I had a MRI today, and afterwards I was given a CD of my scan. The data on the CD was stored in DICOM format, and after some searching I was able to find some open source software to view the data. I especially liked Aeskulap which allowed interactive viewing of the data in multiple dimensions.

I wanted to put my scans online, so I found another set of tools, medcon, that allowed me to convert the DICOM images into png/gif format, and then I used ffmpeg to create the following videos:

I don’t know the exact layout, but on the CD I seemed to have 12 different scans, each with a series of images. The name of the files were all 8 digits numbers, with the first three being the scan number (0 to 11), and the following five digits being (0 to whatever). For example:

DICOM/185723/00000000: DICOM medical imaging data
DICOM/185723/00000001: DICOM medical imaging data
DICOM/185723/00000002: DICOM medical imaging data
...
DICOM/185723/00100000: DICOM medical imaging data
DICOM/185723/00100001: DICOM medical imaging data
DICOM/185723/00100002: DICOM medical imaging data
...

To create videos the first thing I did was to convert the images from DICOM to PNG

sudo apt-get install medcon
mkdir png
for i in DICOM/185723/*; do medcon -f $i -c png -o png/`basename $i`.png ; done;

Now to batch the images I started by creating animated gifs.

sudo apt-get install imagemagick

# Create animated gifs
for i in `seq -w 000 011`; do convert -delay 20 -loop 0 png/$i*.png $i.gif; done;

However, those gifs were huge, up to 20mb. So next I created a set of videos (that were a order of magnitude smaller than the gifs):

sudo apt-get install ffmpeg

# Create MP4
for i in `seq -w 000 011`; do avconv -r 5 -i png/$i%05d.png -r 24 $i.mp4; done;

# Create webm
for i in `seq -w 000 011`; do avconv -r 5 -i png/$i%05d.png -r 24 $i.webm; done;

# Create ogg video
for i in `seq -w 000 011`; do avconv -r 5 -i png/$i%05d.png -r 24 $i.ogg; done;

easy!