gdcm2vtk - Man Page

Convert a file supported by VTK into DICOM​.

Synopsis

gdcm2vtk [options] file-in file-out

Description

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

Parameters

file-in   input filename (DICOM or VTK supported)

file-out  output filename (DICOM or VTK supported)

Options

specific 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​.
     --imageformat      Image Format [1-8] (aka PhotometricInterpretation)​.
     --ipp-sort         When input is directory, sort instances using IOP/IPP​.

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

Description

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​.

Convert Dicom

$ 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​.

Roundtrip Dicom to MHD to Dicom

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

The above refsection 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​.

GDCM2VTK Notes

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​.

See Also

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

Author

Mathieu Malaterre

Main developer

Referenced By

gdcm2pnm(1), gdcmimg(1), gdcmviewer(1).

08/07/2026 GDCM 3.0.24 DICOM Manipulation.