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First Month, Second Year

Photo taken in Lynn Woods Reservation just north of Boston.

I'm a little late with publishing this post. It's really the first month and a half of the school year, and what a roller-coaster ride it's been. I really should get back into writing every week or at least every other week because there is always something significant that happens it seems. Every time I thought I would have some time aside to write, something else came up that was a little more pressing. It was like putting out fires that were popping up everywhere. Whack-a-mole. There still are a million other things I should be doing right now, but I'm going to publish this post today. I must get back on schedule with this.

I didn't realize just how relatively calm the summer was until classes started. One class I'm taking this semester is a quantitative methods course that really focuses on using linear algebra for data analysis through MATLAB. After spending so much time trying to learn linear algebra and wrap my head around these matrix operations on my own, it's great to be able to use code to write and test the application of linear algebra. Try an equation one way. Nope, that's not it. Why? Look around and modify the equation, press run and, haha, it works! Of course, it's never that fast for me. It's not uncommon for me to spend an hour or more on a question trying to obtain the result I'm looking for. Some of the easy MATLAB coding I have down, but it's the implementation of linear algebra through code that makes the class so useful. Most of our researchers are analyzing data through programs available in MATLAB or through MATLAB directly, so it's great they offer a course like this for us. It's a lot of work, but I like this course.

My second class is an fMRI analysis course. Where the quantitative methods course is a math-based course for general analysis (it can be used for anything), this course focused specifically on fMRI acquisition and data processing for research. So far, we've gone over the basics like physics and hardware. Now we are in the beginning stages of data processing, and I have to admit, it's pretty cool. I used to dismiss fMRI data as always being a shadow on the wall, not the real thing. It measures the hemodynamic response of hemoglobin becoming deoxyhemoglobin in the blood, which isn't exactly actual neurons firing. The premise is that as the neuron fires, it requires more energy (more oxygen), and the concentration gradient pulls oxygen atoms off hemoglobin into the tissue surrounding the neuron. The scanner sees that activity as some change in the concentration of deoxyhemoglobin. It is neat to see very "easy" activations with fMRI, like when images are flashed in front of a patient's eyes, or when a participant pushes a button in the scanner. Those types of actions use large areas of the brain to perform the task and are well-correlated with the task, but the difficulty lies in trying to get smaller signal changes to be detectable by the system. The research occurring in neuroscience today involves trying to decode those more complex and diffuse activations. The ultimate goal in my opinion is to figure out what it means to be conscious. How does that mass of tissue in your skull allow you to experience the world around you? Whatever the answer is, we'll need something better than fMRI to find out, but in the meantime, it's what we have, and it's actually pretty rigorously tested by those in the field. I still have my reservations, but I'm warming up to the modality.

In other news, the research projects are moving forward, but always at a snail's pace.

  • Quickly, the coil paper...yeah, still working on it. Got some feedback recently that I'm incorporating and hopefully and push this thing out relatively soon. Then again, I've been saying that for a while now.

  • The fear-conditioning study, still wrapping up some study design changes and should have another amendment submitted soon. It's always slow with these sorts of things.

  • The ultrasound project: I finally built a degassing system, but there are some engineering issues that need to be worked out. In other words, it doesn't de-gas. Does anyone know of a pump that can work against a vacuum (-25in Hg) on one side? Is this the equivalent of drawing up from a source below the pump? Regular valve pumps are just not strong enough for this application. Gear pumps maybe? Still figuring it out.

  • The drug treatments for PTSD: this could become larger than I thought, but why not? I've been networking with several people across the country trying to drum up support for a psychedelic treatment study for PTSD. I think it would be really neat to perform the cognitive neuroscience behind that sort of research. If you're interested in the project, let me know through a comment or message.

