2. Creating .raw files with ImageJ

Any 3D clinical data (CT scans, MRI) must be converted into an image stack in .raw format. Clinical data commonly is stored in DICOM format. In order to convert from .dcm to .raw, we use ImageJ. ImageJ will also have a suite of tools in its default installation to perform a variety of edits on image stacks.

These edits include but are not limited to:

• Changing the relative size and units of voxels (mandatory)
• Altering brightness/contrast in the 3D volume (recommended)
• Removing background noise in the image (recommended)
• Recolouring and built-in labeling
• Resizing the resolution of the volume (recommended)
• Reducing the memory footprint of the image stack (recommended)