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Posts tagged “research

Back to EEG processing…

It’s the day after thanksgiving and I made my annual I don’t want to have to cook for the next week or two spread of tasty foods. I don’t do the traditional Thanksgiving foods though, I prefer Mexican dishes (since I’m Mexican). Namely I make a huge batch of tamales, since they are a bit of work I tend to make a comically large amount, think 100 or more. So while I have food to last, I need to get back to my main focus and that’s work!

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EEG Cleaning: ICA and Dipoles

This is (a very, very, small portion) of the data I’m working with for this post!

Let it be known that I’m a person of my word and today we’re going to give a rather broad overview of ICA and dipoles. Don’t know what those words mean? Well start here and that will give you a high level view of the entire process. Today we’re going to do a slightly deeper dive into what the heck a dipole is, why we use it for ICA and why ICA is so helpful in EEG data processing. Sound like a lot? Well it is, but let’s take a crack at it anyway!

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How to process EEG data

This is what Raw EEG data looks like. That big spike in the middle of the screen across most of the channels, that’s (probably) eye movement.

For those just tuning in, I’ve been busy! I made my deadline, barely. Unfortunately that was one of two. The second requires me to have all the work done, not just part of it. I managed to finish one of ten (yes ten) of the datasets I had, so now I have less than two weeks to finish the rest of it Let’s take it from the top and discuss how we process EEG data!

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More data!

Today marks another day that I got to collect data for my project. The good news is we got a LOT of it, the bad news is I got a LOT of it! Okay, only semi-kidding about that last part. I’m happy I have more data than less data, but it’s also a busy time so I don’t get to process it until I finish all this other work.

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That time I angered my PI

king's roads from Jonathan Strange and Mr. Norell
Navigating the right path isn’t always so easy.

I met my deadline, so now I’m going to take a short(ish) break and tell a quick story. I have been debating about telling it since it’s embarrassing and talking about failures (or really mistakes) is uncomfortable. I had enough uncomfortableness just trying to hit my deadline, but now that I’ve made it I figure I can at least tell the story for posterity’s sake.

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Time to work

So this post is coming a lot later than I would normally do this, but it’s been a day (already) and it’s going to get busier. I’ve had one experiment, one class, and now I need to repair my computer so I can perform the analysis of the data I have to get done before Thursday. Fun times ahead!

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EEG, not quite mind reading

Still one of the best photos showing how we set up EEG, that syringe has a blunt tipped needle and we use it to apply gel to the scalp. Don’t worry, we don’t break the skin, so it just looks scary, but it’s really safe.

Well I’m behind schedule and even though I was given an extra week (6 days now) I don’t know that I’m going to meet my deadline. It’s not me, it’s my computer, things take time to run so I’m stuck waiting for it to do its thing. Today let’s talk about what EEG is and how we make sense of it.

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NDSEG Fellowship Tips

I might as well talk about it, this will be my second time applying for NDSEG, so today we’ll go over exactly what that is, why I’m doing it, and why, if you’re working on a PhD, you may want to do it as well. NDSEG is tricky, but if you get it then you should be pretty well set for funding, it’s a great program, but it also means you’re being funded via the DOD.

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A writing realization

I had one of those shower realizations last night. I was thinking about all the writing I’ve done and how much I still have left and suddenly it occurred to me that I was done with all the writing… for now. That’s not the only thing though, I had the realization that I wrote more the second two weeks than I had the first two, by a lot.

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The abyss of uncertainty

It’s been a day. Meetings, planning, the usual stuff, just a whole lot of it. There is a few things that have been left unresolved unfortunately, namely I’m not sure what my main PI is going to do or how to be ready for it. I get the feeling that he’s trying to move on to the next phase in his career and I’m not the only one.

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Calm before the storm

a painting of a ship at sunset on calm seas
I’m sticking with the sea theme, it’s metaphorical!

Time is a great teacher that eventually kills all of its students. We’re all dying, I mean that in the literal sense. We’re slowly headed to a brick wall that we can’t avoid. I guess the difference between that plodding path forward and what I’m feeling now is just a time-scale difference. You see, I’ve set off a chain of events that are destined to blow up. I just hope I’m not part of the casualties. Am I being dramatic? Well, let’s review and you be the judge.

