Provided by: libgdcm-tools_2.8.8-9ubuntu3_amd64 bug

NAME

       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.

SYNOPSIS

           gdcmimg [options] file-in file-out

DESCRIPTION

       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.

PARAMETERS

           file-in   input filename (non-DICOM)

           file-out  DICOM output filename

OPTIONS

             -i --input     Input filename
             -o --output    Output filename

SPECIFIC OPTIONS

                --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).
             -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.
                --template        Template DICOM file.
                --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, 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)

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 re-compressed.

   Convert RAW to DICOM
       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

   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, 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.

   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

   Specifying a template DICOM file
       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 overriden (eg. image size). On particular case should
       be of concern: the Pixel Representation for the JPEG family.

MULTIPLE FILES

       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.

START OFFSET

       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

WARNING

       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

SEE ALSO

       gdcmdump(1), gdcm2vtk(1), gdcmraw(1), convert(1), dd(1)

AUTHOR

       Mathieu Malaterre
           Main developer

COPYRIGHT

       Copyright © 2006, 2011 Mathieu Malaterre