2020: Identifying the next 20 years of need in In Vivo MR

Or using 2020 vision to visualize the future of Magnetic Resonance

Or Magnetic Resonance, from molecules to space science

Are you doing magnetic resonance research (MRI, MRS, EPR)? Are you keen on learning cool new stuff, brainstorming new ideas and networking with peers and leaders in the field?

Come to the Gordon Research Conference and Seminar this summer!

Gordon Research Conference on in vivo Magnetic Resonance: July 19-24 (open to all)


Chair: Jeff F Dunn Vice Chair: Kim Butts Pauly

Gordon Research Seminar on in vivo Magnetic Resonance July 18-19 (trainees-students/pdocs) Chairs: Manushka Vaidya and Melissa Haskell


Why come?

This meeting has been very influential in the development of magnetic resonance. It is one of those small meetings, in a beautiful setting, where people can meet others in their field and where ideas flow. This is the 20th anniversary meeting. In recognition of this, the meeting will have a bit of a historical feeling as well as a goal of brainstorming the next 20 years. It will cover many aspects of MRI including hardware, sequences and processing. From the first meeting, chaired by Michael Smith, to the 2018 meeting, chaired by Dan Sodickson, this meeting on Magnetic Resonance has been ranked among the top Gordon Research Conference meetings.

If you go farther back, the current GRC evolved from the GRC on Magnetic Resonance in Biology and Medicine, which started in 1974. The last meeting, in 1998, was chaired by David Wemmer, had Alex Pines as a speaker, and MRI was a minor component.

As a special anniversary theme, we are asking speakers to think about major discoveries in their labs, and to wax profound about where thire field might go in the next 20 years.

What is a Gordon Conference?

My students have said that this is the best conference they have ever gone to. It is one of those small group meetings where ideas flow and friends are made. You will hear news from a range of MR fields—expanding your knowledge and contacts.

Gordon Conferences are a special genre. The Gordon organizes sites, and all the meeting logistics. The program is required to have time for discussion and there are no parallel sessions. Speakers are encouraged to include unpublished date. People often come and don’t present. They are there to learn what’s new and to discuss science with leaders and trainees. One of the unique things about the “Gordon” is that it is a closed meeting. You have to submit an application and obtain approval to register. There is no abstract book. Photographs are not allowed without specific permission. Thus everyone’s intellectual property is protected. This conference is aimed at learning what is happening at the forefront of field. People can, and do, discuss what is new in their lab—not just what is already published. It was the Gordon that hosted many of the early meetings where the idea of MRI was tossed around, and developed.

They GRC is about networking and discussions—and so there is plenty of time in the afternoon and evenings for getting to know other attendees. Our GRC is famous for a nice hill walk, swimming, and the famous soccer (football!) games. The GRC starts with dinner on Sunday, an evening session and meetings in the bar (a relaxing venue where you don’t have to have alcohol to have a good time).

Posters are encouraged so bring it on. These will be relaxed sessions where everyone will have time to meet people at the poster sessions.

What is the Gordon Seminar?

 This is a trainee only meeting. It runs from the day before the GRC starts, to the afternoon of the first day of the GRC. Most speakers and discussion leaders are trainees. Get to know your peers.

So—great science, cutting edge AND time to meet people—not just hear them while they blather on behind a podium.


Hints for attending a Gordon Conference/Seminar:

Attendees and speakers are encouraged to stay for the duration so you have time to make friends and go away with new colleagues. There are many late night brainstorming sessions sitting on the lawn with the stars overhead (hope for no rain!). There are organized social events every day including the now famous Kearsarge hike with fantastic views of New England.

Bring walking shoes, a bathing suit for the freshwater lakes and whatever sport gear you might want. Take in organized activities such as canoeing. Partake of the famous “last night” Gordon dinner of lobster (have I mentioned that the food is fantastic and the bar is cheap).

To register follow the links above for the GRC and GRS. Remember that it is a two step process where you apply, obtain permission and then register. We are looking for funding to help people with registrations and note that there is a diversity funding link on the conference homepage.

We look forward to meeting you.

Yours in Magnetic Resonance

Jeff F. Dunn Chair GRC

Kim Butts Pauly Vice-Chair GRC

Manushka Vaidya Co-Chair GRS Melissa Haskell  Co-C

Magnetic Resonance scientists– come resonate with us at the Gordon Research Conference

Are you doing magnetic resonance research (MRI, MRS, EPR)? Are you keen on learning cool new stuff and hanging out with leaders in the field.

Come to the Gordon Research Conference and Seminar

This post was about the 2018 conference. This is short update to say that the 2020 conference is July 19-24 at Proctor Academy and the Gordon Research Seminar for trainees is immediately before this (July 18/19)

Why? Let me count the ways!

Attendees and intrepid hikers from the Gordon Conference on In Vivo Magnetic Resonance—the famous Mt. Kearsarge hike.

My students have said that this is the best conference they have ever gone to. It is one of those small group meetings where you get to talk to everyone.

