View source for Slicer3:Coordinates

== Coordinate Definitions ==

This page describes the coordinate system assumptions for Slicer3

[[Image:Slicer3-coordinates.png|thumb|right|400px]]

=== Volumes ===

IJK refers to voxel index coordinates.

RAS refers to Right-Anterior-Superior subject-referenced coordinates.

Each volume includes a transformation to go from voxel indices (IJK) to world (RAS).  This is obtained with the vtkMRMLVolumeNode::GetRASToIJKMatrix(vtkMatrix4x4).

=== Models ===

Model vertices are expressed in millimeters, in RAS space.

=== Fiducials === 

Fiducial points are expressed in millimeters, in RAS space.

=== Transforms ===

All transforms at RAS to RAS transforms.

== Notes ==

* image data in a volume is laid out in memory in the same order as it is read from disk.  That is, the "infamous VTK Y-flip" is ''not'' applied.
* the reader for each file type is required to provide the IJKToRAS mapping.