On Monday I had a CT scan. If you haven’t already, every visualist should go for a ride in a computed tomography machine. It’s the best mix of futuristic medicine and video geekness I’ve ever encountered. As happens with most medical imaging these days, I came away with both a collection of printed films and a CD full of images. However, unlike previous scans and xrays which were generally disparate grainy stills of amorphous organs or bones, these prints showed hundreds of clear, consecutive slices through my body.

Jaymis CT Scan Slice
Yes, that’s my heart and lungs. I love technology so damn much.

Looking at the films I knew immediately that I should be able to use the frames to create an animation. Checking through the CD I found a folder of images named “CT000000”, “CT000001” etc. Some quick googling informed me that these are DICOM format files, which contain both patient information and imagery.

Anyone on Windows who works with images should know the fantastic, free image viewer/toolkit Irfanview – it’s the VLC of the still-image world! Irfanview has a plugin in its default bundle which allows it to read and operate on DICOM files, as long as they have a .DCM extension. Fortunately Irfanview’s batch functions feature both Rename and Convert, so I was able to quickly go from the aforementioned folders of consecutively named, extensionless files; to folders filled with consecutively named .BMPs, which any visualist will recognize as a Good Thing.

From there it was a quick hop to After Effects [tag on CDM], and I was able to scrub a timeline to look through my organs. Quite the definition of “freaky technology”. The human body is quite full of various blobs and tubes though (well mine is anyway), so instead of turning this into a blobby animation I spent some time colour correcting to isolate just the brightest points: My skeleton.

Inside The Jaymis: Skeleton Animation – Wide Time from Jaymis on Vimeo.

At 25FPS the animation only lasted 11 seconds, so I used After Effects’ time stretch and frame-blending (the “high quality” morphing type) to slow it down and stretch it out. This looks great for the most part, but some sections have quite obvious frame-morphing distortion going on. I also applied the “CC Wide Time” effect, which onionskinned 8 frames before and after. This gives a better feel of the 3D volume, as opposed to the “narrow time” version, which shows only one frame at a time. This is more accurate, but slightly harder to understand.

And yes, I do feel that my skeleton is epic enough to warrant Mogwai Fear Satan.

So I’ve had a great time with my small CT scan, enough to hope that I get sent in for another one soon so I can scam the technician into scanning my whole body. In the meantime, I’m sure there’s more which can be done with this imagery. Looking at the slices, it seems as though I should be able to turn them into a 3D model of my spine… Which I could get printed and give to my girlfriend as ear rings.

I’ve been looking around and haven’t been able to locate any tools which will convert flat slices in to 3D data. I’m sure that at least a couple of CDMsters have done so in the past though. Any suggestions? Would anyone like to send me their CT scan data so I can make a 3D model of their skull?

[Update: I’ve made a “Squishy Bits” version, with organs included, showing both the morphed version and the original frames.]

  • using a mac? try osirix

  • Great idea Jaymis. I didn't know you got given yours scans on CD now, thats awesome. I always wished I got to keep the x-Rays I had as a kid.

    This is a really interesting use of the technology to make something visually stunning. Think I prefer the Narrow Time version personally.

  • That is so cool. I've had scans recently, but have never seen the images, far less been offered a disk of them to take away.

  • very impressive!

  • rhowaldt

    My skeleton.

    What's wrong with blobby animations? You just did this as to avoid people making funny comments about how they could see your manhood.

  • here is what you are looking for, and its free, open source, and for the mac…


    OsiriX is an image processing software dedicated to DICOM images (".dcm" / ".DCM" extension) produced by imaging equipment (MRI, CT, PET, PET-CT, …) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or imaging modality (STORE SCP – Service Class Provider, STORE SCU – Service Class User, and Query/Retrieve) .

    OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT).

    The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT).

    have fun 🙂

  • rich

    Can Photshop do the same thing as IrfanView?

  • HenningK

    Drishti: http://anusf.anu.edu.au/Vizlab/drishti/

    "Volume Exploration and Presentation Tool"

  • Dan

    I love how the vertebrae at 0:17 look like some sort of swimming/flying creature.

    I've been using tomographic animations in a different context:
    rheotomic surfaces

  • check this out: http://www.volumedic.com/
    it converts DICOM files in 3d models. i have been told thats what they use for CSI.

  • http://www.slicer.org/
    The learning curve might be steep, but eh, it's open source…

  • hunter19

    Hi Jaymis
    please consider radiation dose issues before opting for a unnecessary full body scan…
    google a little about that
    just a thought

  • @Lawrie: I've received the CDs from all of the scans I've had done (ultrasound and CT), but not from an Xray. I didn't have to request them or anything, the discs were just included in the package of materials.


    You just did this as to avoid people making funny comments about how they could see your manhood

    If that was my only concern, I could just remove the "offending" frames.. Thought that wouldn't leave much of the animation (OH SNAP!)
    Seriously though, without frame blending, everything goes past too quickly to really understand what's going on. With frame blending, there's too many blobs for the algorithm to understand and it goes from "occasional distracting morphing" to "everything's morphing all over the place", which isn't really an aesthetic I'm in to. I'll render out an example though for completeness 🙂

    @VJrabauke and @exiledsurfer: Nice one on Osirix. I hadn't even thought to look for something on Mac! I'll see if I can get anything meaningful out of it.

    @Rich: Photoshop won't touch DICOM natively, but there does seem to be an impressive and expensive plugin available.

    @HenningK, @manuel and @Sylvain: Thanks for those. I'm sure with all of these possibilities I'll be able to get something more interesting out!

    @hunter19: I did some reading on it, and a single scan seems to be about the same radiation dose as I'd receive living on planet earth for 2-3 years. The increased risk of illness from this seems to be minimal, and considering the other exciting/dangerous things I'm happy to do for fun: Riding planks of fiberglass down mountains etc. and that I'm going to have one of my internal organs removed in a couple of weeks, I'd prefer to grab Art as hard as I can than worry about 0.05% chances of things which could possibly happen.

  • Scratchpole

    Toneburst Quartz composer gem: http://www.vimeo.com/2848308

  • Scratchpole

    Oh yeh forgot to say, the best thing I find about Osirix is the QTVR export function.

  • Ok. Here's the squishy bits version, showing both morphed and single frame styles.

  • yuv

    Finally! Proof that the body is indeed a series of tubes!

  • zach

    I've also been playing with OsiriX, using the 3d surface rendering feature to export wavefront files. There's a ton of great DICOM files (with the patient data removed) available for download on their website. I actually had an MRI recently and was able to get a copy on CD. Unfortunately, MRIs don't make nearly as good 3d models at CTs, due to the focus on soft tissue.

    Anyway, here's an animation I made in Max from the wavefront files: http://vimeo.com/3610906. Obviously, working with such large models can slow down your computer quite a bit. Just when I got the whole thing to run at 30 fps, I realized that I didn't leave any processing power to record it- the stuttery result is what you see.

  • rich

    I pretty sure that Photoshop Extended opened and animated DICOM files in CS3… maybe I'm skimming here too fast.