1GDCM2VTK(1) DICOM Manipulation. GDCM2VTK(1)
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6 gdcm2vtk - Convert a file supported by VTK into DICOM.
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9 gdcm2vtk [options] file-in file-out
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12 The gdcm2vtk takes as input any file supported by VTK (including DICOM
13 file) and will generate as output a DICOM file.
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16 file-in input filename (DICOM or VTK supported)
17 file-out output filename (DICOM or VTK supported)
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21 specific options
22 --force-rescale force rescale.
23 --force-spacing force spacing.
24 --palette-color when supported generate a PALETTE COLOR file.
25 --argb when supported generate a ARGB file.
26 --compress when supported generate a compressed file.
27 --use-vtkdicom Use vtkDICOMImageReader (instead of GDCM).
28 --modality set Modality.
29 --lower-left set lower left.
30 --shift set shift.
31 --scale set scale.
32 --compress set compression (MetaIO).
33 -T --study-uid Study UID.
34 -S --series-uid Series UID.
35 --root-uid Root UID.
36 --imageformat Image Format [1-8] (aka PhotometricInterpretation).
37 --ipp-sort When input is directory, sort instances using IOP/IPP.
38 compression options
40 -J --jpeg Compress image in jpeg.
41 -K --j2k Compress image in j2k.
42 -L --jpegls Compress image in jpeg-ls.
43 -R --rle Compress image in rle (lossless only).
44 general options
46 -h --help
47 print this help text and exit
48 -v --version
50 print version information and exit
51 -V --verbose
53 verbose mode (warning+error).
54 -W --warning
56 warning mode, print warning information
57 -E --error
59 error mode, print error information
60 -D --debug
62 debug mode, print debug information
63 environment variable
65 GDCM_ROOT_UID Root UID
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68 Convert a file supported by VTK into DICOM.
69 Typical usage is:
71 $ gdcm2vtk inputfile output.dcm
73 It uses the internal factory mechanism of VTK to recognize a file
75 (CanRead function). See VTK supported file here:
76 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
78 If your input file has 4 components, the 4th comp (alpha) will be
80 removed from the output file as DICOM does not support alpha component
81 anymore (see –argb option).
82 Special care was taken for the following file format:
84 1. DICOM: Direction Cosines and vtkMedicalImageInformation are passed to the output
86 2. BMP: The file can be saved with a Lookup Table (see --palette-color)
87 3. GE Signa: vtkMedicalImageProperties is passed to the output
88 4. MINC: Direction Cosines is passed to the output
89 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.
90 CONVERT MetaImage (mhd, mha)
92 $ gdcm2vtk inputfile output.mha
93 This command will convert the input DICOM file: inputfile into a
95 MetaImage .mha file. Same goes for .mhd file.
96 CONVERT MHA/MHD
98 $ gdcm2vtk inputfile output.mha
99 or
101 $ gdcm2vtk inputfile output.mhd
103 This command will convert the input DICOM file: inputfile into a
105 MetaImageData .mha/.mhd file.
106 CONVERT VTI
108 $ gdcm2vtk inputfile output.vti
109 This command will convert the input DICOM file: inputfile into a XML
111 VTK ImageData .vti file.
112 CONVERT VTK
114 $ gdcm2vtk inputfile output.vtk
115 This command will convert the input DICOM file: inputfile into an old
117 VTK Structured PointSets .vtk file.
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120 $ gdcm2vtk input.dcm output.dcm
121 vtkGDCMImageReader will be used to read in a DICOM file, not the
123 default vtkDICOMImageReader. See option –use-vtkdicom to use
124 vtkDICOMImageReader.
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127 $ gdcm2vtk input_ybr.dcm output.mhd
128 $ gdcm2vtk --modality US --imageformat 7 output.mhd output.dcm
129 The above refsection shows how to convert a DICOM using the Photometric
131 Interpretation of YBR_FULL (or even YBR_FULL_422 is lossy) into another
132 file format: MetaImage (mhd). Since this file format does not handle
133 color space, we have to explicitly set it using the –imageformat
134 command line option. The –modality command line option is required in
135 this case since the default Secondary Capture Image Storage Class
136 family does not allow for YBR Photometric Interpretation.
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139 IMPORTANT NOTE: The internal VTK structured will be filled from the
140 input DICOM, and then pass to the output DICOM writer. Some information
141 might be lost during the conversion DICOM to VTK to DICOM. This option
142 is mostly used to test the vtkGDCMImageReader/vtkGDCMImageWriter
143 combination.
144 IMPORTANT NOTE: When converting from a lossy format such as JPEG, the
146 information of lossiness is important. The output DICOM will contains
147 the required Lossy Image Compression attribute that indicates that
148 image was lossy-compressed somewhere along the pipeline. See also
149 gdcmimg (better handling of JPEG in general).
150 IMPORTANT NOTE: When using –use-vtkdicom the output DICOM file will
152 always be written as MR Image Storage as this information is not
153 available from the reader itself. This allow setting the Image
154 Orientation (Patient) properly.
155
157 gdcmdump(1), gdcmviewer(1), gdcmimg(1)
158
160 Mathieu Malaterre
161 Main developer
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164 Copyright © 2006, 2011 Mathieu Malaterre
165GDCM 3.0.12 08/02/2022 GDCM2VTK(1)