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A storm ahead

I’m not sure how to even start. Maybe I’m just being overanxious. I’m an anxious person and this happens! Frankly, I think I’m just overreacting, I mean I have to be. My main-PI wouldn’t do something to hurt my career, it just doesn’t make sense, yet I can’t shake the feeling and the email I got today doesn’t help ease my mind.

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The PhD proposal

This horror story from phdcomics.com

Well I was somewhat caught by surprise yesterday when we had our weekly lab meeting and my PI reminded me specifically that I should be working on my PhD proposal. It’s yet another milestone that I need to accomplish on my journey to a PhD. I’m not exactly sure why the reminder caught me off guard, I’ve been planning it for a while now. So today I guess we should talk about what a PhD proposal really is and why I need to do one before I can continue my research.

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Dominoes

It’s going to be a busy week for me. Seems to be a theme in my quest for that PhD to be honest. I’ve got data to process, papers to write, experiments to run, appointments to keep. It’s a lot of moving pieces that all need to be aligned at just the right moment. Dominoes, if I can get everything lined up nicely, the tasks will all fall just as easy.

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The grant proposal

Well today one of my grant proposals is due. Technically it’s due tomorrow, but I always try to submit a day early. Why? Well, technical issues, I’m an anxious person, all that good stuff. This was an equipment grant and I did it at the request of my PI, it’s not the grant I want, but it’s a learning experience, or at least that’s how I’m treating it.

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A lot of changes!

While EEG caps look super high tech, it’s actually a low-tech solution to an environment full of electrical noise. Each channel is pre-amplified at the source to reduce contamination as the signal travels down the cable. The first active electrodes? Made sometime in the mid 90’s, so a surprisingly new advancement in the history of EEG!

Well if there was any doubt that I write these daily I’m sure yesterday’s brief post explaining my panic helped answer that question. It really was a busy day and that’s not a bad thing. Things are… changing and I can’t tell how they will turn out now, but I’m anxious to see the outcome. How very mysterious! Let’s talk about it.

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More on mentorship

It’s dangerous to go alone!

One of the more enjoyable aspects (see: favorite thing ever) of being a PhD candidate and about half way done with my degree (… WAIT. HOW THE HECK DID THAT HAPPEN?!) is that I get to be a mentor. To be fair, I’ve been mentoring since my senior year of undergrad, but my style has developed and I don’t… flail as much as I used to when I first started mentoring students.

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Dataset mining

We use heavy equipment to mine our data around these parts…

I did an experiment! That’s old(ish) news, but now I have some data to play with… lots of data. So now I get to do something somewhat enjoyable and that’s try to get cool and interesting stuff to fall out of it. All you have to do is shake it really hard and hope for the best.

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A breakthrough

Oh yeah!

Well… where the hell do I even start? Yesterday was actually a semi-okay day. I mean the world is still on fire, the pandemic is still killing far too many people( but somehow not enough for the people in charge to care), and I mean let’s face it, it feels like the human race is in the death throes. HOWEVER, all that aside, my microscopic insignificant day wasn’t bad… now I’m worried.

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Path planning

One would think that the pandemic would put a lot of things on hold. Unfortunately (here in the US anyway) that isn’t the case, it just makes things harder to do because everyone expects you to perform at a higher rate now that you’re not commuting to school… how the hell that works is beyond me.

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Into the unknown

Time to cross that bridge…

Today is going to be a somewhat anxious day for me. It’s the day I get to crack open my data and see what spills out. There was a process to get to this point of course, it took me about a week, but today with just a few clicks I’m going to see if I have something or if my idea was never meant to be.

Read more… if you dare!

Day 362: Experiment two

Just a giant case full of the equipment I borrowed from my university for experiments. Pretty sure the school’s office staff thing I was robbing the place though.

Well today is going to be a quick recap of my experiment yesterday. This will be just as much for me as it is for all of you. While I can’t go into the experiment details (since I’m working to publish this) I can give a pretty good overview like I did the last time around.

