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animatedicom

Visualise and animate a DICOM data series

This simple python script allows you to create an interactive 3D visualisation of a DICOM series; moreover, it animates the scene with a camera rotation about the azimuth.

It is aimed at medical physics students who work with DICOM for their research, and who are looking for an eye catching animation for a conference presentation, or are just interested in exploring their data in 3D.

Visit 2MRD's YouTube Channel for example animations.

Usage

Use animatedicom.py to produce a series of frames as .png images.

animatedicom.py [-h] [--dicomdir DICOMDIR] [--output OUTPUT] [--animate]
optional arguments:
    -h, --help              show this help message and exit
    --dicomdir=DICOMDIR     The directory containing the dicom series (default:./)
    --output=OUTPUT         The generated animation output directory (default:./animation/)
    --animate               Animate camera rotation about the azimuthal axis and save each frame

The collection of frames can be rendered into a movie with the following steps:

$> cd ./animation/png/
$> mogrify -format gif  -resize <width>x<height>^ -gravity center -extent <width>x<height>^ *.png 
$> cd .. 
$> mkdir gif
$> cp png/*.gif ./gif/
$> cd gif/

# Create the gif animation using ImageMagick.                               
$> convert -delay 1 -loop 0 frame*.gif final.gif

# Convert the animated gif to mp4 movie.                                    
$> ffmpeg -i final.gif final.mp4