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Posts tagged “neuroengineering

The coding hole

Help, I’ve fallen into a coding hole and I can’t get out! Okay, to be fair I actually DID get out, but at the time it felt like there was no hope and I would be trapped banging my head against a wall trying to figure out what I was doing. Today I figure we can discuss how I code and what my idea of a coding hole is, it will be a fun break for me.

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The science behind an MRI

Today I had an MRI, don’t worry it was for research purposes. It wasn’t a short MRI either, I was in the bore for almost two hours. Yep, stuck in a tube with nothing but my thoughts, some music, and the sounds of the MRI machine doing its thing. I figure we can discuss what an MRI is, why I had one, and why I don’t mind that it took so long. I may even show off some of the scans, but not today I don’t have them yet.

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The art of coding

Well I did it. I got all the code written for the next two (of three) steps for processing my data. I can’t do the third until the second step is done for at least one dataset, but I’m almost there and the last bit of code is to visualize the data, which is substantially easier. So let’s talk about what I did and why I won’t have to do it again now.

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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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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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The due data

It’s time, my data and the results from the experiment are due today. Okay, if we want to get technical the due date is tomorrow. HOWEVER, and that’s a big however, I need to get it to my PI today to review before I submit it. Which means he needs to see it today so I can send it off to the center for review.

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Computer troubles

It’s my baby! The case is unique, but I wanted something that could grow with my needs and this case is not just fun to look at, it’s huge! Unfortunately that makes the computer super heavy.

I had a feeling this may happen, I just didn’t expect it to happen when I was so against the wire to get this project done. I’m having computer troubles. Not my laptop thankfully, but my desktop computer is feeling a little… warm. I’ll explain and then get into what I’m doing to fix it, so today let’s talk about my computer!

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A race to the deadline

Yet another day closer to my deadline for this EEG project and I’m still trying to pre-process my data so that I can make sense of it. We’re racing the clock here and my PI is pushing me to get it done, sure I think I can do it, but then again… maybe not?

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Funding and you, a PhD story

New day, yet another topic for me to talk about. Today I’ve decided to spare everyone from hearing about my data processing woes to instead touch on a topic that I haven’t discussed before (at least I don’t think I have!). Today we’re talking about funding your PhD. Specifically why it’s important and what power you have over the funding you recieve.

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The end of the experiment

Well today was a milestone for me, the end of an experiment I wasn’t too excited to do in the first place! Of course, now comes the semi-difficult part. I need to process the data, draw some conclusions, probably publish a few papers, and get a presentation made. Things need to happen quickly too, so while I’m done, I’m not. At least, not yet.

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Fellowship applications

Well looks like we’re switching gears. That’s right, now that I’ve finished (FINALLY!) writing the draft of my grant proposal, I can move on to some other funding opportunities. It’s fellowship season and since it ’tis the season, I need to iron out my CV and best of all I get to do something different!… wait it’s just more writing.

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The Dissertation Committee

Well it’s been a journey… but every person I emailed has responded and they all agreed to be part of my committee. That’s right, we’re making serious progress on the road to my dissertation proposal. It’s been a little surreal and I’m nervous that even though I’m here I’m not quite ready for it. Today, let’s talk about my next steps and what forming my committee actually means.

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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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Committee selection

Old black and white photo of blindfolded man in a suit reaching out in front of him.
It feels exactly like this somedays…

Well here’s a post that I thought I wouldn’t be writing this soon. Or maybe I’m right on track and I just don’t want to admit that I’ve made progress. Either way, even though it is the weekend I’m taking an important step in my goal to my PhD! I’ve formally submitted my list for my dissertation committee to my PI. Not a PhD or don’t know what that means? No worries, that’s why I do this, so let’s talk about my committee!

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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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Technical writing: How to write gooder

Know your audience, it’s the first rule of technical writing. I’ve taken several technical writing courses during my education and they all start off the same way. KNOW YOUR AUDIENCE! In my experience that is usually the end of the advice given. Most technical writing courses assume you know how to write, an odd assumption when you’re supposed to know your audience. Today I’m going to go over what I do BEFORE I write, in the hopes that it will help some of you. Fair warning, this is long and detailed!

