Spring Break 2017

It’s been a crazy few weeks. We had two deadlines due the Friday of Spring Break, which as we all know in grad school is a productive time to get work done without the undergrads being around. Needless to say, it was a bit hectic!

The first of these deadlines was the American Society of Biomechanics conference abstract submission deadline. My advisor and I have been working on creating a new method to compute Achilles tendon moment arm in vivo, using motion capture and ultrasound (I’ll talk about this in a future post) and by Monday of Spring Break we were ready to start collecting data. I had received IRB approval a week prior, and so was able to test the first of my subjects. Over two days, I ended up collecting data from 8 people. Post-processing the data was a multi-stage process.

Step one involved going over the motion capture data in Cortex, labeling markers, and trimming the motion capture so it was synchronized to the start and end of the ultrasound data. While this sounds simple enough, I hadn’t used the post-processing tools in Cortex before so Monday and Tuesday nights were spent learning the software and labeling my trials. I had 6 dynamic trials plus a static and calibration trial for each participant. Lots of labeling!!

Step two took the .trc files from the labeled Cortex data and imported them into Matlab. I then digitized points from the ultrasound and ran the data through some custom-written scripts. As is always the case, my code needed editing as the results I was getting were a little bit ludicrous (70 cm moment arm?!). Eventually, we fixed it and we got some exciting results. The abstract was written by 6pm Friday evening and I was excited to sit back and relax for the weekend.

On Tuesday of this week, Snowstorm Stella hit State College and we got a rare snowday. While knee-deep in grading and doing all the jobs I’d postponed during deadline season (including tackling American tax returns for the first time), my email pinged. It was an acceptance to my first conference – ISBS in Cologne, Germany. I can’t tell you how excited I was. Of course, a flurry of activity ensued – applying for travel grants, editing the abstract in response to the reviewers comments, figuring out timing and costs and all the logistics that come with conference acceptances.

That’s a quick catch up of the craziness of Spring Break and the following 5 days. I’m hoping to update the blog shortly with some more detailed posts, and some interesting talks I’ve sat in over the past month or so. For now though, it’s time to get back to grading…

Finding your lab feet

Today I want to write a little about my frustrations in learning how to use different versions of equipment you already can use. I’m currently working on advancing a method of identifying Achilles tendon moment arm using ultrasound and motion capture. In both my undergrad and masters training, we learnt how to use MoCap – using the Qualysis system in a very guided step-by-step process in undergrad and using Vicon with a lot more freedom in my masters. I felt I had a relatively competent grasp on how to collect movement data using a passive 3D motion system. And then I started my PhD.


I came into a lab at a time where very little data collection was actually going on in the lab, and had to figure out how to use the systems here predominantly solo (with a little guidance from our lab tech). We run off the Eagle cameras and use the Cortex software from Motion Analysis Corp, neither of which I had prior experience with.


As with all motion systems, the first step was calibration. After opening all the cupboards in the lab, I found our calibration L and wand (in hindsight, asking our lab tech where things are should have been my first step. Oh well, you live and learn!). I figured calibrating would be the same as before – place the L on the center of the capture space (normally on the force platform), enter the capture space and wave the wand high and low making sure all the cameras see it sufficiently. This is how it works, but it took me a few times messing up before I found the screen in the software that shows all camera views and turns green when each camera is properly calibrated (data views, all cameras for those of you querying this).


Next up of course is data capture. My current testing involves markers on rods and an ultrasound probe so this is what I learnt the system with. A few trial and error attempts and I figured out the system. After testing a few times, I think I’ve got a handle on the way it works but I’ll feel more confident once I’ve run a few more pilot tests. My main apprehension at the minute is processing the data in Cortex after it’s been collected – especially with dynamic tasks which have the risk of marker drop out. I’ve been doing my analysis in MATLAB (which again is a whole new set of skills I’ve had to learn), and have been surprisingly pleased with how I’ve been getting on. It’s always a wonderful feeling when you show your advisor something they didn’t previously know – even if it is as obscure as playing a video in Matlab!


We also had to figure out the ultrasound system – a Telemed LogicScan 128. This is a PC based system that plugs in via USB, and all the controls are on the computer, which makes saving data and editing settings nice and straightforward. For the most part, learning this has been fairly intuitive despite having very little prior experience with ultrasound (observing its use in a single class in my masters).  Integrating the two systems with synchronization is still a problem we’re figuring out – while we have an analog signal that shows when the ultrasound is collecting data (on/off), it would be excellent to get the sample rate of the ultrasound system (frames/second) so it can be linked to the MoCap accurately.


