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Chad Haney
I'm the medical imaging, Red Wings, Formula One, Tech guy.
I'm the medical imaging, Red Wings, Formula One, Tech guy.

Chad's posts

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Medical visualization, it's what I see and do
I was going to summarize an article about the history of medical visualization that was discussed in MIT Technology Review in 2012.
The Future of Medical Visualisation
However, I think that the #OpenAccess  article that they reference does a good job on its own. It's kind of strange to think of a review of a review of a review article.
From individual to population: Challenges in Medical Visualization

Rather than review the review of the review, I'll add a few comments and answer your questions. So read either the MIT Tech Rev article or the journal article and ask questions. This is an opportunity to talk to a scientist that works in the medical imaging field.

The article mentions multi-modal volume visualization. If you have been following my  #CHMedicalImagingSeries then you know that each imaging technique (modality) has strengths and weaknesses. Combining imaging modalities, like the MRI and CT below of my head, allow you to take advantages of the strengths and minimize the weaknesses. To get the best out of multi-modality imaging you need to be able to fuse the images. The technical term is image registration or some like image co-registration. There is a lot of research in just this technique to make it more automated. One common technique is called mutual information. Our brains can easily tell that the dark material in MRI is bone (e.g. my skull) and it should match the bright material in CT. Mutual information tells the computer to consider that bright could equal dark by normalizing the images first. The principal axes of the objects are also used to register (align/fuse) the two images. For therapy planning, both surgery (cosmetic) and tumor resection/radiation, multi-modality imaging can have a huge benefit. They mention that in 1993 Altobelli used multi-modality imaging to visualize the possible outcome of complicated craniofacial surgery.

Another use of medical imaging visualization is virtual colonoscopy. Visualization tools that you need are surface/volume rendering, skeletonization, and segmentation.
UCSF Radiology: What Virtual Colonoscopy CT Scans Look Like

Surface/volume rendering is just what it sounds like. The data is analyzed and the surface can be identified and displayed with shading and lighting such that it looks 3D. You can make it true 3D with the right equipment (3D glasses, 3D monitor, and software to split the data into left and right views) but that's not essential. It can't be emphasized enough that modern GPUs have made these difficult calculations become trivial. Some of the early animation work and medical image visualization required high end UNIX workstations. Now that same level of visualization can be done with a low-end gaming PC.

Segmentation is also, just as it sounds. There are automated and manual segmentation tools. For example in the heart and skeleton images below, the tissue of interest has been segmented out of the "background" tissue, e.g., the internal organs, muscle, etc. Again, there is research in this technique alone. Our brain can look at a medical image and identify parts of the brain or organs quickly. "Teaching" a computer program to do that automagically is very difficult, especially if there is motion due to breathing. In that case, you may have to use image registration to get rid of the motion blurring first.

Skeletonization is a process of identifying paths. For colonoscopy, that would be teaching the program to traverse the path of the colon. I've done work where we were measuring blood vessel diameters in a pulmonary hypertension model. Skeletonization was used to automatically identify each part of the vascular tree. From there, it was easy for the software to measure each diameter.

The first three images are fused images of a CT and MRI of me. The yellow surface rendered part is from CT as it shows bone (skull) very well. The grey-scale part of the image is MRI which shows soft tissue very well. The rest of the images are from a Toshiba 320 slice CT. In CT technology, a ring of detectors is used capture the signal from the x-ray source. Each ring is called a slice in clinical CT machines. For a while 64 slice was considered the best. Now 256 and 320 slice machines are becoming available. More slices means you can cover a larger area in a shorter amount of time. So highly detailed images of the heart can be acquired without motion artifacts from the beating heart. Likewise for the lungs.

Here's a few older posts that will hopefully help you understand the article.

Medical Imaging 101 pt 1 (
Medical Imaging 101 pt 2: CT (
Medical Imaging 101 pt 3: MRI (
Functional vs. anatomic image (
Visible Human project (
Eye of Horus post (

Image sources other than the above article:
Lung and brain CT images (

CT Heart (
Medical Imaging Visualization
8 Photos - View album

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Converting Housing Projects to Mixed-Income Housing
WBEZ just put together an informative article about the Chicago Housing Authority's failed plan on mixed-income housing. You often hear about the gun violence in Chicago. You often don't hear that the gun violence is concentrated in basically two neighborhoods, the far south side and the near west side. You also don't hear about how heavily segregated Chicago is. The segregation and gun violence are intertwined. Some of the areas with the highest unemployment are the same areas with high rates of gun violence.

So the promise of converting some of the crime infested housing projects into mixed-income housing sounds like a great plan. Unfortunately there really wasn't a plan, just a goal. Read on to learn some of the details.

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Here's an excellent summary of the connection of the Trumpelthinskin administration and Russia.
There have been so many news stories about the Russia investigations in the past week – from Comey's testimony to Flynn's possibly turning state's evidence – that I sat down and tried to pull everything into one place. Here you go.

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The Frisbee is mine, all mine!
but I can't throw it, if you don't give it back.
OK, but I must kill it first! <shake, shake, shake>

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Happy #FloralFriday 24 March 2017
My bulbs are doing pretty good. Snow drops are more or less over. Crocuses are still coming up. That's about it for now.

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For those who know +Philip Plait, you'll get an extra kick out of this Oatmeal.

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You otter have a break from politics

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Facts no longer matter
§ Confirmation Bias - the tendency to favor information that supports your existing view.

§ Cognitive Dissonance - action that contradicts reasoning, e.g., continuing to smoke when you agree it is unhealthy.

§ Motivated Reasoning - accepting information that supports what you already believe and giving extra scrutiny to information that is against what you believe.

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Go Away Snow, You're Late
Cleaned off my wipers, got back in the car, and this is how much snow covered my windshield (windscreen for the Brits).
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