gdcmgendir(1) [debian man page]
gdcmgendir(1) GDCM gdcmgendir(1) NAME
gdcmgendir - Tool to generate a DICOMDIR file from a File-Set. SYNOPSIS
gdcmgendir [options] file-in file-out DESCRIPTION
PARAMETERS
file-in DICOM input filename file-out DICOM output filename options Parameters options -i --input DICOM filename or directory -o --output DICOM filename or directory -r --recursive recursive. --descriptor descriptor. --root-uid Root UID. 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 Typical usage NOTE
One may have to run some preliminary steps in order to get gdcmgendir to generate the DICOMDIR file. Namely two steps: o Batch renaming of the DICOM filename into something compatible with ISO 9660 filename convention o Convert all DICOM file into the Explicit VR Little Endian Uncompressed (1.2.840.10008.1.2.1) Step 1. can be solved in a numerous way. Eg. on UNIX environment this could either be solved using the mkisofs command line tool. filename should not contains any extension since the VR CS does not allow for the '.' character. Only upper case, digit 0-9, the space ' ' and the underscore '_' character are valid in VR CS, with a maximum of 8 bytes. Another simple tool that can be handy is 'rename' in conjunction with 'basename'. Step 2. can simply be achieved using the gdcmconv command line tool: $ for i in `ls IMG*`; do gdcmconv --raw --force $i /tmp/out/$i; done SEE ALSO
gdcmconv(1), gdcmanon(1), rename(1) COPYRIGHT
Copyright (c) 2006-2011 Mathieu Malaterre Version 2.2.0 Tue Feb 5 2013 gdcmgendir(1)
Check Out this Related Man Page
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)