That’s a little overview of the equipment I’m using, and some of the challenges I’ve faced and am working on in understanding it. I’m hoping my next post will also be informative – I recently submitted an IRB (ethics) proposal so I’ll detail that process soon.

End of Semester 1 – Research Update

“Science is competitive, aggressive, demanding. It is also imaginative, inspiring, uplifting.” —Vera Rubin


I love this quote from an amazing woman the world unfortunately lost in 2016. Science is competitive, it can be aggressive and it can definitely be demanding. That’s what makes it so rewarding. When you’re working on a problem, stuck on a specific element in that problem, science can be incredibly frustrating. But when you find a solution to the issue, when you come up with a creative approach, science can be uplifting. Other scientists can be inspiring, but so can their work. When you find a paper that is well-written and communicates its findings clearly, it can rejuvenate your own work.


But how do you decide what is going to be your “thing”? How do you figure out your research area? How do you whittle it down to the relatively niche area required for a PhD and beyond? There was a post the other day asking the readers what their “aha” moment was when it came to picking their research topic. I realized that I didn’t specifically have one.


I first discovered sports science was a viable option to study at university when I was 14. Our phys-ed teacher arranged a trip to visit the sports science facilities at a university about an hour away. I was awed, walking around all the physiology testing rooms, the sporting facilities, and was literally breathless when I was made to do a Wingate test! But it was visiting the biomechanics lab, where a harness was suspended from the ceiling harness and a tripping mechanism embedded in the floor, that I realized what I was interested in.


Over the three years of undergrad, my interests remained in biomechanics, but became more refined towards understanding injuries. My research project at the culmination of my time there ended up being an epidemiological study on injury risk factors in university sports. It involved 8 weeks of daily questionnaires from approximately 120 students and athletes based at the university. The data analysis still gives me nightmares! I have a lot of respect for those of you in statistically-heavy, questionnaire-focused fields after that experience!


Initially, I thought my next steps after graduating would be to study physiotherapy. Life happened, and I came to the realization that I wanted to do the science that drives the techniques used. I applied for a masters in Sports Biomechanics, and started in September 2015. Around January 2015, I figured out my dream career. To get there, I’d have to do a PhD. I started researching advisors and labs (see post here), and fine-tuned my interests while starting the masters. The university had recently opened a sports medicine center and brought in new faculty members with diverse research backgrounds. Learning from them and the other established faculty in the department, learning a broad history of key papers, literature and theories in biomechanics and how they relate to performance and injury, I started getting excited about the application of biomechanics in orthopedics.


Shortly after arriving at Penn State, my advisor and I sat down to discuss research ideas. The lab I work in focuses on joint mechanics and function – a lot of work looks at joint structure, moment arms, why our joints work the way they do. I knew that my research would fit somewhere into this theme, and I’d just finished a project looking at a specific injury mechanism for ankle sprains for my masters.


I was leaning towards something to do with ankle joint structure when my advisor brings up an idea he’s been wanting to look at for a while. We developed the idea further before I started work on the first project. Essentially, the theme of my PhD is how total ankle replacements affect joint mechanics, including changing Achilles tendon moment arm. The hope is, by changing the leverage of the Achilles tendon through a joint replacement, it will shed light onto how changing the moment arm at the ankle affects joint function.


So at the end of my first semester, I am about a third of the way through my first project – a methods paper. Conference abstract/submission season is well and truly upon us, and I’m working on three submissions. One is a conference in Europe, which my masters advisor suggested I apply to. That conference submission is a summary of my MSc thesis work. There is also another conference in September next year which might also be an option if the Europe submission gets rejected. The other abstract I’m working on has a deadline in March, but is based off the work I’ve been doing this first semester of my PhD. It’s a good kick up the backside to be productive so I have something to write about and present!


I’ll write more posts about the conference process as things happen, but for now, I have to focus on semester 2. My goals for this next semester are to get all the code written for this first project, with just data about me. I’d like to get this done by March, when that abstract is due, and then work on getting more data and writing up a paper later in the year. I also have my qualifying exams in April/May time which will take up some of my time this semester. I still have classes and TA duties, but I my main goal this semester is to get my research really flying.