MINC File World Coordinates

The MINC file format explicitly specifies which axes should correspond to designated brain axes. For example, the z-axis coordinates should increase when moving from inferior to superior and the y-axis should increase when moving from posterior to anterior. Although often ignored, the same y- and z-axis conventions apply to Analyze format images. However, the conventions for MINC and Analyze images differ for the x-axis. MultiTracer flips MINC images to correspond to the Analyze convention such that the x-axis coordinates increase from right to left.

The MINC file format also allows negative voxel dimensions, which effectively cause real world coordinates to run in the opposite direction of voxel coordinates. MultiTracer flips the voxel order in such cases, so the corner of the image that corresponds to voxel (0,0,0) in the MINC file may correspond to any of the following voxel coordinates in MultiTracer:

When displayed in MultiTracer, the MultiTracer coordinate (0,0,0) of a properly formatted MINC image should be at the right, inferior, posterior edge of the image.

MINC files maintain not only a voxel-based coordinate system, but also a real-world based coordinate system that may be rotated with respect to the voxel-based coordinate system. The origin of this coordinate system need not lie at the edge of the image (for example, MINC files often reference the Tailarach atlas, where the origin is defined as the anterior commisure). A command line interface associated with MultiTracer will allow you to save a .air file that can be used to map contours drawn using MultiTracer into the MINC file's real-world coordinate system. To save a .air file 'test.air' associated with the MINC file 'test.mnc' , use the following command:

java -cp MultiTracer.jar MincWrapper test.mnc test.air
Fully qualified pathname prefixes may need to be applied to the 'java', 'MultiTracer.jar', 'test.mnc' and 'test.air' arguments. No prefix should be applied to the 'MincWrapper' argument

The MINC file's world coordinate system will correspond to the standard file in the resulting .air file. The AIR program reslice_ucf can be used to map contours exported as UCF's into this coordinate system.

Back to main MultiTracer page ©2001-2003 Roger P. Woods, M.D.

Modified: April 22, 2003