Gordon Conferences are a special genre. The Gordon organizes sites, and all the meeting logistics. The organizers can focus on creating a great program. The program is required to have time for discussion and there are no parallel sessions. People often come and don’t even present. They are there to learn what’s new and to discuss science with leaders and trainees. One of the very unique things about the “Gordon” is that it is a closed meeting. It isn’t “invitation”, but you do have to submit an application. There is no abstract book. Photographs are not allowed without specific permission. What this means is that everyone’s intellectual property is protected. This conference is aimed at learning what is happening at the forefront of field. People can, and do, discuss what is new in their lab—not just what is already published. It was the Gordon that hosted many of the early meetings where the idea of MRI was tossed around, ridiculed, and formalized.

The original meeting was “Magnetic Resonance in Medicine and Biology”. It ended for a while and was reborn in 2000 as “In Vivo Magnetic Resonance” with the late Chris Sotak https://www.wpi.edu/news/sotakinmemoriam at the helm. The chair this year is also the president of ISMRM, Dan Sodickson http://cai2r.net/people/daniel-k-sodickson

Challenging Assumptions About Magnetic Resonance Technology and Applications in a Changing World

July 15 – 20, 2018

Proctor Academy, Andover New Hampshire

Applications for this meeting must be submitted by June 17, 2018.


Posters are encouraged so bring it on. These will be relaxed sessions where everyone will have time to meet people at the poster sessions.

For the first time, this Gordon conference will have a “Gordon seminar” just before the main meeting. This is aimed at giving trainees a leg up about learning the technology and new concepts.

The Changing World of Magnetic Resonance: Old Physics, New Techniques July 14 – 15, 2018

Chairs: Scott C. Beeman and Carson A. Hoffman

Apply by April 14 to be eligible for consideration for an oral and June 16 for the conference.


So—great science, cutting edge AND time to meet people—not just hear them while they blather on behind a podium. Attendees and speakers are encouraged to stay for the duration so you have time to make friends and go away with new colleagues. There are many late night brainstorming sessions sitting on the lawn with the stars overhead (hope for no rain!). There are organized social events every day including the now famous Kearsarge hike with fantastic views of New England.

Kearsarge for fantastic views. Bring walking shoes, a bathing suit for the freshwater lakes and whatever sport gear you might want. Take in organized activities such as canoeing. Partake of the famous “last night” Gordon dinner of lobster (have I mentioned that the food is fantastic and the beer is cheap).

Yours in Magnetic Resonance

Jeff F. Dunn, co-chair and excited Gordon conference attendee

Communicating science—some ideas for newbies

I was asked by the international society of magnetic resonance in medicine to talk about twitter and blogging for science communication. Take home: Excite people with a story that is relevant to their experience, remove jargon (so much for including the jargony society name) and give the conclusion first! Here are some tips to get you started.

We are entering a new phase of science. In this new world, we are expected to make a more concerted effort to reach out and communicate with both scientists AND non-scientists. Why do this? How to do this?

Photo some @ismrm twits at #ismrm17     @jeffreyfdunn @Alex_leemans @badjiatef @silascribbles

I know blog is too short to answer all these questions but I hope to include enough to get you started. We scientists have isolated ourselves so much that the public don’t understand most of what we do. Many actually don’t trust scientists to be unbiased. You want to reach out but are a bit uncomfortable doing that. Many scientists don’t want to speak in public. The internet is designed for you. Twitter and blogging make it pretty simple.

Aim to excite, not to preach. Although we are tempted to explain why alternate facts are bad, leading by example will have more impact. If people get interested they will naturally learn. Keep blogs short, focused and backwards. By this I mean put the conclusions first and build the information as you go. Make it so one can read the first few lines and know what you are going to say.

Blogs can be useful to describe papers in layperson terms. You can use them to teach a subject. Research papers which are blogged about actually tend to have more citations. You might blog on a disease if you are working on that disease and target the public interest groups and patients. You might blog on how imaging works.

It is important to define your audience (demographic, etc). The style of writing and the subject should be consistent if you want to attract a particular group. Perhaps start with an anecdote about something that may relate specifically to your audience. Think of the elevator speech. Make a statement that will attract the person or group you are targeting. Try to understand your audience, whether a single person or a group. Who are you talking to? You would start a conversation differently if you are meeting your family, your research colleagues, a layperson who is sitting on a grant committee, a senior university administrator, etc etc. Have different opening lines or ideas for each audience regardless of whether you are sending a tweet or writing a blog.

How to blog can be a bit overwhelming. Ask another blogger. Blog software allows for creating categories so your blog might have different subjects with links to each subject.


It will take a bit of research to create your first blog. You need a site. You can go full on and buy your own domain. I use “godaddy” to purchase my domain and have an online host. I use wordpress to design the site. Universities often have software that allows you to create and host a website on the university server for free. Lots of websites also have free blogging options—do a search on blog software sites. Using the university is great if you are focusing on your own work. If you decide to blog about personal or other science topics, you might want your own site so there are no control or IP issues.