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The ambiguity of language

Well we made it, it’s Friday. I’ve finished my experiments, done most of the things that I needed to do and now I can focus on writing for once. No, not my blog. It’s finally time for some technical writing. I’m not thrilled about it, I mean I don’t mind technical writing as a general rule, but it does get tedious with all the edits. Maybe that’s why I like my blog so much, I can just write and be done with it.

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Yet more experiments?!

Sticky notes are the best.

Another long day for me. Back to back experiments (with a short break in between thankfully). It’s a lot, but I’m hopeful that after it’s all done things will slow down at least for a moment, hint they won’t. In any case, I just need to make it to tomorrow then I get a break for a few days.

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A week of experiments

Don’t mind me, just trying to turn back time… lol

Most times work can be a trickle, we get one or two subjects a week and that’s all. 6-8 hours in the entire week dedicated to collecting data and the rest of the time I’m free to process data, work on other things I need to do, basically live day to day like I didn’t live in a lab. Most of the time. Sometimes it’s a flood, like this week and next, then I’m reminded that I definitely need to work.

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Catching up

This feels about right, I’ve been running on empty!

Sunday means getting ready for the rest of the week and what a week it will be. In my Co-PI’s lab we typically have a steady stream of people coming and going for experiments, this week (and probably next) it will be a flood. We’re trying to make my main-PI happy.

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Meeting a potential postdoc

Comic from phdcomics.com

Well today has been interesting to say the least. It wasn’t planned, but I went into the lab to meet my Co-PI and the new potential postdoc for the lab. I sort of rushed in last minute and the coordinator apologize, but I hadn’t planned anything that would’ve been hard to do in the lab anyway, so it wasn’t a big issue.

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Data results!

light bulb in the sunset

About a week ago I collected some data randomly. Well let me start over, not randomly my Co-PI decided it would be a good experiment to collect the data using my “super secret” technique to verify that it worked. We had six different conditions and I’ve only processed two of the conditions, so there’s still some work to be done to determine if this is real or not, but I have my initial results and my Co-PI has seen them.

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Grant writing!

writing spelled out in letter tiles

It’s time to help write another grant! In this case, it’s one I actually want. One of these days I’ll write a little tutorial on how I like to do my writing, I think it’s a good system, but then again what works for me may not work for you. This one is particularly complicated though so it needs a lot of attention. It’s not that it’s long, it’s because it’s short.

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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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Exoskeleton experiments

Just a few of the exoskeletons we have in the main lab, two of them are self balancing the other two in the shot are not, but they all have different purposes.

Well let’s toss something else into the pile of “things I’m going to talk about, but can’t share the details because we’re working on a publication.” I’ve got yet another new project I’m working on! This is going to be so freaking cool and I’m super excited to start it. So let’s go over some of the details, at least the bits I can talk about. Eventually when all this stuff gets published, I’m going to have a ton to write about.

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Experimental failure

Well that was a …flop. Today I had an experiment, had. There are a lot of moving parts when it comes to an experiment, especially in my line of research. Technology, can’t live with it, can’t live without it. Still, somedays I wish I was living in the future, one where I didn’t need to reset my router randomly. Then I would know for sure the singularity was close.

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More data!

Old wooden treasure chest with strong glow from inside.
Old wooden treasure chest with strong glow from inside.

It was a surprise to me, but I somehow ended up with a new dataset from a single subject. One that, after processing, could be the key to convincing my Co-PI once and for all that we have something real… or it could just be one giant mess, but if we don’t look we may never know.

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Problem solved

Sometimes we don’t need to think outside the box, the box can stay closed for the moment…

Everyone go back to what you were doing, nothing to see here! Yesterday I had an existential crisis, one that could’ve derailed my technique and any hopes I had at introducing something new into the world. With it, my PhD dissertation topic, meaning I would be over two years in and I would need to reevaluate my goals. Let’s talk about what happened!

