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/*!
\page gdcm2vtk Convert a file supported by VTK into DICOM.
\section synopsis SYNOPSIS
\verbatim
gdcm2vtk [options] file-in file-out
\endverbatim
\section description DESCRIPTION
The \b gdcm2vtk takes as input any file supported by VTK (including DICOM file) and will generate as output
a DICOM file.
\section parameters PARAMETERS
\verbatim
file-in input filename (DICOM or VTK supported)
file-out output filename (DICOM or VTK supported)
\endverbatim
\section options OPTIONS
\subsection options options
\verbatim
--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.
\endverbatim
\subsection compression_options compression options
\verbatim
-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).
\endverbatim
\subsection general_options general options
\verbatim
-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
\endverbatim
\subsection environment_variable environment variable
\verbatim
GDCM_ROOT_UID Root UID
\endverbatim
\section description DESCRIPTION
Convert a file supported by VTK into DICOM.
Typical usage is:
\verbatim
$ gdcm2vtk inputfile output.dcm
\endverbatim
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:
\verbatim
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.
\endverbatim
\subsection convert_meta CONVERT MetaImage (mhd, mha)
\verbatim
$ gdcm2vtk inputfile output.mha
\endverbatim
This command will convert the input DICOM file: inputfile into a MetaImage .mha file. Same goes for .mhd file.
\subsection convert_mha CONVERT MHA/MHD
\verbatim
$ gdcm2vtk inputfile output.mha
\endverbatim
or
\verbatim
$ gdcm2vtk inputfile output.mhd
\endverbatim
This command will convert the input DICOM file: inputfile into a MetaImageData .mha/.mhd file.
\subsection convert_vti CONVERT VTI
\verbatim
$ gdcm2vtk inputfile output.vti
\endverbatim
This command will convert the input DICOM file: inputfile into a XML VTK ImageData .vti file.
\subsection convert_vtk CONVERT VTK
\verbatim
$ gdcm2vtk inputfile output.vtk
\endverbatim
This command will convert the input DICOM file: inputfile into an old VTK Structured PointSets .vtk file.
\section convert_dicom CONVERT DICOM
\verbatim
$ gdcm2vtk input.dcm output.dcm
\endverbatim
vtkGDCMImageReader will be used to read in a DICOM file, not the default vtkDICOMImageReader.
See option --use-vtkdicom to use vtkDICOMImageReader.
\section round_tripmhd RoundTrip DICOM to MHD to DICOM
\verbatim
$ gdcm2vtk input_ybr.dcm output.mhd
$ gdcm2vtk --modality US --imageformat 7 output.mhd output.dcm
\endverbatim
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.
\section gdcm2vtk_notes 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.
\section see_also SEE ALSO
<b>gdcmdump</b>(1), <b>gdcmviewer</b>(1), <b>gdcmimg</b>(1)
\section copyright COPYRIGHT
Copyright (c) 2006-2011 Mathieu Malaterre
*/
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