Read blogs. Get ideas. It is a wonderful and glorious online community of people writing because they are excited and want to reach out to people like you.

Check these out:

Magnetic Resonance in Medicine Highlights

just an editorial note: the MRM link above works of you click ismrm but not if you click the share symbol on the right. I don’t know why JFD




So, TWITTER. Short. Snappy, and with a lot of potential. Here are a few tips:

If you don’t want to tweet yet—fine. It is the best online newspaper around. Use the search icon to search for keywords. Start following people, universities, interest groups, newspapers, journals, magnetic resonance etc. How about the organizers and some members of the scicomm panel: @mrm_highlights @jeffreyfdunn @stikov @erikaraven @fmrib_karla @mrimark @Dee_Kay_Jay

When using twitter to communicate science, it is OK to tweet a lunch photo and some travel pics now and then, this makes the person seem human. Make sure you are polite. Bad tweets can haunt you forever. Consider the audience (again). If you post a photo of a scientist, put something interesting in to say why someone might want to know about this person.

Put something in your bio that relates to the image you want to project in your twitter account. Put in a photo. You may not want one of yourself but put in something-an image, hardware, cartoon, you doing something that you like to do. The bio is short but without it you won’t get many followers. Why would someone follow you if they don’t know what you are going to tweet about?

-include a photo in your tweets when you can. People love images, pictures, etc.

-include weblinks. If you publish a new paper you could tweet the link to the paper or pubmed citation. Tweet your lab website. These links make twitter very powerful in terms of conveying news. The tweet then becomes just a title pointing to the longer article you want to communicate

-include hashtags. #MRI #ISMRM17 related to the topic. Think about what someone might search for. Most hastags in twitter are too long and not too searchable.

-include @etc. By including someones twitter handle, the tweet will show up in their software as a mention. They will see it and have a higher probability of retweeting or reading it.

In conclusion, more info:

Thoughts on using social media as a scientist:


Thoughts on using twitter as a scientist:


AND, a peer reviewed article saying blogs will increase your publication readership! Enjoy cyberspace.

  1. Hoang, J. K., J. McCall, A. F. Dixon, R. T. Fitzgerald and F. Gaillard “Using Social Media to Share Your Radiology Research: How Effective Is a Blog Post?” J Am Coll Radiol 12(7): 760-5.

PURPOSE: The aim of this study was to compare the volume of individuals who viewed online versions of research articles in 2 peer-reviewed radiology journals and a radiology blog promoted by social media. METHODS: The authors performed a retrospective study comparing online analytic logs of research articles in the American Journal of Neuroradiology (AJNR) and the American Journal of Roentgenology (AJR) and a blog posting on Radiopaedia.org from April 2013 to September 2014. All 3 articles addressed the topic of reporting incidental thyroid nodules detected on CT and MRI. The total page views for the research articles and the blog article were compared, and trends in page views were observed. Factors potentially affecting trends were an AJNR podcast and promotion of the blog article on the social media platforms Facebook, Tumblr, and Twitter to followers of Radiopaedia.org in February 2014 and August 2014. RESULTS: The total numbers of page views during the study period were 2,421 for the AJNR article and 3,064 for the AJR article. The Radiopaedia.org blog received 32,675 page views, which was 13.6 and 10.7 times greater than AJNR and AJR page views, respectively, and 6.0 times greater than both journal articles combined. Months with activity above average for the blog and the AJNR article coincided with promotion by Radiopaedia.org on social media. CONCLUSIONS: Dissemination of scientific material on a radiology blog promoted on social media can substantially augment the reach of more traditional publication venues. Although peer-reviewed publication remains the most widely accepted measure of academic productivity, researchers in radiology should not ignore opportunities for increasing the impact of research findings via social media.





Act your Science: improvisation training at U Calgary

Dennis Cahill, Loose Moose Theatre: improvisation with science graduate students

Your talk is next. There are hundreds of people in the audience. Your heart is beating so loudly you wonder if the person beside you can hear it. What if you screw up? You can’t focus on the speaker even though you had wanted to hear her for years

Is this you before your talk—or before your thesis presentation, or a job interview? What if you could train to reduce that anxiety? What do actors do? These thoughts led me to create “Act your Science?” at the University of Calgary. Did it help? Read on!

I came across the idea of using improvisation training to improve science communication skills years ago through Youtube. Alan Alda, a well-known actor (including the “MASH” television series), applied his acting and improvisation training to help scientists improve their communication. He developed the Alan Alda Centre for Communicating Science at Stony Brook University. You can see some information here


There is a testimonial from Boston University in this link.


I stored that info. After all, I did drama in high school—this could be fun and interesting.

My interest in scicomm led me to setting up such an improvisation course although the journey didn’t start with that goal. I took the Banff Science Communication course with amazing communicators like Jay Ingram, Mary Anne Moser, John Rennie and more. I was surprised to see that improvisation was  included. The next incentive for starting an improvisation course came after I joined the Canadian Science Writers Association (now now the Science Writers and Communicators of Canada). I met Janice Benthin, the Executive Director. She had been thinking about organizing improvisation with Calgary members and had made contact with Dennis Cahill—artistic director of the Loose Moose Theatre company in Calgary and one of Canada’s top improvisation trainers.

