gdcm2vtk (1)

gdcm2vtk [options] file-in file-out

The gdcm2vtk takes as input any file supported by VTK (including DICOM file) and will generate as output a DICOM file.

file-in   input filename (DICOM or VTK supported)

file-out  output filename (DICOM or VTK supported)

OPTIONS

     --force-rescale    force rescale.
     --force-spacing    force spacing.
     --palette-color    when supported generate a PALETTE COLOR file.
     --argb             when supported generate a ARGB file.
     --compress         when supported generate a compressed file.
     --use-vtkdicom     Use vtkDICOMImageReader (instead of GDCM).
     --modality         set Modality.
     --lower-left       set lower left.
     --shift            set shift.
     --scale            set scale.
     --compress         set compression (MetaIO).
  -T --study-uid        Study UID.
  -S --series-uid       Series UID.
     --root-uid         Root UID.

compression options

  -J --jpeg             Compress image in jpeg.
  -K --j2k              Compress image in j2k.
  -L --jpegls           Compress image in jpeg-ls.
  -R --rle              Compress image in rle (lossless only).

general options

  -h   --help
         print this help text and exit

  -v   --version
         print version information and exit

  -V   --verbose
         verbose mode (warning+error).

  -W   --warning
         warning mode, print warning information

  -E   --error
         error mode, print error information

  -D   --debug
         debug mode, print debug information

environment variable

  GDCM_ROOT_UID Root UID

Convert a file supported by VTK into DICOM.

Typical usage is:

$ gdcm2vtk inputfile output.dcm

It uses the internal factory mechanism of VTK to recognize a file (CanRead function). See VTK supported file here:

  What image file formats can VTK read and write? http://www.vtk.org/Wiki/VTK_FAQ#What_image_file_formats_can_VTK_read_and_write.3F

If your input file has 4 components, the 4th comp (alpha) will be removed from the output file as DICOM does not support alpha component anymore (see --argb option).

Special care was taken for the following file format:

   1. DICOM: Direction Cosines and vtkMedicalImageInformation are passed to the output
   2. BMP: The file can be saved with a Lookup Table (see --palette-color)
   3. GE Signa: vtkMedicalImageProperties is passed to the output
   4. MINC: Direction Cosines is passed to the output
   5. TIFF: vtkTIFFReader is currently in bad shape in VTK (different behavior in VTK 5.2 and git/master). Only use it, if you know what you are doing.

CONVERT MetaImage (mhd, mha)

$ gdcm2vtk inputfile output.mha

This command will convert the input DICOM file: inputfile into a MetaImage .mha file. Same goes for .mhd file.

CONVERT MHA/MHD

$ gdcm2vtk inputfile output.mha

or

$ gdcm2vtk inputfile output.mhd

This command will convert the input DICOM file: inputfile into a MetaImageData .mha/.mhd file.

CONVERT VTI

$ gdcm2vtk inputfile output.vti

This command will convert the input DICOM file: inputfile into a XML VTK ImageData .vti file.

CONVERT VTK

$ gdcm2vtk inputfile output.vtk

This command will convert the input DICOM file: inputfile into an old VTK Structured PointSets .vtk file.

$ gdcm2vtk input.dcm output.dcm

vtkGDCMImageReader will be used to read in a DICOM file, not the default vtkDICOMImageReader. See option --use-vtkdicom to use vtkDICOMImageReader.

$ gdcm2vtk input_ybr.dcm output.mhd
$ gdcm2vtk --modality US --imageformat 7 output.mhd output.dcm

The above section shows how to convert a DICOM using the Photometric Interpretation of YBR_FULL (or even YBR_FULL_422 is lossy) into another file format: MetaImage (mhd). Since this file format does not handle color space, we have to explicitly set it using the --imageformat command line option. The --modality command line option is required in this case since the default Secondary Capture Image Storage Class family does not allow for YBR Photometric Interpretation.

IMPORTANT NOTE: The internal VTK structured will be filled from the input DICOM, and then pass to the output DICOM writer. Some information might be lost during the conversion DICOM to VTK to DICOM. This option is mostly used to test the vtkGDCMImageReader/vtkGDCMImageWriter combination.

IMPORTANT NOTE: When converting from a lossy format such as JPEG, the information of lossiness is important. The output DICOM will contains the required Lossy Image Compression attribute that indicates that image was lossy-compressed somewhere along the pipeline. See also gdcmimg (better handling of JPEG in general).

IMPORTANT NOTE: When using --use-vtkdicom the output DICOM file will always be written as MR Image Storage as this information is not available from the reader itself. This allow setting the Image Orientation (Patient) properly.

gdcmdump(1), gdcmviewer(1), gdcmimg(1)

Copyright (c) 2006-2011 Mathieu Malaterre