Imaging coordinate system
The imaging coordinate system is defined solely by the type of object/specimen under investigation. It serves as a normalized reference frame, sometimes also called the “patient coordinate system”. Many important parameters refer to the imaging coordinate system, i.e. scan planning information, slice positioning, slice orientation, image labels, slice offsets and DICOM metadata. The origin of the imaging reference frame is always aligned with the origin of the physical coordinate system of the MR instrument.
ParaVision supports four different object or specimen:
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- Materials: For an intuitive representation, the imaging reference coordinate system of materials corresponds has been arbitrarily selected to correspond to the head supine human position. This is especially useful for microscopy applications of material in vertical MR instruments. Image labels are given in the right-handed Cartesian coordinate system as shown in (1) below.
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- Rodents: The imaging reference coordinate system is defined by standard animal nomenclature and the DICOM anatomical orientation type “QUADRUPED”. Independent of the animal position inside the magnet, image labels are given in the right-handed Cartesian coordinate system as shown in (2) below.
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- Primates: The imaging reference coordinate system is defined by standard primate (human) nomenclature and the DICOM anatomical orientation type “BIPED”. Independent of the primate position inside the magnet, image labels are given in the right-handed Cartesian coordinate system as shown in (3) below.
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- Others: This imaging reference coordinate system is identical to the coordinate system of primates, see above. It can be used if the object under investigation does not belong to any of the predefined specimen.
Coordinate System for Images
For rodents, primates and others, the correct transformation between imaging coordinate system and the physical coordinate system of the MR instrument is automatically done by ParaVision and depends on the relative position of the object with respect to the MR instrument. The relative position of the object with respect to the scanner is defined during the study registration and cannot be changed within one study, i.e. head first / prone for a rodent that enters with the head first and which is in the natural prone position.