It began to feel like we had an idea that might be achievable.

Who would come, and how would we pay for it?

I wanted to do something special for graduate students in the area of STEM research at the University of Calgary. I approached the Graduate Students Association for funding through their “Quality Money” program and voila—we had funding. I approached the Faculty of Graduate studies for administrative help and ideas—and voila, we had rooms and a recruitment plan.

A month later, “Act your Science” was born. I was in a room at the University of Calgary together with 15 graduate students, Dennis, and a lot of uncertainty about whether this was going to work.

In short, we had an absolute blast. The main theme running through the course was the idea of learning to fail gracefully in front of an audience. Training with this in mind greatly reduced “presenter anxiety”. The group began very tentatively as expected. There were a lot of pauses and embarrassed looks to each other. By the end, people were jumping up from their seats to volunteer. The transition from not wanting to be in front of people, to knowing you can  have a good time even if you make a mistake, was complete. The comfort level with presenting, even in those where English is a second language, was much higher. In the final evaluations, everyone said that their ability to communicate was improved.

And, bonus, we learned even more. A second big theme was to “be in the moment”. We learned how to focus on the message, the story, and the others on stage—all while maintaining connection with the audience. We learned to trust that a story will unfold, even if it is not memorized. This lead to the presentations being much more relaxed and less forced. The presenters became communicators and not just scientists repeating memorized sentences. We learned to trust that if we walked up in front of an audience, we had the skills to engage without memorizing. During the first course, one of the “English as a second language” students attended a conference where they won the best podium presentation! Don’t just rely on my word. Here is a blog from Jennifer, one of the students.


So, success. And fun.

We played games and laughed. We bonded as a group, through shared embarrassment and success. We learned to steal each other’s hats, to speak in one voice, to think in the moment, to make connections with the audience and to be acutely aware of others. This was all done through games, many off which would sound a bit silly if I just described them.

The games gave us the practice and confidence to talk to an audience (not just AT the audience) and, when you forgot your line or idea, to fail gracefully. After all, isn’t worrying about those problems what makes you anxious before speaking to an audience.

Imagine not having that anxiety.


Should science communication societies like the Canadian Science Writers Association limit senior roles to journalists

Photo from a David DiSalvo article http://www.forbes.com/sites/daviddisalvo/2011/08/08/why-scientists-and-journalists-dont-always-play-well-together/#42935dcf1dec
Photo from a David DiSalvo article

In Canada and the USA, the role of media based science journalists in societies focused on science communication vs. people who write about science (scientists, public information officers, bloggers) is currently under debate. Contrary to the idea that truth and integrity will suffer with an open door policy, I expect that impartiality and “truth” in science writing will be improved if non-journalists are allowed equal access to science communication organizations and societies.

Some background: I’m a Professor in the University of Calgary. My job is to create new knowledge and to teach (mostly graduate students). I need grants to do what I do. Given the shortage of funding in Canada, I spend a most of my time applying for grants to do my work.

For good reasons, there is a growing requirement to undertake “Knowledge Translation”. Agencies are encouraging scientists to take a more active role in communicating what they discover. KT in my field could be working with clinicians teaching them about new discoveries in MRI. It also includes reaching out to disease based societies and to the general public. Big research grants have been turned down when this KT portion is underdeveloped. KT is also a growing portion of my annual report. Not only do I list my papers and students, but also what activities I do that fall under a communication heading. Since I enjoy communicating, this isn’t a hardship. My biggest reason for committing my time though, is that regular people pay my bills—mostly through their taxes. We, as scientists, need to let people know what has been discovered and, equally importantly, what remains to be discovered. Why do science!

I’m excited being encouraged to reach out. I want people to share my excitement about discovery, and I hope that by doing so our society will become more engaged. OK, this is a tall order. I aim to engage one person at a time and I assure you, there have been wonderful moments when I’ve been able to change a response from “huh?” to “wow!”

I’ve been asked if I’m a science communicator. After replying with what I do, I’ve had both a “yes you are” and “no you aren’t”. I was puzzled. Surely if I communicate science, regardless of my job, I’m a communicator.

Ahem, this is sacrilege, according to some. Why?

Mainstream, or media journalists were the founders of many science communication societies. In the good old days, these people dominated the science communication environment, both in skill and in numbers.

Things are changing. Everyone with access to a computer and the internet can set up a blog site and do science communication. One notable communications group include those that make press releases for universities and other research organizations. It is the clear job of these people to make the discoveries sound amazing, groundbreaking, game changing and unique. Scientists themselves are doing more communication.

So, what is the problem? As well laid out by the President of the CWSA, Tim Lougheed, in an email to the CWSA membership, there is concern that some individuals, such as a public information officers (PIO), are not bound to the same high standards of academic journalism and so may mislead people with inappropriately positive press releases. I would add that scientists may also distort their own work for their own benefit. In addition, those with products to flog or agenda’s to support could actually lie about their findings.