The program is starting to guide us in the direction of applying for fellowship grants to support us and our research after the qualification exam. This is a sum of money that companies and government agencies put forward to support graduate students pursuing research in an area they feel is important. It's not quite a full-on grant where you would need to have a budget and sign a contract to perform the work, but the expectation is that the student will at least graduate with a project that was similar and legitimate. Not every applicant gets a fellowship, and not every fellowship covers the full cost of tuition here, so the ones that are the best are highly competitive. I have to admit, knowing the line of research that I want to head and having access to the avenues I need to make it happen allow me to put forth a compelling story, but I just hope the agencies to which I am applying feel the same way. I'll be sure to let you know if I am awarded a fellowship.

Finally, on a more personal level, since the start of the school year I've been thinking about how I want to make this year different somehow. It was as if last year I felt like I was more along for the ride and this year I wanted to be more in charge of what what happening. I think I started off that way, but I think it wasn't long that I started to become a bit overwhelmed. I did have the summer without class, and the research pace wasn't so rapid, so by the end of September I was beginning to feel a little frazzled. Don't get me wrong, I love every minute, but I just don't have enough minutes to go around, and maybe I have taken on too much?

Then last week I was hit by a truck while I was riding my bicycle. One morning I was riding into the office and as a truck passed me going the other way, I crossed the street to enter a driveway and head to my little parking spot. What I didn't expect was the truck to stop and reverse quickly into that same driveway. He didn't see me and I didn't have time to react. He hit me going about 15 or 20 with the bed of his Dodge Ram. Luckily, it had been raining a bit and my bike's tires were skidding on the road as I was crushed up on his tailgate, otherwise the bike may have gone under and likely I would have too. I hit the truck and made some noise. He stopped. I pushed off the truck and actually rode away. I thought I was fine. Nothing broken. No blood. Ah, but those two lovely spinal fusions...the adrenaline masked the pain that I have been in since. Left knee, hip, ribs, shoulder, neck, and back....I thought about trying to locate that guy, but the damage is done. No insurance claim will undo what has happened. All I know is that I haven't been the same since. I'm trying to stay as active and mobile as possible, but these things never leave the body completely.

The accident got me thinking about a whole lot of things. How many times in my life have I almost died? What am I doing with my life right now? How do I want my life to be? Who do I want in my life? These are many of the same existential questions I ask of myself from time to time, but after this event, it seems more of a wake-up call. Like it or not, we are all going to die. I'd like to hope that for me it's while I'm sleeping in a bed in my 90s, but maybe it's on a road in my 30s. I need to live the life I want to lead today. I just might not get the chance to make that change later. Easier said than done though, isn't it? I must admit, the event knocked me off my rhythm. Pun intended. I still feel a little disoriented. I don't think I hit my head, or at least not very hard, but I'm lacking that motivation and drive I know I had just a few weeks ago. Maybe this is the early stage of burnout, which is a little unfortunate because the semester has just begun. I need a better support network.

Have any close calls that make you question everything? Are you more the type that brushes it off and shrugs after a close call? Do you rely on a support network, or are you pretty good on your own? Have you been so lucky as to never have had a close call? I'd love to hear from you. Let me know your story in the comments.


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Omar Rutledge
Omar Rutledge
Nov 02, 2019

Jeff, thanks for the words of encouragement. I am definitely one to isolate if given the chance, and that's certainly been the case after the bike incident. I'm going to start reaching out to connect more with the people around me as well as those not so near. Reciprocation and vulnerability are certainly quite the challenge, and I'll keep working on it through practice.


You're a fighter bro. Sucks hearing about the truck and resulting effects. If close calls were someone else's fault, I'd evaluate the time investment relative to reward (money, moral obligation,..).

Existential crises seem to come and go regardless of any inciting event. Actually whenever close calls do happen, I get the crisis for like a few hours and then it disappears lol. Not sure if that's a good thing. Anyway, what's worked for me is like you said, everyone dies; Might as well fight tooth and nail to find whatever happiness is and set your mark.

I was always a lone tough guy and had the mindset that I can only depend on myself. Recently, just being more open and…


Omar Rutledge
Omar Rutledge
Oct 17, 2019

Everything seems so slow until 10 years have passed and there's no way to get them back. I think you're heading in the right direction. You're moving forward, even if you feel like it's at a snail's pace. I need to take a page from your book and focus on keeping myself happy and peaceful here and now.

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