Convert NII.GZ to AVIF

Technical note

Before you convert NII.GZ to AVIF

NII.GZ stores a volume rather than a picture: a three-dimensional grid of voxels, each with a physical size in millimetres, plus an orientation matrix that ties the grid to the patient's anatomy. AVIF holds a flat image, so the conversion cuts the volume into slices along the axis most commonly used for viewing and writes each slice as its own numbered file. A 1 mm structural brain scan has somewhere around 180 slices, so a single NII.GZ comes back as a folder of about that many images, in order from one side of the scan to the other. Voxel values in NII.GZ are measurements. Depending on the scan they are MRI signal intensity, Hounsfield units from CT, or the result of an analysis such as a statistical map, where values run negative as well as positive. They are stored as 16-bit integers or 32-bit floating point, often with a scale factor in the header, and AVIF stores brightness levels for display. The conversion maps one onto the other, which is the right result for a figure or a teaching slide and the wrong one for measuring anything.