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A snag

No tears, please. It’s a waste of good suffering.

You know… that’s how it goes sometimes. You’re cruising along and everything looks great then, BAM! Totally derailed. What happened? Turns out I have a problem with my data. Not a problem persay, more like an anomaly, one that throws a rather large wrench into what WAS a perfectly running operation. Things were looking good, but now… I have a doubt.

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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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A busy day!

Well it’s been… a day, which for me started at 5am. It’s not over either! Our experiments ran long so I haven’t had a chance to get a break in between the different experiments and now I have class, so basically this is the post. It’s a busy day and I still have so much work to do! Good luck to everyone out there who is also swamped. Hopefully the weekend will give us a break!


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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The Nyquist frequency

Parts to a wave (top left) a example wave (bottom left) and different examples of how waves change based on frequency (top right) and amplitude (bottom right)

A few days ago I realized I had never bothered to explain the nyquist frequency. Considering it’s been over a year now since I explained some of the frequency domain things that I do in my lab, I’m actually surprised I missed something so important. Well, better late than never today we’re going to explain the nyquist frequency and why it matters… to my work at least.

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Neuralink: Beyond the hype

The sewing machine like robot that is the linchpin for neuralink.
The sewing machine like robot that is the linchpin for neuralink.

Brain machine interfacing, as someone who does research in the field and is getting a PhD in a brain machine interface lab, I think I’m qualified to comment on the progress neuralink. There’s a lot of hype out there, curing disease, ending paralysis, a world where we are part of the machine and the machine is part of us. Is it science fiction, or is there more to it?

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Fact or artifact

Does it belong in a museum though?

A new turn in the saga of my data processing. There has been some concern that the artifact from the stimulation is causing the thing I am seeing in my data. There are arguments to be made for both sides, but let’s go over what that could mean for me.

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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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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 334: 3D printing, my final summer class

Robot parts

One of the slides I used in my 3D printing course, this was the robot I designed and 3D printed (prior to assembly) for my Masters degree.

Well I got a chance to give my last lecture yesterday (virtually of course) on 3D printing. I worked literally weeks to get everything ready and it went off (mostly) without a hitch. The world of 3D printing is full of vast, multifaceted, and divergent technologies with more applications than I could possibly list in a single lecture. In fact, they offer entire 12 week courses on 3D printing, so I had to cram everything together into a nice 1-2 hour presentation, where to start?!

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Day 333: Solid modeling course day 3

3D printer

My 3D printer still working hard, but I’m still having troubles!

Yesterday was the last day for my solid modeling class and surprisingly I got more questions than the previous days so that made me very happy. Today is my 3D printing course, so we’ll talk about how that went tomorrow (and push back our online 3D printing course by a day sadly).

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Day 332: Solid modeling course day 2

Printer

Yep, still dealing with printing issues so I have the dual extruder on. Ugh!!!!!! 5 HOURS still left on this print. Why does 3D printing have to be so sloooooooow?!

Well yesterday was day 2 of my solid modeling course, today is my last day of the class. Unfortunately tomorrow is my 3D printing course and I still haven’t got my printer well behaved yet. I guess we get to see all the 3D printing troubles! In any case, let’s talk about how the class went yesterday and what I have planned for today.

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Day 331: Solid modeling course day 1

20200715_134927

The dual extruder attachment, the current bane of my existence!

Well can’t complain too much about the first course. I’m used to people talking to me so it was an odd feeling talking into a screen with no one talking back. I had a few questions, but mostly the course was on how to think about solid modeling, so maybe not a lot of room for questions?

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Day 330: I’m teaching this week!

Harbinger

I love mass effect, so I really thought this was a perfect header image for the post since I am… assuming control!

Well I mentioned it a few days ago, but it’s day one of four today. I’m teaching three courses on solid modeling and one on 3D printing * Shakes fist at 3D printer who keeps giving me problems * and I figure I can talk about how my classes go after the fact, but let’s talk about my prep for these classes so my students get the most out of what I have to teach them.

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