.TH "gdcm2vtk" 1 "Mon Sep 5 2016" "Version 2.4.4" "GDCM" \" -*- nroff -*-
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.SH NAME
gdcm2vtk \- Convert a file supported by VTK into DICOM\&. 

.SH "SYNOPSIS"
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.PP
.nf
gdcm2vtk [options] file-in file-out
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.PP
.SH "DESCRIPTION"
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The \fBgdcm2vtk\fP takes as input any file supported by VTK (including DICOM file) and will generate as output a DICOM file\&.
.SH "PARAMETERS"
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.PP
.nf
file-in   input filename (DICOM or VTK supported)

file-out  output filename (DICOM or VTK supported)
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.PP
.SH "OPTIONS"
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.SS "OPTIONS"
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.nf
     --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.
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.PP
.SS "compression options"
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.nf
  -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).
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.PP
.SS "general options"
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.nf
  -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
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.PP
.SS "environment variable"
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.nf
  GDCM_ROOT_UID Root UID
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.PP
.SH "DESCRIPTION"
.PP
Convert a file supported by VTK into DICOM\&.
.PP
Typical usage is:
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.nf
$ gdcm2vtk inputfile output.dcm
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.PP
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It uses the internal factory mechanism of VTK to recognize a file (CanRead function)\&. See VTK supported file here: 
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.nf
  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

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.PP
.PP
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)\&.
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Special care was taken for the following file format:
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.nf
   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.
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.PP
.SS "CONVERT MetaImage (mhd, mha)"
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.nf
$ gdcm2vtk inputfile output.mha
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.PP
.PP
This command will convert the input DICOM file: inputfile into a MetaImage \&.mha file\&. Same goes for \&.mhd file\&.
.SS "CONVERT MHA/MHD"
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.nf
$ gdcm2vtk inputfile output.mha
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.PP
 or 
.PP
.nf
$ gdcm2vtk inputfile output.mhd

.fi
.PP
.PP
This command will convert the input DICOM file: inputfile into a MetaImageData \&.mha/\&.mhd file\&.
.SS "CONVERT VTI"
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.nf
$ gdcm2vtk inputfile output.vti
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.PP
.PP
This command will convert the input DICOM file: inputfile into a XML VTK ImageData \&.vti file\&.
.SS "CONVERT VTK"
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.nf
$ gdcm2vtk inputfile output.vtk
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.PP
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This command will convert the input DICOM file: inputfile into an old VTK Structured PointSets \&.vtk file\&.
.SH "CONVERT DICOM"
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.nf
$ gdcm2vtk input.dcm output.dcm
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.PP
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\fBvtkGDCMImageReader\fP will be used to read in a DICOM file, not the default vtkDICOMImageReader\&. See option --use-vtkdicom to use vtkDICOMImageReader\&.
.SH "RoundTrip DICOM to MHD to DICOM"
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.PP
.nf
$ gdcm2vtk input_ybr.dcm output.mhd
$ gdcm2vtk --modality US --imageformat 7 output.mhd output.dcm
.fi
.PP
.PP
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\&.
.SH "gdcm2vtk notes"
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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\&.
.PP
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)\&.
.PP
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\&.
.SH "SEE ALSO"
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\fBgdcmdump\fP(1), \fBgdcmviewer\fP(1), \fBgdcmimg\fP(1)
.SH "COPYRIGHT"
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Copyright (c) 2006-2011 Mathieu Malaterre