DICOM CONVERSION

Some format conversions are provided by this package:

DICOM to Nifti

Relies on dcm2niix, which must be installed and in path (or set in config file).

DICOM to HTML

Will build a standalone .html file to display DICOM series in ParaView Glance renderer.

DICOM to VTK

A DICOM to VTK format conversion is provided. See VTK format documentation here.

Format conversions are:

  • DICOM to image data (vti format). Suitable for 3D image volumes. This format is axis-aligned (there is no embedded transformation). But “Field Data” embedded in the file are included as “ImageOrientationPatient” which, along with the Image Origin and Image Spacing methods can be used to construct a transformation matrix allowing conversion from image to real-world coordinate space.

  • DICOM to structured dataset (vts format). This will result in a dataset that is in the true real world (patient) coordinate space. NOTE: Due to VTK format such a file has a larger (disc) size than a VTI file.

  • DICOM to image data format but in the true image coordinates. This will be an axis-aligned image but covering the true image coordinates - image dimensions will be different from the original. This is basically a resample of the VTS output to a VTI dataset.

  • Work In Progress: DICOM to planar dataset (vtp format).

GENERAL CONVERSIONS

For general DICOM manipulation and analysis the class PatientMeta found in dcmVTKTK.py is useful. It provides a number of properties that can be used to get the basic dicom meta data.