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Day 361: Accidental history

Impostor syndrome
Art by: xkcd

Ever wake up one morning and realize you’re exactly where you wanted to be. That you’re in a place you never even dared to dream you could reach because, well it was silly to think you could accomplish something like that. Dreams that big weren’t meant for people like you, so you didn’t even bother to think you could get there. Yet… here we are.

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Day 360: Second experiment

Computer

The computer I use to process all my data, even with this it takes FOREVER to finish processing.

Well tomorrow is my second experiment. To be clear, it’s technically the same experiment, just a second person, so maybe it would be better to call it trial two? In any case, while the last one went (mostly) well, there are a few things I’m changing to make this next one even better. Sometimes when you prep for an experiment, you don’t realize what you’re forgetting until you can’t do it, so we’re correcting that this time.

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Day 358: One small step

Dream big

Sometimes are points in life that you can clearly define as the before and the after. As a child sometimes those points are simple milestones growing up, starting a new school for example or moving to a new town. There is the before and the after. As you get older those points become few and far between. For example, you started a new job. Unless it’s your dream job, you don’t really think of it as one of these points and everything just blurs together. Thus the bar seems to get higher and higher as we age. Today I had one of those points.

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Day 357: Thoughts from the lab

Case

My giant very suspicious case full of equipment from my school lab.

Well today is a busy day! I’ve got a lot going on so hopefully by the time you read this I’ll have all the setup taken care of. Working in two labs seems like a fun and interesting way to do experiments and it is! It’s also a huge pain.

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Day 354: Even more paper edits…

bad writer

These feels brought to you by: phdcomics

Whhhhhyyyy!!! Okay it’s not that bad, or maybe it is. I have yet more paper edits to do. It’s frustrating I just really want to be done with this paper and it doesn’t seem to want to end. I’m trying to keep my eye on the prize and do this right, it’s just soooo freaking difficult. I just want this done.

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Day 353: Experimental prep

Matlab

Sometimes a parfor loop in just doesn’t cut it because the things you want to do in that loop aren’t allowed (like save or load data a certain way). In those cases (see above) I can run multiple instances of MATLAB and process my data much more efficiently than if I did it one at a time. In this case I had 8 subjects that needed a rather long mathematical operation performed, so I did it all at the same time. It’s a little silly, but it worked! If you didn’t know you could do that, now you do!

Yesterday I told the story of how we got to this point, a long two year journey and next week I finally get to take the next step. It’s exciting, but it also means because of my flare-up, I’m behind on what I need to do to be ready. Not to worry though, I’m taking it slow so I don’t make whatever I have worse. What goes into an experiment like this? I’m glad you asked!

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Day 352: My experiment is coming!!

EEG Cap

I just really like how this photo came out. Here’s one of my lab mates gelling the electrodes for a pseudo-experiment. The scary looking syringe has a blunt tipped needle, we don’t break the skin in our lab so no pain, just a bit of gel to wash out of the hair once completed.

Okay I’ve got an experiment update today and I’m really excited to share because it feels real finally. I know I already wrote about some of this, but when I reread my previous post, it felt disjointed so let’s go over how we got here and what’s coming. I’m excited, are you excited? I’m excited!

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Day 350: In construction…

extruder

I redesigned my extruder to make it beefier, this has nothing to do with the post, but I’m really proud of it and wanted to share. Haha

Well today despite feeling like refried dog poop I have to go do experiments. It’s part of the job and to be honest I want to do it even though I feel like dried monkey vomit. I could go on, but you get the picture. I do have some more good news not related to yesterday’s news. So that is the conversation for the day.

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Day 347: The precipice of … something

precipice

Today is a mash of things, because frankly I still am not feeling good. My the scaly bits on my hands, face, and apparently elbows (missed that one until last night) haven’t gotten worse (yay), but they haven’t gotten better either (boo). On one hand it’s a realization that whatever is wrong with me was worse than I had thought, on the other, the world still moves forward and unfortunately I have work to do, so what’s a guy to do?

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Day 345: Undergrad research presentations

Virtual classroom

Well today is day one of three for wrapping up our undergrad/high school research experience. We had a group of about 50 I think, just in our lab and a good portion of them were high school students. Because we’re living in a pandemic, this was all done virtually! Today we get the first glimpse into how we did as mentors.

