Animation from CT scan images

Craft & Design

Jaymis on Create Digital Motion writes:

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.

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.

I can’t wait to do this with my MRI images!

16 thoughts on “Animation from CT scan images

  1. Xray says:

    Except for the fact that CT gives a very high dose of ionizing radiation, I couldn’t agree more. MRI would be safer.
    If your running a Mac, google Osirix and you can d/l CT images that don’t mean you need a large dose of xrays!

  2. Stephen says:

    Computed Tomography is just a way of processing the images – tomography is a way of building up a 3-dimensional image of an object by using 2D slices and computed is because it’s faster that way.

    Saying that CT gives you a high dose of radiation is kinda up there with saying that Photoshop’s Polar Coordinates filter gives you AIDS. The problem is that those 2D slices are generally generated with a powerful X-Ray machine but the technology does date back to 1971 and that’s what they were using back then. Even CNN has used a form of tomography, it’s a pretty powerful image processing technology.

  3. Xray says:

    Lol! I am sorry! Have I missed something with your analogy? Jaymis suggests “very visualist should go for a ride in a computed tomography machine”. So, if you toddle off to your local CT machine and have them scan you, you will receive a high dose of ionising radiation. Period. Your radiation dose (depending on weight) would be around 14mSv, around 20x greater than a plain film x-ray. All ionising radiation carries a risk of developing cancer and so exposure should be medically justified.
    If you do want to see images like these, MRI scans would be better.
    Now, how do I get rid of photoshop? I sure don’t want to catch AIDS from that pesky polar co-ordiante filter…

  4. Animation from CT scan images Becky Stern says:

    Hey folks, Im sure Jaymis had a medical reason to get a CT scan, he just wanted to do something fun with the imagery! Just like me and my MRI; I never would be able to afford to get one if my insurance weren’t footing the bill, so the animations (or in my case, embroidery) are just a happy byproduct of a medical procedure.

  5. Adolph Trudeau says:

    One of the things making a movie misses out on is the way that medical imaging software adjusts levels/contrast/etc to better see different types of body tissue. Bone is interesting but soft tissue is pretty neat too!

    In the below link, someone who had an MRI made a neat wood block puzzle/model of the diagnostic image:

    I think he later processed the data into a 3d fly-through but I couldn’t find that immediately.

  6. Aion says:

    yep, did this and more with my brain scan
    raw data animated:

    3D voxelized data:

  7. says:

    Hi guys. There was indeed a legitimate medical reason for this particular scan.

    I’ve also done another version with the organs included:


  8. Neuroscientist says:

    You can try Brainvoyager for your MRI data. They have a free Viewer that allows some neat stuff.

    Or, can also use SPM if you have a version of MATLAB available. (Just google SPM, download the software and look at the good documentation.) It’s released under GNU, but still you need Matlab.

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Becky Stern is a Content Creator at Autodesk/Instructables, and part time faculty at New York’s School of Visual Arts Products of Design grad program. Making and sharing are her two biggest passions, and she's created hundreds of free online DIY tutorials and videos, mostly about technology and its intersection with crafts. Find her @bekathwia on YouTube/Twitter/Instagram.

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