Posts tagged ‘medical’

All my computer does anymore is fold proteins

The last month has been fairly painful for me. My leg currently sits wrapped in several layers of gauze with an immobilizer surrounding it all to keep me from moving it. This is because of the surgery I recently went through to repair a torn meniscus. For the last few days it has felt like there is hot lava pouring out of my leg through the incisions and my arms feel like they’re going to fall off from walking on crutches. But the worst (I think) is now over. I’m very thankful to say everything feels like it’s healing properly, I’m just waiting for the doctor to see it tomorrow and tell me exactly how long I’ll be like this.

Due to the fact that I cannot at all bend my left knee, it gets very painful to sit at my computer for more than about fifteen minutes at a time. About all that I’ve done on my computer recently is watch my computer bust out Folding@Home workunits and mess around with Google+.  I’ve also decided to move on from xmonad in search of something a little more casual. I’ve since fallen in love with Fluxbox & conky. I like the more casual approach to computing. It almost feels more fun. It almost feels more natural to size and place windows all over the desktop, as opposed to the tiling I’ve done over the last few months.

Aside from all of that, I’ve been thinking I want to get back into programming. I don’t really want to learn something new, just expand my current knowledge. I figure let’s go back to the basics, my first real interest in programming was with C++. I already have a great grasp over the basics and a decent understanding up to pointers and object oriented programming, so why not go for broke? I want to master C++ by the time I recover from this injury.

I’d like to ask you, reader, what are your favorite C++ programming resources? I would like to do some touch-ups to my basic skill set and then delve into more advanced articles and examples. Do you have any recommendations for projects, articles, chat rooms, anything? Does anyone have some words of wisdom for staying on track with projects? I’ve noticed in the past many times I would start off a project great and just burn-out or lose interest. How do you combat that?

How to view an MRI using ArchLinux

In my previous post I mentioned a knee injury and that I would like to be able to view my own MRI images on my desktop. After some googling and experimentation, I have done it.

To start off with, I’m going to mention that the images provided to me were in the DICOM format. It also appears there is a windows executable on the cd, possibly for viewing the images natively, but I didn’t check into that much so your mileage may vary if you choose that route. I managed to find a hardware accelerated OpenGL MRI viewer, however, it reads images in the NIfTI image format, so I had to convert. I used a program called dcm2nii to convert everything. It features a command line interface, as well as a GUI, I personally used the GUI with no issues.

After the conversion, I found myself with about 15 different images of varying resolution, angle and depth. Not being a doctor, I really had no idea what to look for in terms of diagnosing the injury. That really wasn’t my goal though. My goal was simply to see the inside of my knee, finding the injury myself would be a plus. On that hand, I think I may have found the spot on the meniscus that was torn, just bragging points if I got it right I suppose. Either way, it was still very cool to have a 3D image of my knee which I could freely move around, rotate or pull individual frames from. I highly recommend looking at your own MRIs if you have any. Just for the coolness factor of looking inside your own body.

The website which acted as a portal to all the MRI information I needed is on Chris Rorden’s web page. There are links to all of the software I mentioned as well as additional software and image format information. None of the programs I used are in the Arch Repositories or AUR, so I may package them at some point if there is a demand.

Chris Rorden’s Home

On the hunt for some MRI visualization software

In a very unfortunate turn of events two nights ago, I managed to tear my meniscus (bucket-handle on the lateral). After meeting with my orthopedic, he recommended an MRI to get a better idea of whether or not I will require surgery to repair it, I’ll be going in for that later on tonight. I also understand that the imaging center will give me a CD containing the images for me to bring to the doctor. I fully intend on at least viewing the images myself as opposed to the two weeks until my follow-up appointment.

Now I’m on the search for some way to visualize this data on my computer. I really have no knowledge on actual MRI data formats, so that will be my research project for today. What I would like to know, is there any great MRI visualization software for Arch? How can I view these images on my computer as a 3D model as opposed to the 2D slices I see sometimes?