DICOM data orientation

From IGSTK

Contents 1 Introduction 2 Viewing Convention 3 Observations 4 Miscellaneous 5 Dicom related issues in IGSTK 6 Further information

Introduction

Dicom uses patient-centered coordinate system convention. In patient-centered convention, the coordinate axes are oriented in the same direction regardless of the patient's position on the scanner. Dicom standard contains tags that provide information about image position and orientation

1. Image Position (0020,0032): specifies the x, y, and z coordinates of the upper left hand corner of the image. In other words, this tag specifies the coordinates of the the first voxel transmitted.
2. Image Orientation (0020,0037): specifies the direction cosines of the first row and the first column with respect to the patient. The direction of the axes are defined by the patients orientation to ensure LPS system ( x-axis increasing to the left hand side of the patient, y-axis increasing to the posterior side of the patient and z-axis increasing toward the head of the patient )
3. Patient position( 0018,5100) : Patient position descriptor relative to the equipment. Required for CT and MR images. Possible values: HFP= head first-prone, HFS=head first-supine, HFDR= head first-decibitus right, HFDL = head first-decubiturs left, FFP = feet first-prone, FFS, FFDR, FFDL.

Viewing Convention

Viewing convention is NOT part of the DICOM standard. However, there are two widely used viewing conventions

1. Radiological convention: Images are viewed as though looking upward from the feet of the subject ( feet to head ). "Right is Left"
2. Neurological convention: Images are viewed as though looking from the top of the head downward ( head to feet ). "Right is right"

DICOM-compliant scanning devices transmit pixels for radiological viewing convention. The scanning device orders the pixels depending on the patient orientation during the scan. Hence, the image technologist must indicate the patient orientation before scanning starts.

Observations

1. When patient position is "HFP", the image orientation direction axis will be [-1 0 0, 0 -1 0] to ensure LPS orientation
2. Slicer 3.0 displays the "HFP" patient oriented image correctly ( 3D view shows the orientations correctly )

Miscellaneous

1. DICOM uses millimeter units
2. DICOM stores the upper left pixel as the first pixel in an image. However, VTK stores the lower left pixel as the first pixel in an image (Flipped in the y-axis)
3. Slicer3 stores image data in memory consistent with DICOM convention ( unlike Slicer2 which stores image data in VTK convention.

Dicom related issues in IGSTK

1. How do we incorporate clinician viewing preference (Radiological or Neurological) into IGSTK pipeline?
2. How to use the direction cosine information in DICOM image data?
   1. Currently, we get the direction cosine from itkOrientedImage and generate image transform based on the direction cosine and image origin information. In the ImageSpatialObject representation class, a vtk transform matrix is generated using this image transform and then gets applied to the image actor for correct viewing.

Further information

1. Discussion in the ITK wiki
2. Paper on DICOM coordinate definitions and parameters that need to be considered for conversion to another coordinate system
3. Orientation and Voxel-order terminology