If the CSWA allowed everyone who does science communication an equal role in the society, then, according to Tim Lougheed, members are concerned that “the CSWA would lose credibility as a touchstone of journalistic integrity.”

An important point was made by Tim–that the CSWA played a significant role in highlighting the muzzling of scientists by the last government. Only an independent journalist could have worked against that mandate. Unfortunately, this is not a clear reason to protect journalist roles in the society. I’m sorry to have to point out that I know journalists who would not speak out because they held federal grant funding in the area of science communication. What would have happened if they had been President of the CSWA during this period? I could also imagine a situation where a journalist works for a publication with an editorial view that could reduce the impartiality of the journalist. Just by having a journalist at the helm, does not ensure an unbiased or unfettered leader.

I agree with the problems. But I disagree with introducing protectionism. Be careful about labeling people within a group as universally having a lack of integrity. As a scientist looking at the field of science journalism, I am often appalled by the extent that media journalists will happily buy into the “groundbreaking” jargon, writing headlines and text that are clearly aimed at improving readership or being “click bait”. One has weak legs to stand on when describing media journalists, as a group, of having a higher level of integrity than any other science writing group.

For these reasons, I strongly disagree with limiting the role of members in the CSWA. I think the main argument is unfounded.

On top of that negative argument, I have a positive one. We need to work together and to learn from each other. People who are doing press releases for universities are often just rephrasing what the scientist themselves have written. The scientist, in turn, often sees the publicity as a good way of improving their annual report or the justification section of their next grant. All of us need to find a way to guide the general public to accurate and unbiased science based information.

If we put these communicators in the same room through chapter meetings, the annual conference, emails etc, and truly get to know the goals and limitations that each group has, then the results will certainly be better communication. If enough scientists and PIO’s hear the concerns of journalists, perhaps press releases will be more appropriately tempered. The scientist may learn better writing skills and the PIO’s may feel more empowered to obtain clarification from the scientist. Journalists will have more access to members in all aspects of science communication—which gives them more opportunity to find stories and to fact check. Working together will promote a common good.

Perhaps instead of targeting a group, the CSWA should focus on how the constitution and mandate of the society could be written to clarify the role of the society and its officers, to write in an obligation of impartiality and the option of abstention if an officer is restricted by pressure from their own work.

Also, the society president is elected by the society, which puts some limitation on the individual. Don’t make this a two tiered organization.

I only see benefits to inclusion. I, for one, look forward to working with the CSWA, and learning from media journalists, as my career evolves to include more science communication.

Let’s learn from each other instead of putting up artificial barriers based on emotionally driven perceptions of who has more integrity.


DSC_1776Moreau F1, Yang R2, Nambiar V3, Demchuk AM4, Dunn JF5.

Near-infrared measurements of brain oxygenation in stroke.

Neurophotonics. 2016 Jul;3(3):031403. doi: 10.1117/1.NPh.3.3.031403. Epub 2016 Feb 11.


You are having a stroke. Luckily you know “FAST” an acronym that stand for Facial drooping, Arm weakness, Speech difficulties and Time. These are key symptoms. You or a friend called for an ambulance.

“Time is brain”. The quicker you obtain treatment the better. The current care is to arrive at a hospital and have CT imaging quickly. The CT will tell whether there is bleeding. Some CT’s give an excellent view of the size of the stroke. What the doctor doesn’t know, is how severe the stroke is within the stroke region. A stroke is a low flow condition. The blood oxygen carrying protein—hemoglobin—looses oxygen. The tissue becomes hypoxic (low oxygen). The severity of the hypoxia is likely to relate to outcome. CT doesn’t tell you much about severity.


So, is there another option?

Yes, near-infrared spectroscopy (https://en.wikipedia.org/wiki/Near-infrared_spectroscopy). As a plug, the main society interested in this technology in brain is the society for functional near—infrared spectroscopy or fNIRS (http://fnirs.org/ )

NIRS involves shining light into the brain and measuring the light coming back. In effect, we are measuring the color of the blood as it goes from the red oxygenated blood to blue deoxygenated blood. This provides us with a measure of how hypoxic the brain is. The photo shows me with a NIRS pad placed on the forehead. The fibres are fibre optics that carry the light to and from the head.

This year we published one of the first attempts to apply NIRS in the hectic acute care setting of a stroke patient arriving at the hospital. We used a NIRS method called frequency domain spectroscopy, which adds the key ability to quantify oxygenation between subjects. With this, in a few seconds, we could obtain a measure of the level of oxygenation in the brain of the patient. We could get a marker of severity.

This was a small pilot project to show proof of principle. Thanks to the journal “Neurophotonics” (http://spie.org/publications/journals/neurophotonics) for letting us publish this observational study. In future, perhaps a NIRS measurement will be used in an ambulance to help assess the severity of the stroke even before arriving in emergency.