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Day 337: The end of summer mentoring

virtualconference

Still trying to get used to the idea of virtual conferences.

Well we still have a month of summer break left, but we do have the end of summer courses coming. In just a week we’re having our undergrad researcher conference (virtually of course). Everyone will get a 5 minute block to showcase their poster, talk about their experience, and get a chance to answer questions about the projects they worked on (another 5 minutes max). The whole thing will take three days to get though.

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Day 336: A close call

Teddy Bear wearing a face mask to protect against COVID-19 spread

Teddy Bear wearing a face mask to protect against COVID-19 spread

Wear the mask!!

I was up bright and early today, 4:30am to be exact. We had two experiments planned for the day, one first thing in the morning, the other in the afternoon. Being the dependable person I am, I was up and out on time, arrived here early and setup to get started. That’s when it all fell apart.

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Day 326: Review: The state of spinal cord research

Figure 2 from and yet it moves

Figure 2 from and yet it moves

Facilitation of stepping-like volitional oscillations using non-invasive transcutaneous electrical spinal cord stimulation in SCI subject. (A) Position of the participant in the gravity-neutral apparatus. (B) Biphasic electrical stimulation was delivered using unique waveforms consisting of 0.3–1.0 ms bursts filled by 10 kHz frequency that were administered at 5–40 Hz. (C) EMG activity of right soleus (RSol), right tibialis anterior (RTA), right medial gastrocnemius (RMG), right hamstrings (RHam), right vastus lateralis (RVL), right rectus femoris (RRF) and angular displacement in the knee and hip joints of both legs during leg oscillations with a voluntary effort alone (Vol), stimulation at T11 (Stim), and Vol + Stim are shown. (D) Schematics demonstrating the approximate location of transcutaneous electrodes above the lumbosacral enlargement, in relation to the location of the motor pools based on Kendall et al. (1993) and Sharrard (1964).

Well it’s been two weeks (roughly) and my PI asked specifically that this week I do a review on the state of spinal cord research, with emphasis on the spinal cord stimulation work I’m doing. So this review is going to look slightly different, namely it has a rather long references section (15 total). If you find this research fascinating I recommend “And yet it moves” (reference 5). It’s long, but open access and worth the read. I’m a little bias though, my Co-PI is one of the authors. In any case, I had two weeks to write this, so hopefully it is a good dip into what we know about the spinal cord and a lot of what we don’t. Enjoy!

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Day 310: Review – Interfacing with alpha motor neurons in spinal cord injury patients

Figure 1 from the paper showing EMG recordings and the transformation using deconvolution to motor neuron spike trains

Figure 1 from the paper showing EMG recordings and the transformation using deconvolution to motor neuron spike trains

Spatiotemporal spinal maps of ipsilateral a-MNs. (A) Experimental set-up for ankle plantar flexion. (B) HD-EMG is decomposed into a-MN spike trains using a convolutive blind-source separation technique. (C) The spinal output to generate the neural drive to muscles is estimated from the a-MN spike trains.

The world is on fire, we’re protesting for a future, but today I have my review paper due so instead of writing about my frustrations I’m going to share my review. Today we’re looking at the effects of trans-spinal direct current stimulation (tsDCS) on alpha motor neurons and how we can determine that effect using electromyography. It’s actually a very cool paper, the work is well done, and it’s open source so you can read it if you’re interested.

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Day 296: Review – Spinal Rhythm Generation by Step-Induced Feedback and Transcutaneous Posterior Root Stimulation in Complete Spinal Cord–Injured Individuals

Black and white diagram showing the front and back of a human with the the placement of electrodes over the lower abdominal area and separate electrodes over T11-T12 of the spinal cord a third image to the right shows the side of the spinal column with spinal cord to depict the location of the back electrodes with relation to the spinal cord

Black and white diagram showing the front and back of a human with the the placement of electrodes over the lower abdominal area and  separate electrodes over T11-T12 of the spinal cord a third image to the right shows the side of the spinal column with spinal cord to depict the location of the back electrodes with relation to the spinal cord

Transcutaneous posterior root stimulation: Paravertebral and abdominal skin electrode placement (this is just a portion of figure 1 of this paper.

