We're a little crazy, about science!

A few new skills

Not working on anything serious today. Nope, not doing it. I took yesterday for myself and I’m taking today for myself. So instead of working on something strictly productive, I’m going to spend some of the day, maybe just a few hours, looking over some of the skills I’ve been meaning to pick up that I haven’t had time to learn/read about. Will this help my work? Yeah, of course, but it’s also something fun I wanted to learn. I’m a sucker for learning something new and that’s exactly what the plan is for the day.

The problem with publishing or doing research in general is that things are always changing. Journals want better graphics, the way we do analyses change, even best practices don’t stay best for long. Since starting my PhD the way we do things in the lab has evolved and it’s one of those things that we need to keep up with or else we get left behind. I really don’t mind learning new skills, it’s a fun thing for me. It’s why I got into research, it’s why I’ve been a student for most of my adult life, and it’s why I enjoy the work I do.

Unfortunately, between the constant drive to publish (speaking of which, I have a new second author paper that just came out I need to write about…) and the constant stream of research that needs to happen to keep up with the publish or perish research world we live in, there is simply not a lot of time to learn anything new. Certainly not anything beyond a cursory understanding of something. It’s just the way the system works and I can complain (and do complain!) about it all day, but there it is. So when I have some down time, either because I feel like crap or because there’s a lull in the work, I try to take advantage of it.

So what’s on the agenda for the day?

I’m not going to lie, I’m probably not going to get much done in the way of learning, but I do plan on relaxing with a nice book. The goal though (if there is one) is to learn some new tricks with medical scans. You may or may not recall I’ve been working with medical scans (CT and MRI) basically since my undergrad days, way back when! I’ve created several different things using those scans, from my robot (here) to 3D printing my own spinal column (here)(how to). But the times are changing and the way I do it is probably severely outdated. There are easier (?) ways to do it, or at least that’s what I’ve been lead to believe.

There are also new things we can do with scans and I want to learn it all, but mostly I want to apply some of this useful information to the figures and videos I make. My latest first author paper (this one) is a good example of that. Using a 3D brain model I overlaid a lot of information from the study we did. But that was using the average of several medical scans that someone else created for use in the software package I use to do some of the analysis and I really want to be able to create things that are person specific for at least some of the studies I am working on or have planned.

How to do that, that’s the question. Well there are ways using the software I am most familiar with that I haven’t learned, both new and old ways. My preferred software for medical scans by the way (for those who didn’t click the links on the spinal column sentence) is a software called 3D Slicer and has been my favorite open source software to use for medical scans of all types really. It’s super flexible and does basically anything and everything I’ve ever needed it to do, buuuuut…

There are other things I want to play with, some of which are far outside my skill set, which is part of the reason I want to learn them. The one in particular that I have my eye on is called Spinal Cord Toolbox, which is a way to process and analyze MRI spinal cord data. It’s super fancy, does a lot of things I don’t understand, and uses things I don’t even know where to start learning how to use. I’m going to need docker to use it and that alone has me stumped because I’ve never needed to use docker for anything.

Basically there’s about a dozen steps I need to figure out before I can even use the software and I haven’t had any real time to start poking around and learning them all. While I may not get to the fun tutorial part today, I hope to at least get to the open the software and see what it looks like part. Maybe, it just seems like a lot, but that’s why I’m taking it one step at a time. I’ve had my eye on it for months now (in a mostly ignored chrome tab), so I figure why not mess around with it a little today to see if I can get further than I did last time I tried to install/open it.

Yeah, okay I’m weird. It’s like a little puzzle. People enjoy puzzles in their free time. This is just how I like to unwind a bit. Maybe I won’t get very far, maybe I’ll get to a tutorial, I don’t know yet, but regardless, today is another day for me to relax, so if it gets too stressful or I find that I’m not enjoying the challenge, I can (and will) walk away from it.

There are other things I want to learn anyway, but this is certainly near the top of the list. I doubt I’ll ever use it for anything in my research, but it just looks like a cool thing to learn and I am a big fan of the spinal cord (in case that hasn’t become apparent over the last few years of writing).


6 responses

  1. That 3D slicer is amazing!

    Liked by 1 person

    September 5, 2022 at 3:47 pm

  2. In industry we don’t have “publish or perish” but we do have “keep up with the competitors.” There are always new parts and new software tools coming out (and for FPGAs the software tools aren’t optional – they’re the only way you can build code for the part). Once the new things are available, everybody wants to be among the first companies using them. Sometimes when we’re too fast we end up helping the manufacturer find all the bugs they shipped in their software, heh.

    And I guess that’s a case of competition doing what it’s supposed to do, encourage constant innovation. It’s just a little frustrating to become master of a part and then get to use it on two or three projects before it’s obsolete. At least at work they do explicitly schedule time to test new technologies and get people trained on them.

    The effect on my hobby projects is even worse, since they follow a much slower cycle. I have something that works, think “time to start developing this again” or “I’ll build another one,” and then find out some of the parts are discontinued, the software is all different, code’s broken because libraries changed, blah blah blah. The lesson is, if you find something you like buy a hundred of them. And keep a backup of your software installers somewhere.

    Liked by 1 person

    September 7, 2022 at 4:25 pm

    • Oh I didn’t even think about how it must be in a company like that. I’m glad they give you time to test out and learn new equipment though, I feel like that would be helpful in my field as well.

      My hobby projects are mostly at a standstill these days. I’m looking forward to being done with school so I (hopefully) will have free time to get back into it, but I’m not even sure what the state of the art is anymore! At least I know most of the stuff I use still works… for now!

      Liked by 1 person

      September 7, 2022 at 6:32 pm

  3. And then I forgot to even ask you how far you got. Did you end up playing with anything exciting?

    Liked by 1 person

    September 7, 2022 at 4:27 pm

    • Haha yeah a little bit. I had some data laying around that I plugged in and got something that looks like it makes sense. I’m just confused how I did it at this point, but I’m going to have to keep trying.

      Liked by 1 person

      September 7, 2022 at 6:33 pm

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