Are the wires in the brain damaged after concussion?


cropped-mouse-spinal-cord-DTI-600-1.jpgDiffusion tensor MRI showing breaks on long fibre tracts when myelin is lost. This example is from a model of multiple sclerosis. See explanation below. Thanks to the team at the Experimental Imaging Centre and Dayae Jeong.


What is injured in your brain after a concussion? It is pretty obvious that something isn’t quite right. There is a list of symptoms in the sport concussion assessment tool three, the SCAT3, that you can look at for a range of symptoms.


The brain has long communicating fibre bundles called nerve tracts. These are clearly visible on MRI. The problem that MRI researchers have had in the past is that the changes are very subtle and not visible on standard MRI’s.

To overcome this problem, MRI groups have been working intensely to make the images more sensitive to the injury. There are MRI methods, called “sequences” by MRI specialists, which are showing promise as being sensitive to structural injury. These sequences are sensitive to the amount of myelin. Myelin is the covering on nerves that helps the signal travel down the nerve. When you lose myelin, as occurs in conditions such as multiple sclerosis, the nerve doesn’t function as well. If the myelin doesn’t regrow, the nerve may die.

Clinical MRI systems are actually imaging protons and the most abundant source of protons in the body is in water. So MRI is really imaging water. The trick to making contrast in the image is to make the sequence sensitive to things that can change in the water.

For instance, water can diffuse or move. In the brain, water diffuses fairly readily along fibre tracts but does not readily diffuse across a tract. This is because myelin is similar to soap, and it repels water. An MRI sequence called diffusion tensor imaging has emerged which is sensitive to the amount of water and the direction the water is diffusing. If water diffuses randomly in all directions, it is called anisotropic diffusion. If the diffusion has a directionality, it is isotropic. The measure of this is the fractional anisotropy or FA.

If myelin is damaged, water can more readily diffuse in all directions and the FA will decline. Such changes have been observed indicating that myelin may be damaged in certain regions of the brain after mTBI.

Dean, P. J., J. R. Sato, G. Vieira, A. McNamara and A. Sterr Long-term structural changes after mTBI and their relation to post-concussion symptoms. Brain Inj: 1-8.

Shenton, M. E., H. M. Hamoda, J. S. Schneiderman, S. Bouix, O. Pasternak, Y. Rathi, M. A. Vu, M. P. Purohit, K. Helmer, I. Koerte, A. P. Lin, C. F. Westin, R. Kikinis, M. Kubicki, R. A. Stern and R. Zafonte A review of magnetic resonance imaging and diffusion tensor imaging findings in mild traumatic brain injury. Brain Imaging Behav 6(2): 137-92.


Another sequence that looks at myelin is called quantitative T2. A very specific, not widely available variant is called imaging myelin water fraction or MWF. The University of British Columbia MRI group has been a leader in this area. They looked at MWF in athletes and, indeed, found reduced MWF along major fibre tracts in brain. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150215

Again, this supports the idea that damage to myelin occurred.


Wright, A. D., M. Jarrett, I. Vavasour, E. Shahinfard, S. Kolind, P. van Donkelaar, J. Taunton, D. Li and A. Rauscher (2016) Myelin Water Fraction Is Transiently Reduced after a Single Mild Traumatic Brain Injury – A Prospective Cohort Study in Collegiate Hockey Players. PLoS One 11(2): e0150215.


Another sequence is called magnetization transfer imaging or MTI. This one looks at how water interacts with surrounding chemicals and how those chemical transfer some of their MRI related characteristics (or magnetization) to water. This is where the label “magnetization transfer” arose. One can design a sequence such that a lot of magnetization is transferred to water if myelin is present, but not much if myelin is not present. So the MT declines as myelin is lost.

There has been less work on MTI, but I expect to see a lot more. What has been done though, is consistent with the other methods. A decline in MT has been observed.


McGowan, J. C., J. H. Yang, R. C. Plotkin, R. I. Grossman, E. M. Umile, K. M. Cecil and L. J. Bagley (2000) Magnetization transfer imaging in the detection of injury associated with mild head trauma. AJNR Am J Neuroradiol 21(5): 875-80.

Narayana, P. A., X. Yu, K. M. Hasan, E. A. Wilde, H. S. Levin, J. V. Hunter, E. R. Miller, V. K. Patel, C. S. Robertson and J. J. McCarthy (2014) Multi-modal MRI of mild traumatic brain injury. Neuroimage Clin 7: 87-97.

So, there are three MRI methods that have been used to show a loss of myelin after concussion or mTBI. This is worrying as it is very difficult to re-grow myelin to its original form. It is encouraging as there are imaging methods on the horizon that may help identify the extent of injury after concussion.

Diagnosing concussion is one thing, and we probably do that pretty well now. However to manage the injury we need to know the magnitude of the injury, where the injury has occurred, and whether the injury has recovered. This is the holy grail of brain imaging in the field of concussion research.

CONCUSSION: Stealing your mind

DSC_1776Dear everyone suffering from concussion, or trying to help someone who has a concussion:

Here is a podcast series on concussion.

