If you go for an ultrasound or some other imaging procedure, they may give you a CD with the images that requires some overly complicated and under-featured Windows viewer. Chances are these images are in DICOM format, which is like the AVI of the medical world.

Your first clue will be that file might report the file as an unoptimised QuickTime movie, e.g.

$ file ./QMAG0001
./QMAG0001: Apple QuickTime movie (unoptimized)

After figuring out the file type wasn't actually anything to do with QuickTime, I tried some of the many different tools and methods to convert this to something viewable. Unfortunatley, the DICOM viewer in GIMP and ImageMagick (probably the same thing?) didn't like the files at all, and neither did a range of other tools. I finally managed to do it with the dcm2pnm tool from the Debian dcmtk package -- just point it at the file and it spits out a PNM which is easily converted by all graphics tools.

You can also encapsulate a series of images in a DICOM file, like a little movie. dcm2pnm extracts these easily, but requires the --all-frames options. An ffmpeg recipe to turn these extracted files into a more easily viewable movie is:

$ ffmpeg -qscale 5 -r 20 -b 9600 -i foo.%d.ppm movie.mp4

I certainly can't guarantee this will actually work for you, as DICOM appears to be an extremely complicated format with many possible vendor extensions. But hopefully it's a starting point!

posted at: Sun, 08 Feb 2009 14:11 | in /linux/tips | permalink | add comment (2 others)