NAME
gdcmimg - .TH "gdcmimg" 1 "Sun Aug 8 2010" "Version 2.0.15" "GDCM"
NAME
gdcmimg - .SH "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)
* 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 (case insensitive)
$ gdcmimg --size 512,512 --depth 16 -i input.raw -o output.dcm
the image will be a Secondary Capture
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
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) 2006-2010 Mathieu Malaterre