Convert NII.GZ to JXR

Technical note

NII.GZ to JXR: what to expect from the conversion

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. JXR 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. The voxel size does not survive. JXR has no field for millimetres per pixel, and in clinical scans voxels are often far from cubic, for example 0.5 mm across a slice and 5 mm between slices. The images look correct, but anything measured on them comes out in pixels rather than in anatomy. For distances and volumes, keep the NII.GZ original or convert to TIFF, which preserves the spacing.