CONCUSSION: Stealing your mind

Episode 1 is about concussion–what is it

Concussion is also called mild traumatic brain injury or mTBI. It is a brain injury. The symptoms are extremely variable.

Episode 2 is about diagnosis of concussion.

I interviewed Dr. Karen Barlow from the Alberta Children’s Hospital.

For most people, diagnosis is done with a low bar—by this I mean few things are needed for you as a coach or parent to consider concussion as being likely.   I recommend you download and read a great resource—the statement on concussion in sport (or the SCAT3).


Consensus Statement on Concussion in Sport—the 4th International Conference on Concussion in Sport Held in Zurich, November 2012 Paul McCrory, MBBS, PhD, Willem Meeuwisse, MD, PhD, Mark Aubry, MD, Bob Cantu, MD, Jiri Dvorak, MD, Ruben J. Echemendia, PhD, Lars Engebretsen, MD, PhD, Karen Johnston, MD, PhD, Jeffrey S. Kutcher, MD, Martin Raftery, MBBS, Allen Sills, MD, and Coauthors: Brian W. Benson, MD, PhD, Gavin A. Davis, MBBS, Richard G. Ellenbogen, MD, Kevin M. Guskiewicz, PhD, ATC, Stanley A. Herring, MD, Grant Iverson, PhD, Barry D. Jordan, MD, MPH, James Kissick MD, CCFP, Dip Sport Med, Michael McCrea, PhD, ABPP, Andrew S McIntosh, MBiomedE, PhD, David L. Maddocks, LLB, PhD, Michael Makdissi, MBBS, PhD, Laura Purcell, MD, FRCPC, Margot Putukian, MD, Michael Turner MBBS, Kathryn Schneider, PT, PhD, Charles H. Tator, MD, PHD


Episode 3 is about concussion management. In this Episode I interviewed Dr. Karen Barlow from the Alberta Children’s Hospital (and Alberta Children’s Hospital Research Institute) and Dr. Chantel Debert from the Foothills hospital (and the Hotchkiss Brain Institute).

I hope this series gives you some good ideas.


I do research into brain—I study new imaging methods and I use those imaging methods to unlock secrets about brain injury and disease. We are working on a large project using light to image brain—a method that can monitor brain activity (functional near-infrared spectroscopy or fNIRS) while sittng comfortably in a chair (or on a bike, a sports facility or medical clinic).

One of my main projects right now involves brain injury and concussion.


@imaginer (both the same twitter accounts)

Why are oxygen levels in brains of MS patients unusually low?

A photograph of blood vessels in the brain of an animal model of MS. They are green in this image because a green fluorescent dye was added, making capillaries visible under a microscope.
A photograph of blood vessels in the brain of an animal model of MS. They are green in this image because a green fluorescent dye was added, making capillaries visible under a microscope.

Yang, R. and J. F. Dunn (2015) Reduced cortical microvascular oxygenation in multiple sclerosis: a blinded, case-controlled study using a novel quantitative near-infrared spectroscopy method. Sci Rep 5: 16477.

link to paper here (open access)


Runze and I just published this paper. It has two major new findings. One is that, in about ½ of patents with MS, the brain shows signs of hypoxia (unusually low oxygen levels). This is based on quantifying the amount of oxygen bound to hemoglobin in the microvessels. The other news is that we could obtain a measure of brain oxygen using a method that is easily translatable to a clinic, doesn’t hurt and only takes a minute. It is less inconvenient than having your blood pressure measured in your arm. As we move forward, we have to find out why this hypoxia exists—could it be a totally new measure of the amount of inflammation in brain? I’m sure it will tell us something new and may become a new method for detecting treatment response.

In my opinion, this paper opens up a totally new way of looking at MS—much like MRI did when they first showed that plaques existed. We are taking steps towards understanding what is changing in the brain of patients with MS.

Let me explain.

Hypoxia is a term for low oxygen. If you climb a mountain, there is less oxygen and your body is hypoxic relative to a person living at sea-level. Different methods are used to measure oxygen in brain because a direct measurement is pretty difficult—unless you implant a probe to quantify oxygen. In our study, we used a method called near-infrared spectroscopy or NIRS.

Hemoglobin is a protein in the blood that carries oxygen. If all hemoglobin has oxygen bound, then the oxygen saturation is 100%. Light is absorbed differently if the hemoglobin is bound to oxygen or not. That is why blood in arteries is red and blood in veins is more purple or bluish in color. With NIRS, we shine light into the head and quantify the amount of oxygen bound to hemoglobin, by looking at the different color of light coming to our detector. The method focuses on the small vessels, like the ones in the image above, where oxygen is being transferred into the brain (the capillaries and microvessels). Most NIRS can’t quantify between subjects. Our method uses frequency domain NIRS to obtain absolute values. Big words, but the main point is that we can get an absolute measurement of the oxygen saturation of hemoglobin.

We found that about ½ of patients with MS were hypoxic—using the definition that the amount of oxygen bound to hemoglobin was lower than in control subjects. This wasn’t caused by low inspired oxygen, or an inability of the lungs to work. The low oxygen related to a low delivery of oxygen to the brain relative to how much is being used. A kind of supply problem.

