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
http://arxiv.org/pdf/1206.1148v2
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 (http://goo.gl/LTWUf)
Medical Imaging 101 pt 2: CT (http://goo.gl/IHaFw)
Medical Imaging 101 pt 3: MRI (http://goo.gl/UVbiU)
Functional vs. anatomic image (http://goo.gl/UTPK7)
Visible Human project (http://goo.gl/cv2xU)
Eye of Horus post (http://goo.gl/qpxyh)
Image sources other than the above article:
Lung and brain CT images (http://goo.gl/HHhqSJ)
CT Heart (http://goo.gl/eqbFde)
#ScienceSunday
The MIT article mentions the omission of a discussion of cost for these new technologies, and the importance of spreading the already existing imaging techniques to the entire world and not just the richest parts of it, but I’d be interested to know how feasible you see such a thing being. These imaging techniques all rely heavily on processing power, which is expensive, and use imaging machines which are large and expensive and require a degree of precision in production that makes local third-world manufacturing infeasible.
Processing power gets cheaper every year, but is the same true of MRI or CT machines? Or is there a way to make a “netbook” MRI that may not be as precise but still provides the same essential utility of a more expensive unit to enable wider availability?
Thanks for the question Stephen Baird. Manufacturing these imaging systems in a third world country isn’t feasible and also isn’t necessary. Many emerging countries have CT and MRI. They might not have the latest but they surely have something. The processing power really isn’t an issue as they would likely not be using them for research. Many of these 3D techniques can be done with a graphics card that you can get off the shelf. The image scanners and software is more expensive than the graphics or computational processing.
There are less expensive, i.e., lower magnetic field MRIs but they are not really applicable. The easiest solution is to purchase older imaging technology, second hand.
Chad, very nice images. Can you comment on the benefit spatial resolution can have on the visualization work? And do you see the emergence of increasing field strenghts for clinical MRI as an important tool for visualization of smaller sized structures, like the hippocampus for example?
Thanks Jose Muniz for the question. I’ll get to it later today.
Sorry for the delay Jose Muniz. In general higher spatial resolution is always a benefit. You can see finer details. For 3D visualization work, you have smoother transitions from one slice to the next. You can see the slice boundaries in the CT image of my skull. You don’t want to trade spatial resolution for signal. So as you mentioned, higher field strength allows for higher spatial resolution. Some hospitals have 7 Tesla systems. I don’t see a huge push to go higher than that, in general. 3T images of the hippocampus good in many cases. For some of the diffusion tensor imaging, working is being done to great better gradients rather than pushing for higher field, clinical scanners.
Thanks for the reply! I’m always curious about the perspective of those that work with clinical MRI. I’m a grad student that works with high field MRI for preclinical work. Do you attend ISMRM?
Yes, Jose Muniz I attend the ISMRM as much as possible. I think Milan might be out of the question due to the sequester and recent gov shutdown. I don’t do a lot of clinical work. I did some work on human prostate DCE-MRI. Other than that, most of my work is pre-clinical and multi-modality. Where are you doing your grad work?
I’m at Florida State University and the National High Magnetic Field Lab
A friend of a friend just graduated from there.
Cool. Not sure about ISMRM here too, although Milan sounds awesome. Any conferences out there for medical visualization?
SPIE http://spie.org/x12166.xml
and ISBI http://biomedicalimaging.org/2014/category/uncategorized/ are two conferences that come to mind.
My friend Christian Wietholt, who works for FEI that makes Amira, might have suggestions for you.
Awesome. Thanks!
I don’t think there is anything specific for medical visualization. RSNA might be your best bet.
IEEE MIC isn’t bad either.
very cool
Thanks Global Health Lab and Chasing Orgasm author Roland J. Ruttledge
You’re a fraud as well
You are a troll, Hayden. Goodbye.
A cell isn’t an organism ! Got it ! Why don t you ask vets who know plenty ( at least they should ) about animals how this or that might affect their organisms … even in the theory one could devellop something instead of relying on hard evidence ( which looks like hard cash to me ) and so on … you are not interested because the science nerds always come back with ” can you prove this ? … well sure Nixon wasn t guilty of any regularities untill someone came
and could provide the evidence … same with you … the myth of science helping humanity … you are bound to the private sector who is heavily financing your research … and who is the private sector ? Well pharmacical companies … what do they want ? The market ! Like the German car industry is responsable for climate change having cheated for years and now OH wonder we all discover it … and when soneone before said this ?
