all medical images are 3D. However, to save time, the third dimension, which we often call a slice, is thicker than the in-plane resolution. So a 100 micron in-plane resolution MRI scan with a slice thickness of 0.5 mm, would have a voxel size of 100 × 100 × 500 micron.

Another misnomer is "fMRI machines became available in the early '90s". There is no such thing as an fMRI machine. Any MRI scanner can do fMRI and fMRI means more than just BOLD-MRI as mentioned already.

In terms of a 'replication crisis' mentioned in the news article, they fail to mention that there is and has been a 'funding crisis' so scientists can't replicate experiments even if they want to.

Medical Imaging 101 pt 3: MRI
http://goo.gl/UVbiU

fMRI - What is love?
http://goo.gl/7gxK2

Whale of a story
http://goo.gl/xcAqX

Meta-consciousness Brain
http://goo.gl/MgJiA

Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates
Eklund A, Nichols TE, Knutsson H.
Proc Natl Acad Sci U S A. 2016 Jun 28. pii: 201602413
http://www.pnas.org/content/early/2016/06/27/1602413113.full

#fMRIblob #ScienceSunday  

h/t +Kee Hinckley 

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Helium Cache to the Bank?
Helium is important for MRI and MRI is important to literally see what's wrong with people. Think about it before buying a helium filled balloon. I wrote more about the helium reserve here:
https://plus.google.com/u/0/+ChadHaney/posts/99SpR28xBme
So does this newly found cache of helium mean we can resume wasting helium in balloons? I think it depends how fast and how economically they can start collecting the helium.

ETA
It's worth emphasizing that we can't make helium and it's so light that it escapes earth's atmosphere. Unlike nitrogen, for liquid nitrogen, we can't collect and liquefy it from our air.

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Betting on Nyquist
I placed my very first bet on a horse for today's Kentucky Derby. I have $20 on Nyquist who is a 3-1 favorite to win. There is a confluence of connections with Nyquist that relate to my interests: hockey and MRI.

Gustav Nyquist
In the attached article you can read about the owner of the horse Nyquist and his history of naming his horses after Red Wings players. Gustav Nyquist is a young-ish (26 years old) center from Sweden, who plays for the Detroit Red Wings. Although his production dropped a bit this season, he's still considered a pretty good player. Nyquist the horse, is slotted in the 13th position to start the race today (determined by lottery, I believe). My favorite Red Wing player is number 13, Pavel Datsyuk. Good bet so far?

Harry Nyquist
Dr. Harry Nyquist was a Swedish electrical engineer that emigrated to the USA in 1907, eventually working at Bell Labs. His contribution to science is used daily for people involved in communication systems and MRI.

The Nyquist sampling theorem states that the sampling frequency, i.e., how often you acquire the data, should be twice the frequency being sampled. The maximum frequency that you can measure is, therefore half the sampling frequency. In MRI, when the frequency of the sample is higher than the Nyquist limit, aliasing occurs. If you aren't familiar with aliasing in imaging, it's when undersampling causes a wrap around or fold-over artifact. See figure 15b in the review article by Morelli et al, linked below. You can also read my previous post about MRI basics to learn what k-space is and what frequency has to do with MRI.

What do you think, a good bet?

Links and references:
https://en.wikipedia.org/wiki/Harry_Nyquist

An Image-based Approach to Understanding the Physics of MR Artifacts
Radiographics. 2011 May-Jun;31(3):849-66. doi: 10.1148/rg.313105115. Review.
http://pubs.rsna.org/doi/full/10.1148/rg.313105115

Medical Imaging 101 pt 3: MRI
http://goo.gl/UVbiU

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Joy and Luck of Fixing a Leech
A group of researchers have used microCT to examine and describe a new species of leech, which they named after Amy Tan (the author of Joy Luck Club). The most important part is kind of buried in the Science Daily piece.

For objects smaller than a human, CT has horrible soft tissue contrast. MRI has significantly better soft tissue contrast, regardless of the size of the sample. However, microCT has better spatial resolution compared to preclinical or 'microMRI' if you will. This group used a microCT that is not intended for live specimen and can reach 5 micron resolution.

The research presented here is a fantastic example of how science works, i.e., building on previous work, especially if it is in a different area. For those of you who remember high school biology, you probably had to dissect a frog or something from a jar. That stinky liquid is formaldehyde, which is what preserves the specimen. It's known as a fixative. So this group looked at fixatives that are typically used in scanning electron microscopy. One of them was osmium tetroxide, which binds the metal osmium to give better contrast. The recipe that worked best was using AFA (alcohol, formalin (which is a variant of formaldehyde), and acetic acid) as the primary fixative, followed by osmium tetroxide.

Unlike the BaSO4 method I wrote about earlier, this method involves soaking the sample for several hours (6-12).

The other key part is in the visualization and image analysis tools. Identifying the various internal organs uses a tool called segmentation. Sometimes it's automated and sometimes you have to do it manually.

Since I'm heading out to walk my dog, I'll keep this short and give you a few links if you wish to read more.

Medical Imaging 101 pt 2: CT
http://goo.gl/IHaFw

Fast CT from GE Healthcare
https://goo.gl/AV6Z59

BaSO4, X-ray Contrast
https://goo.gl/O3GBgU

Medical visualization, it's what I see and do
http://goo.gl/PrwLx6

GE phoenix v|tome|x s scanner
https://goo.gl/aOsbv2

edit
Here's the Science Daily article.
http://www.sciencedaily.com/releases/2016/01/160121130702.htm

Full article here:
1. Michael Tessler, Amalie Barrio, Elizabeth Borda, Rebecca Rood-Goldman, Morgan Hill, Mark E. Siddall. Description of a soft-bodied invertebrate with microcomputed tomography and revision of the genusChtonobdella(Hirudinea: Haemadipsidae). Zoologica Scripta, 2016; DOI: 10.1111/zsc.12165
http://dx.doi.org/10.1111/zsc.12165

h/t +rasha kamel 

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Heart of a Knight
I meant to post this back on 3 December when the story was fresh. I was hoping more information would become available. However, it seems that it was only reported at the recent RSNA meeting and that's it. I'm very disappointed that they didn't show any CT or MRI images.

A group of imaging experts were called when five heart shaped urns were found during an excavation of the basement of the Convent of the Jacobins in Rennes, France. Several grave sites dating back to the late 16th or early 17th century were unearthed. The initial CT and MRI images were good but not diagnostic. The embalming fluid likely has alcohol which would cause chemical shift artifacts (read my MRI post to learn more). The CT would not have good soft tissue contrast and therefore would not have been helpful by itself. After removing the embalming fluid and "re-hydrating" the hearts, one was found to be healthy, three had signs of plaque on the coronary arteries and atherosclerosis and the fifth was poorly preserved.

I was also considering saving this until St. Valentine's day as they mentioned that one of the male hearts was buried with a female, likely his wife. You can read the whole news blurb here: https://goo.gl/gt51RS  

Medical Imaging 101 pt 2: CT
http://goo.gl/IHaFw

Medical Imaging 101 pt 3: MRI
http://goo.gl/UVbiU

#ScienceSunday  
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