It is too early to say if this hypoxia is damaging to the brain. The brain is pretty tolerant of low oxygen. It is very likely that the hypoxia will change how the immune response functions in the brain. Hypoxia could make the immune response worse.

A second large benefit to our paper is we show that our NIRS method is capable of detecting the hypoxia. The method is easy to use and only takes a few minutes of your time. It involves holding a small pad against the forehead for a minute.

Now that we have shown that hypoxia exists, and that we can measure it, the next chapter begins. Why is it there? Is it a marker of unregulated inflammation? Could we use it to tell if anti-inflammatory drugs are working? Inflammation can damage the blood vessels in a way that changes how flow is regulated. Cells responsible for Inflammation can also use a lot of oxygen. Should we re-investigate oxygen therapies? Could it be that major oxygen therapy trials didn’t show significant results because they only worked in the patients that were already hypoxic? At the time of the trials, we had no way to tell, before treatment, if the brain was hypoxic or not so all patients were treated equally.

We have a new method and are now showing that it is sensitive to changes in the brain of patients with MS.

Another cool part of this study is that the funding to do it came from undergraduate student salary grants. This was not a big, well funded study. We cobbled together money for Runze (we wrote this while he was an undergraduate student). Most of his funding was from Alberta Innovates Health Solutions. The equipment funding came from AIHS and Canada Foundation for Innovation.


The skiers guide to growing your own heel spur

An earlier version was Published in the Fortress Alpine Ski Team newsletter


An earlier version was Published in the Fortress Alpine Ski Team newsletter

Our adventure into heel spur growth began last year when our son was 12, and skiing every moment he could. There was a two week period where they were racing 3 days each week and adding training on top. Everyone was exhausted—too much tuning, being cold, sore muscles and general fatigue. At the end of this, “Manchild” pulled his socks off to show his coach his sore heels and, “ voila”, he had large growths on the back of both heels, just outside of the centre line. They were over a cm deep, large enough to name, angry red and very sore.

So what happened, what is it, how can you prevent it and what can you do about it? Depending on the location on your foot, these bumps can mean different things. The ones at the back of the heel, like my son Robert’s little friends, are at the insertion of the Achilles tendon and the bone.

Here is the sum of my meager knowledge. The boot fitting community is, to a large extent, sure that the growth is due to poor boot fit. This is usually because they are too tight, but they also might be too loose. The latter can cause your foot to bang against the back of the boot. Good fitters can find the sensitive site and grind a pocket or blow the boot out to relieve the pressure. But hold on—is this all there is?

I dug more into the literature and pestered my colleagues at the University of Calgary. Their input is unofficial—in that I nabbed them by email or in the halls, and launched into my characteristic gambit “This is really interesting what do you think?” You see, I don’t totally agree with the bootfitters. If it was just mechanical, why was there no other bruising? If something is growing, the body has to also grow new blood vessels to feed the bump, and that usually involves inflammation. If the tendon is inflamed, can the bump also be caused by Achilles tendon injury?

Dr. Benno Nigg is the Director of the Human Performance Laboratory at the University of Calgary. He is also a good neighbor, although he feeds the deer– much to the consternation of the gardeners in the neighborhood. He has worked with Nike and Adidas on high performance shoe design, and has had contracts with the national ski team concerning boot fitting. Benno thought the tendon injury theory had some merit, and thought that pre-exercise active stretching of the tendon may help a lot to prevent further injury. What the heck, good stretching won’t usually hurt so it’s worth a try.

Dr. Preston Wiley is a sports medicine physician in interested in “overuse injuries” in the Roger Jackson Sports Medicine centre at the UofC. He had a PhD student working on reducing pain associated with the bone spur. When I told him Robert was 12 when it happened he exclaimed—“Sever’s disease, it’s relatively common when boys are 12 and girls are 11”. http://kidshealth.org/parent/medical/bones/severs_disease.html# .

Sever’s disease is an acute injury to the growth plate at the site of insertion of the Achilles tendon. It comes on quickly, it will generate a bump, and the pain will go away in 1-2 years as the site heals up. Older athletes get bumps in the same area, but these are called “pump bumps” which alludes to the fact that ladies in high heels get them too. This is more what the boot fitters are thinking of, in that it’s caused by a combination of tension on the tendon and rubbing of the insertion. So the bump might be from rubbing, but keep in mind it may be a growth plate injury, and in part it relates to tendon injury. Also, it isn’t usually bone. It’s usually scarring of the tendon.

So, the bump can be caused by more than one thing. I suggest that f there is acute pain when you are young, try to see a sports medicine physician. The standard pump bump is only alleviated by VERY active icing after your sport and reducing the rubbing. Get on the problem early and fast. Working through the pain in this case will only cause you more problems. Work on the boot fitting. Once the bump hardens and calcifies, there may not be much you can do about it. From our experience, naming them at least makes it more fun to have them.