Coordinate Systems

Written by Andrew Taylor

9MB

Coordinate_Systems.pptx

• Image Spaces (associated with distinct coordinate system)

  • Native space – coordinates unique to subject’s head placement in MRI scanner

  • Standard space – standard defined world coordinates across all images in this space define anatomy location (images in this space can have differ resolutions)

• Coordinate Systems

  • Voxel coordinates

    • no units; integers

    • voxel count in each dimension reflecting matrix size

    • Origin: corner of image (e.g., 0,0,0 or 1,1,1)

    • Origin and axes naming conventions differ in programs

  • World coordinates

    • Have units in mm; floating values

    • Denote anatomy

      • Handedness system

        • Right-handed (RAS) system

          • x+ Left-Right

          • y+ Posterior-Anterior

          • z+ Inferior-Superior

          • Default for: MNI152 space, NifTi

        • LPS system

          • Default for: Dicom

    • Origin: can differ in programs, standard space (e.g., MNI152 space origin at anterior commissure)

• qform and sform Matrices

  PURPOSE: Used to convert voxel coordinates into world coordinates

  o qform & sform stored in the Nifti File

  o Historically, both matrices in a file to keep track of scanner coordinate system (qform) and standard space coordinates (sform); in practice not used; one matrix usually set to 0)

  o Meaningful only if have a NON-ZERO code (0=unknown)