Wrong thread Charlotte Boisson. You clearly don’t know what you are talking about. Rajini Rao and I are funded by the federal government. You can look it up. We have nothing to hide. We are not funded by pharmaceutical companies. Funny you should mention German cars. I drive a VW. Clearly my checks from big pharma are going to the wrong address or I’d be driving a Ferrari.
I am happy for you if you have good ethics ! But clearly some people don t … and they are linked to research … bad or good I cannot tell … animal right activists always check … if your work is clean .. I am sure they won t mention you … but your work has consequences … and they are not always good !
I am not a vet or a person in direct contact with them but all these associations working on it have made things progress … and I am sorry but I don t think you make science progress … on the contrary … that s my opinion ! Off course ! You think main stream … that s why ….
Sorry that you have to deal with these incoherent ramblings, Chad Haney . I had to remove her from the SoG+ community.
O.K ! I will read your link !
And tell you about it ! Have a nice evening ! No hard feelings !
Charlotte Boisson, if you really want to learn from reputable sources, I can provide you with more information. You are clearly misinformed. Perhaps English isn’t your primary language because your comments are rambling.
You say that I think mainstream. What does that even mean? You say that you are not a vet or a person in contact with them. I work with veterinarians all the time. You say my work has consequences and they are not always good. You don’t know about my work. I would argue that you don’t know anything about the topic of biomedical research.
I’ll give you one example. I was in the emergency room once and overheard the lady in the next bed. She had cancer and she said she was responding well to an experimental drug, sorafenib. At the time, I was working on that drug to show that it works with a type of cancer that it was not initially intended for. I’m not trying to say that my research helped that lady. However, that experience confirmed that what I am doing is meaningful and helpful for people. There are positive consequences for the work that I do. What do you do to help people?
I dare you to go to a hospital and walk up to a cancer patient and tell them they should die because your ignorance prevents you from understanding and appreciating research that involves animals. When your loved one is ill, tell them they should not take medicine because you are against research that uses animals.
When I meet a cancer patient, it makes me more determined to continue the work that I do.
The work I do actually helps reduce the number of animals being used as I develop non-invasive techniques. You should read more about the Three Rs.
Replacement, reduction and refinement.
http://www.ncbi.nlm.nih.gov/pubmed/12098013
Monitoring anti-angiogenic therapy in colorectal cancer murine model using dynamic contrast-enhanced MRI: comparing pixel-by-pixel with region of interest analysis.
http://www.ncbi.nlm.nih.gov/pubmed/22905809
+ Chad
I can not talk about cancer since I don t know much about it but I know there are cures to diabetes known since antiquity and were successfully used for milleniums but no since molecular medecine is the thing ( only 100 or 200 years ago mind you … you prefer to developp your so calle I save the world medecine using animals who are only the victims of your ignorance 1 As for cosmetics
and research for cosmetics it has been banned only because intelligent human beings pointed out how useless and unnecessary it was ! And you are not one of them !
Devellopping cancer drugs is good in only 50 % of cases … talk to doctors they will tell you the same ! Because human beings are not an organism to be studied as a body but a whole complex person with emotions ( which you don t have ) and influence the course of the disease … frankly I don t think you are a big step forwards like another idiot says … when I talked
about main stream is that you aim to find a cure for millions of people and that cannot be good … where does that diseace come from ? Native American in the jungle never once in their entire life visited a physician and yet they are perfectly healthy … they have a good knowledge of plants ( those not contaminated by your heros ) and can do without you !
Research on animals is no necessacity contrary to what you say … it s unjustified … and not for the well beings of animals … I think you just talk bullshit … I will read your link though and take a closer look at your arguments.
Charlotte Boisson, why is it not good to find a cure for millions of people? Indigenous people have a life expectancy of 10 – 20 years less than non-Indigenous people.
http://www.aihw.gov.au/WorkArea/DownloadAsset.aspx?id=60129548468
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3796865/
In the healthiest cultures in the 1,000 years before Columbus, a life span of no more than 35 years might be usual.
http://goo.gl/vEV0R5
You have not given one shred of evidence to support your wild claims.
