gdcmimg(1)							       GDCM								gdcmimg(1)

NAME

       gdcmimg - Manipulate DICOM image file.

SYNOPSIS

       gdcmimg [options] file-in file-out

DESCRIPTION

       The gdcmimg command line tool can be used in two fashions:

       o 1. Converting a recognized file format into its encapsulated DICOM counterpart,
       o 2. Anonymizing a rectangular portion of a DICOM file.
PARAMETERS

       file-in	 input filename

       file-out  output filename
options
   PARAMETERS
	 -i --input	Input filename
	 -o --output	Output filename
   options
	    --endian %s       Endianness (LSB/MSB).
	 -d --depth %d	      Depth (8/16/32).
	    --sign %s	      Pixel sign (0/1).
	 -s --size %d,%d      Size.
	 -C --sop-class-uid   SOP Class UID (name or value).
	 -T --study-uid       Study UID.
	 -S --series-uid      Series UID.
	    --root-uid	      Root UID.
   fill options
	 -R --region %d,%d    Region.
	 -F --fill %d	      Fill with pixel value specified.
   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
Supported File Format (appropriate file extension)
       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, gray, rgb)
	 * RLE	     (rle)
	 * PNM	     (pgm, pnm, ppm)
	 * JPEG-LS   (jls)
	 * JPEG 2000 (jp2, j2k, j2c, 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.
Typical usage
   Remove a rectangular part of the image
       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 recompressed.
   Convert RAW to DICOM
       Recognized extension is .raw, .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 explicitely 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
   Convert PGM/PNM/PPM to DICOM
       Recognized extensions are .pgm, .pnm, .ppm (case insensitive)
       $ gdcmimg -i input.pgm -o output.dcm
       the image will be a Secondary Capture
   Convert RLE to DICOM
       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
   Convert JPEG to DICOM
       Recognized extensions are .jpg, .jpeg, .ljpg, .ljpeg (case insensitive)
       $ gdcmimg -i input.ljpeg -o output.dcm
       the image will be a Secondary Capture
   Convert J2K to DICOM
       Recognized extensions are .j2k, .jp2, .jpc (case insensitive)
       $ gdcmimg -i input.j2k -o output.dcm
       the image will be a Secondary Capture
   Specifying a SOP Class UID
       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
Multiple Files
       gdcmimg handle nicely a set of files (for instance jpeg):
       $ gdcmimg 1.jpg 2.jpg 3.jpg 4.jpg output.dcm
Warning
       There are a couple of issues with gdcmimg implementation: 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
SEE ALSO

       gdcmdump(1), gdcmdump(1), gdcmraw(1), convert(1), dd(1)
COPYRIGHT

       Copyright (c) 2006-2011 Mathieu Malaterre

Version 2.2.0							  Tue Feb 5 2013							gdcmimg(1)