Normally I’m somewhat excited to post these, but with everything going on you’ll have to pardon my lack of joy. However, it’s been two weeks so I need to review another paper so I’m sharing it here as well as sending my PI a copy. The study is a few years old, but it’s open access so you can read it if you’re interested. Transcutaneous spinal cord stimulation (TSS) is one part of my research in case you couldn’t tell from all the spinal cord and TSS studies and posts. I find it interesting and it gives me hope that we can help a whole lot of people living with spinal cord injury. Anyway give it a read and get out there and protest for a better world.

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Day 282: Review – Transcutaneous spinal cord stimulation of the cervical cord modulates lumbar networks

Experimental Setup and tSCS electrode placement (A) H-reflexes were evoked via stimulation of the tibial nerve and recorded in the soleus muscle during a consistent background contraction of ≈5% peak muscle activity. The left leg was held static in an extended position, and stimulation to evoke the H-reflex was delivered with the left arm at 0°. (B) tSCS was delivered via two 2.5 cm round cathodic electrodes placed midline at C3-4 and C6-7 (cervical) or T11 and L1 (lumbar) spinous processes. Two 5 × 10 cm rectangular anodic electrodes were placed bilaterally over the iliac crests.

Experimental Setup and tSCS electrode placement (A) H-reflexes were evoked via stimulation of the tibial nerve and recorded in the soleus muscle during a consistent background contraction of ≈5% peak muscle activity. The left leg was held static in an extended position, and stimulation to evoke the H-reflex was delivered with the left arm at 0°. (B) tSCS was delivered via two 2.5 cm round cathodic electrodes placed midline at C3-4 and C6-7 (cervical) or T11 and L1 (lumbar) spinous processes. Two 5 × 10 cm rectangular anodic electrodes were placed bilaterally over the iliac crests.

Experimental Setup and tSCS electrode placement (A) H-reflexes were evoked via stimulation of the tibial nerve and recorded in the soleus muscle during a consistent background contraction of ≈5% peak muscle activity. The left leg was held static in an extended position, and stimulation to evoke the H-reflex was delivered with the left arm at 0°. (B) tSCS was delivered via two 2.5 cm round cathodic electrodes placed midline at C3-4 and C6-7 (cervical) or T11 and L1 (lumbar) spinous processes. Two 5 × 10 cm rectangular anodic electrodes were placed bilaterally over the iliac crests.

It’s that time again! My biweekly critical review paper is due for my PI. He gets a copy and so do all of you. This is a particularly interesting study that falls in line with a lot of research that I am doing, so it’s interesting to see how other groups are progressing. Overall I think this is a great study and while it is behind a paywall, I think I summed it up very well. The drawing they did (above) is awesome, especially for a scientific journal where we normally use simple line figures. Anyway, let’s get to it.

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Day 275: Summer Mentorship

planting a tree

It’s summer, so we’re taking a break from my DI…why?! series to talk about my favorite thing about working over the summer. We get to do mentoring! As you may recall, mentoring is my favorite part of the job. Over the summer we get students from high school, international students, as well as undergrad students from all over the place to visit our little lab.

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Day 268: Review – Magnetospinography visualizes electrophysiological activity in the cervical spinal cord

Reconstructed currents of MSG from the cervical spondylotic myelopathy subject. There are two different sets of plots, the furthest left shows the electrophysiological recording taken from the epidural space and the other set shows the reconstructed currents using MSG. They agree fairly well.

Reconstructed currents of MSG from the cervical spondylotic myelopathy subject. There are two different sets of plots, the furthest left shows the electrophysiological recording taken from the epidural space and the other set shows the reconstructed currents using MSG. They agree fairly well.

This is the results of the cervical spondylotic myelopathy subject. The left graphs are the ascending spinal cord evoked potentials (this was electrophysiological recordings taken from the epidural space) by stimulation of the lower thoracic cord showing conduction block at the C4/5 disc level. The right graphs are the reconstructed currents at the midline of the cervical spinal canal (red) and 2 cm lateral (blue). The leading component (the first waveform in red) attenuated and disappeared through C4–6, and the trailing component (the second waveform in red) disappeared at C5/6. The perpendicular inflow components greatly attenuated at C4/5 (the second waveform in blue).

