3D Slicer is an open-source program that allows for the three-dimensional visualization and processing of CT scans. The steps to go from a raw CT image sequence to a segmented 3D mesh are outlined below.
Total time: ~10 min
Morphosource is a great place to find sequences of CT scan images if you do not already have a dataset.
To import your images into 3D Slicer, you will need an .nrrd file. If you do not already have an existing .nrrd file, you can generate one using Fiji, a free image processing package available here: https://fiji.sc/
Generating an NRRD File
Open Fiji and go into: File → Import, and select Image Sequence
Select the file that contains your desired image sequence.
If your file is large, you can increase the increment size
Here, you can also determine which portions of the sequence you wish to export, and also change parameters such scaling.
To save your .nrrd, go to: File → Save As→ Nrrd
You now have a 3D Slicer-compatible NRRD image sequence!