]> MathieuMalaterreMain developer 20062011Mathieu Malaterre gdcmimg 1 GDCM &version; DICOM Manipulation. gdcmimg Manipulate DICOM image file. gdcmimg is a low level tool to allow de-/encapsulation from/to DICOM image. This tool does not understand Transfer Syntax conversion. It will encapsulate the raw data as-is. This has some impact in some cases, see special warnings below. It is important to note that gdcmimg can only encapsulate proper input file, for instance JPG and or JP2 are accepted since an associated DICOM Transfer Syntax can be found. However input such as TIFF and/or PNG are not, since DICOM does not support those. See instead a tool such as gdcm2vtk. gdcmimg [options] file-in file-out The gdcmimg command line tool can be used in two fashions: 1. Converting a recognized file format into its encapsulated DICOM counterpart, 2. Anonymizing a rectangular portion of a DICOM file. file-in input filename (non-DICOM) file-out DICOM output filename -i --input Input filename -o --output Output filename --endian %s Endianness (LSB/MSB). -d --depth %d Depth (Either 8/16/32 or BitsAllocated eg. 12 when known). --sign %s Pixel sign (0/1). --spp %d Sample Per Pixel (1/3). --pc [01] Change planar configuration. --pi [str] Change photometric interpretation. --pf %d,%d,%d Change pixel format: (BA,BS,HB). -s --size %d,%d Size. --offset %ull Start Offset. -C --sop-class-uid SOP Class UID (name or value). -T --study-uid Study UID. -S --series-uid Series UID. --template Template DICOM file. --keep-meta Keep meta info from template file (advanced users only). --root-uid Root UID. -R --region %d,%d Region. -F --fill %d Fill with pixel value specified. -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 GDCM_ROOT_UID Root UID gdcmimg will base it's conversion process based on the file extension. Follows the list of recognized file extension. When no extension is found, DICOM file is assumed. input format * RAW (raw, rawl, gray, rgb) * RLE (rle) * PNM (pgm, pnm, ppm) * JPEG-LS (jls) * JPEG 2000 (jp2, j2k, j2c, jpx, jpc) * JPEG (jpg, jpeg, ljpg, ljpeg) * DICOM () output format: * PGM (pgm, pnm, ppm) * DICOM () For RAW file format, you should take special care of the –endian option. For the (old) JPEG file format, both the lossy and lossless format are supported, user should pay attention to the –sign option. For file format such as RLE or RAW, user is expected to fill in information required to find the dimension and type of input data as there is no other way to find this information. For all other file format, the properties are derived from the file format itself. PNM file are supposed to be big endian (important for depth > 8) To fill the region [0,100]x[0,100] of a DICOM image simply do: $ gdcmimg --fill 0 --region 0,100,0,100 -i input.dcm -o output_black.dcm Warning: if the Pixel Data is compressed, the image is first decompressed so that pixel can be set to 0, but it is not re-compressed. Recognized extension is .raw, .rawl, .gray or .rgb (case insensitive) $ gdcmimg --size 512,512 --depth 16 -i input.raw -o output.dcm the image will be a Secondary Capture. When the input is 3 component, one need to specify explicitly the Samples Per Pixel: $ gdcmimg --size 512,512 --spp 3 input_rgb.raw output_rgb.dcm When the filename contains .rgb as file extension output is automatically recognized as RGB no need to specify –spp $ gdcmimg --size 512,512 input.rgb output_rgb.dcm You can use the dd cmd line to skip any header you would like to discard, for instance, if you would like to skip the first 108 bytes, simply do: $ dd skip=108 bs=1 if=input.raw of=output.raw .raw and .rawl extension are equivalent. You need to explicitly specify the endianness manually: $ gdcmimg --endian MSB --size 512,512 --depth 16 -i input.raw -o output.dcm or $ gdcmimg --endian LSB --size 512,512 --depth 16 -i input.raw -o output.dcm Recognized extensions are .pgm, .pnm, .ppm (case insensitive) $ gdcmimg -i input.pgm -o output.dcm the image will be a Secondary Capture Recognized extension is .rle (case insensitive) $ gdcmimg --size 512,512 --depth 16 -i input.rle -o output.dcm the image will be a Secondary Capture Recognized extensions are .jpg, .jpeg, .ljpg, .ljpeg (case insensitive) $ gdcmimg -i input.ljpeg -o output.dcm the image will be a Secondary Capture Recognized extensions are .j2k, .jp2, .jpc, jpx, j2c (case insensitive) $ gdcmimg -i input.j2k -o output.dcm the image will be a Secondary Capture. All Pixel information (Bits Stored/Allocated...) will be derived from the image itself, and not from the command line options. Instead of the default Secondary Capture Image Storage, one may want to specify, say VL Photographic Image Storage. $ gdcmimg --sop-class-uid 1.2.840.10008.5.1.4.1.1.77.1.4 input.jpg output.dcm Instead of the default Secondary Capture Image Storage, generated with default values, one may want to specify a DICOM file that will serve as template to fill in the DICOM attributes. $ gdcmimg --sign 1 --template template.dcm input.jpg output.dcm Pay attention that any values from template.dcm that are not consistent with what is found inside the reference image will be overridden (eg. image size). On particular case should be of concern: the Pixel Representation for the JPEG family. gdcmimg handle nicely a set of files (for instance jpeg): $ gdcmimg -C 1.2.840.10008.5.1.4.1.1.12.1 1.jpg 2.jpg 3.jpg 4.jpg output.dcm It is important to specify an SOP Class that supports multi-frames images otherwise gdcmimg will fail. In some case, one may want to create a 2D slice from an arbitrary volume (e.g 3D). In which case –offset becomes handy: $ gdcmimg --offset 4954104330 --size 1673,1673 Input3D_1673_1673_1775.raw slice_1770.dcm There are a couple of issues with gdcmimg implementation: For RAW file, one should pay attention that when using –endian MSB the Pixel Data will be encapsulated as is (not touched by gdcmimg). Therefore the only possible transfer syntax available is Implicit VR Big Endian DLX (G.E Private). GDCM does handle this private Transfer Syntax. So if you need to convert this Transfer Syntax to another one (and allow Pixel Data manipulation), you can use: $ gdcmconv --raw --force input_big_endian_dlx.raw -o output_implicit_vr_little_endian.dcm For JFIF file and JP2 file (with header) the header is copied into the Pixel Data element which is illegal for JP2. Use gdcmconv to properly re-encode a JP2/JFIF file into J2K/JPG. $ gdcmimg input.jp2 output_jp2.dcm $ gdcmconv --j2k --force output_jp2.dcm output_j2k.dcm For RLE file, no check is done for crossing the row boundary. It is recommended to use gdcmconv –rle to re-encode into a proper RLE file in case of doubt. Of course if the compression is not ok with your setup, you can always de-encapsulated the DICOM file (typically JPEG) to a non-encapsulated form, using gdcmconv: $ gdcmconv --raw input_jpeg.dcm output_raw.dcm gdcmdump(1), gdcm2vtk(1), gdcmraw(1), convert(1), dd(1)