You say you cannot talk about cancer because you don’t know much. Well that’s one of your first true statements.
If you know the cure to diabetes, please share it with the rest of the world otherwise you are ten times more cruel than anyone doing research with animals. If you don’t know the cure to diabetes then you are confirming that you are an ignoramus spewing bullshit.
Yes ! Since the colonists from Europe destroy their inhabitats , not before !
There are well known plants used since antiquity used against diabetes … I will find the name … ( physicians in ancient Greece 2000 years ago described the symptoms
and knew it welll )
As for the pathways being blocked you are talking about the nerve system … this is also known since Antiquity in Chinese medecine they know how to block the transmission to the brain using the nerves centers or knots … nothing new here … why using drugs for this ?
How do you inject step by step a virus in a chimp and not let him suffer ? In the end when fully contaminated he will !
You inject morphine ? So the monkey is high all the time ?
Either he feels the virus either he is in a second state ? Please explain !
Charlotte Boisson, I’m not talking about the nervous system. Cell signalling involves cytokines, https://en.wikipedia.org/wiki/Cell_signaling, not the nervous system. You don’t even know what acupuncture is and yet claim it obviates the need for drugs.
You still have not provided any references for your claims.
Since you are not capable or willing to have a debate using substantiated evidence, I’m not going to waste my time any longer. I’ve been very patient with you. Again, you have provided nothing to support any of your statements.
Chad Haney Sounds like someone with PETA affiliations. Most impressed with your patience and tolerance.
Thanks Meg L.
Chad Haney You are probably more versed in this than I, but here goes anyway; During my period of “fandom” over Pixar, I gleaned that Pixar was originally a company developing medical imaging devices. John Lassiter was hired to animate said images and being an animator he began animating other things, setting Pixar on the way to becoming a movie studio.
Tomm Gundal, I think the Wiki on the Pixar Image Computer will answer your question.
https://en.wikipedia.org/wiki/Pixar_Image_Computer
My former boss had an old Pixar sign, probably from when Pixar was giving away Pixar Image Computers to try to get traction. I don’t know if he ever used the Pixar Image Computer or if it was just leftover from a sales pitch.
Good evening Chad Haney, how are you?
I have a research paper to write and I need radiological topographic anatomy images, I was wondering if there is an online source that you might know about that can help me with the images?
Susana M., off the top of my head, try Washington University in St. Louis, Radiology case studies.
https://www.mir.wustl.edu/Patient-Care/Clinical-Specialties/Nuclear-Medicine/Teaching-File
Thank you Chad Haney, will check it out.
Susana M., what’s your time frame? I might be able to image something for you using microCT.
Chad Haney, I have till Monday 23rd, I’m late on this one, had no idea it will be difficult to find the images online with proper description. So yesterday, I went to the campus’ library and found this book, http://www.editoradcl.com.br/Produto/394/manual-radiologia/13 , I’m going to use it as a reference, it has the images with detailed description, I think it will be enough. Thank you so much 😉
Susana M., just send me a message if you have any questions.
Thanks, very interesting
well-known about people’s have insomnia how should be the solutions for the persons can’t get sleep well! please if u have and idea could u explained to me doc;
Mercy Micumao, I’m not a physician and my research is in oncology. Sorry I can’t help.
A ciência está bem avançada em países que se importam com as pessoas. Será que em 2018 teremos mesmo o remédio para esclerose múltipla?
So nice sir
Just trying to find out what this is on me
Take over
Very interesting Chad, I just had catscan of head and neck and an mri of same area. I had fallen in April and by back hit cement first then my head it twice as hard. I have a concussion
Lisa Faro I hope you feel better.
hi Chad Haney. I need help with interprition of mri of patient with hemolytic uremic syndrome and deep hyponatremia. would you help me please?
Khayala Salmanova I can’t do that for HIPAA reasons. I’m also not a licensed radiologist. I’m an engineer, scientist.
One of my fave things on Flickr back in the day was a medical imaging technician who would post images from their trauma unit. Some of these were fascinating looks at how traumatic injury looks from the inside.
Lex Larson I wonder if I can find it.