Getting Ahead

3 minute read

As I mentioned in my earlier post, Who Knows What my Nose Knows, I had a CT scan of my head earlier this month. The CT scan uses magnetic imaging X-rays to produce a series of stacked images. Each image is composed of a 2-dimensional grid of voxels (basically the 3-D equivalent of a pixel). A voxel represents the density of material found at a certain X, Y, Z coordinate within the scan.

My doctor asked me to go back to Washington Imaging Services for another scan. After fighting through ice and snow I got to their office yesterday afternoon. They checked their records and found that they had already done the scan. In the interest of efficiency the technician said “I’ll just burn it on a CD for you and you can take it with you when you go in for your procedure on Monday.”

When I heard that I knew what I had to do.

A few minutes later she handed me a CD and I was on my way to the office. As soon as I got there I pulled the CD out of its protective case, shoved it into the drive, and fired up Windows Explorer to see what was on there. I found a single file called DICOMDIR and a folder with 108 numbered files, each about 500KB. A quick Google search for DICOMDIR told me that it was a standard format — Digital Imaging and Communications in Medicine. Another search, this time for free DICOMDIR viewer, and I found what I needed.

I downloaded the Sante Dicom Viewer Pro, installed it, and pointed it at the CD. A few minutes later I was staring into my brain:


Using the viewer was pretty straightforward. I was able to zoom in and out and to switch from slice to slice with ease. I put it away and worked until late in the evening and then went home to continue.

Arriving home I copied the CD onto my hard drive for safekeeping, and spent some more time looking through the slices. It was actually kind of cool to locate anatomical features such as vertebrae, teeth, eyeballs, ears, nose, and and so forth.

After a search for DICOM viewer 3d I found a really great page of DICOM resources. I scrolled through the extensive list of viewers and chose the Able 3D Doctor application. I downloaded and installed it and started out by viewing the same slices in 2D form. After some poking around I figured out how to do a 3D rendering. The program has a ton of features, most of which I ignored. It allows you to map specific voxel values to colors (different densities, representing different materials) and it also allows for specification of a range of values which should map to a particular color. I used default values for all of these and generated a rendering, which took about 15 minutes on my rather fast desktop machine. The first rendering was a bit strange. I could see my skull, but the slices weren’t in the right order. After staring at the raw slices in 2D form for about half an hour I figured out the right order, and did a pair of move operations in 3D Doctor to set them right. There were 108 slices in all. I moved slices 77 through 107 into position 35, and then moved slices 88 through 107 to position 66. I did another couple of renderings and was rewarded with some very cool pictures.

Here is the 3D Volume View:


And here is the 3D Surface View:


I interrupted the rendering process partway through and accidentally managed to get this amazingly cool view:


This was all pretty cool stuff, and not at all creepy. How often do you get a chance to look into your own skull? Rotating and zooming in on all of the features is quite interesting. There’s actually a lot more asymmetry inside than I would have expected — a feature on one side isn’t always matched exactly with one on the right.

If you ever get a scan, I’d urge you to ask for a copy on a CD. Its your body after all, and you should be entitled to your own data, right?

Anyway, my procedure is scheduled for Monday morning. I’ll post a status report just as soon as I am up and around.