Another two weeks, another critical review. This time I was more critical than review, unlike the last one where I was blown away at the possibilities. Why was I more critical with this one? Well in my opinion, the authors took a baby step when they should’ve taken a leap. All that aside, it is an interesting study and one I hope has several follow up experiments. This one is open access as well, so have a read for yourself if you’re interested.

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Day 266: Pandemic research pressure

Pandemic

Think of research like the post office, nor rain, nor sleet, nor snow, nor pandemic, we will be there working. My dumbass had to make the transition from design to human experimenting the year before a pandemic. I could be safely at home designing cool robots in solidworks, but no we need to collect human subject data and despite the pandemic, I’m feeling the pressure.

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Day 264: Summer Research

EEG cap

Pay no attention to my messy desk… instead look at the cool EEG cap I set up.

It’s supposed to be a busy summer for me. With the pandemic going on, I’m not sure how that will play out. Since we don’t know yet, let’s talk about how it was planned and then we can discuss how that changed thanks to the COVID-19 pandemic. This may be bad as far as my research timeline… maybe.

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Day 216: So I’m “essential” now…

pandemic

Fun fact, I love pandemic movies. Movies, not so much living through one. As humans we are selfish, greedy, prone to panic, and for being “evolved” we are so very, very stupid. Basically every dumb choice you see the characters in those movies make while screaming, “you idiot, that would never happen in real life!” Well, it’s happening and wow does it do a number on a persons mental health. But hey guess what? I’m essential, so let’s figure out what that means in a time where the world is practically on fire.

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Day 215: What now?!

look ahead

Social distancing is important, but maybe not this distant…

Well if you missed it, yesterday was our final post in the know your spinal cord series. I’m not crying, you’re crying! Now the question is, what does that mean for the blog? An excellent question, one I wish I would’ve asked myself!  Let’s take a look at some of the things that we will (probably) be discussing now that our designated topic has run its course.

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Day 136: A look forward

a look forward

The obligatory photo of a path that goes on into the distance (taken from the hike we went on during the neurotech confrence).

Yesterday we took a look back at the past decade. I’m not a fan of looking back, it’s not how I’ve survived this long, it’s not something I’m particularly comfortable with, and even though it wasn’t a bad thing to do, I would rather look forward and talk about the things that will be happening (hopefully) this year. Let’s ring in the new year with the to-do list for this year!

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Day 101: Holiday

Well today is thanksgiving, not a holiday I celebrate, but I’m happy to have the day off at least. I’ll be taking the day to get some work done and relax some. Deadlines are coming so I can’t take the whole day to myself, but at least it’s a low stress day.

Until next time, don’t stop learning!


Day 100: Graduating lab members

Day 100 - PhD defense offense

Image from: xkcd.com

Wow, time flies, we’re already on day 100. Still not half way done, but it certainly doesn’t feel like 100 days of writing. Today has been a busy day, which is why I’m writing so late. With the end of the term comes other projects that need to be addressed, namely my qualifying exam, final exams, and other lab members having their Ph.D defense. Yep, we have not one, not two, but three people defending their Ph.D this term.

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Day 99: Data request, a update

letters vs email

Sometimes emails can still be exciting!

I’ve got news! In my last post on the subject I said that I wasn’t expecting a response from the lab I was requesting data from until Monday, if at all. Well would you believe I got a response! It wasn’t a “here’s the data response,” but it is progress. Let me explain why.

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Day 98: Laptop troubles

Well it finally happened. My laptop looks pretty dead. Right now I have it in pieces while I try to figure out what went wrong with it. Thankfully I have a desktop computer that I use for all my heavy computing as a back up. Just one more expense I guess, I should be grateful that it wasn’t something more serious like the hard drive going out.

So short post, I know, but I have to get this fixed or find some sort of resolution since my laptop is an important part of how I get work done. I’ll have a longer post tomorrow, but for now I think that is it.

Until next time, don’t stop learning!


Day 97: Neural network models

Neural net

Today should be an interesting day for me. I plan to do a deep dive into the world of neural networks to better understand how they work and the best type to apply to my data. There are a few, quite a few in fact that I could use and really it depends on how I want to frame my problem, so let’s look at what I’ve got planned.

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