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)

gdcminfo(1)							       GDCM							       gdcminfo(1)

NAME

       gdcminfo - Display meta info about the input DICOM file.

SYNOPSIS

       gdcminfo [options] file-in

DESCRIPTION

       The gdcminfo command line program takes as input a DICOM file, or a directory and process it to extract meta- information about the DICOM
       file processed.

PARAMETERS

       file-in	 DICOM input filename

options
   options
	 -r --recursive 	 recursive.
	 -d --check-deflated	 check if file is proper deflated syntax.
	    --resources-path	 Resources path.
	    --md5sum		 Compute md5sum of Pixel Data attribute value.
	    --check-compression  check the encapsulated stream compression (lossless/lossy).

   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_RESOURCES_PATH path pointing to resources files (Part3.xml, ...)

Simple usage
   gdcmData
       Using data from gdcmData:

       $ gdcminfo gdcmData/012345.002.050.dcm

       MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
       NumberOfDimensions: 2
       Dimensions: (256,256)
       Origin: (-85,21.6,108.7)
       Spacing: (0.664062,0.664062,1.5)
       DirectionCosines: (1,0,0,0,0,-1)
       Rescale Intercept/Slope: (0,1)
       SamplesPerPixel	  :1
       BitsAllocated	  :16
       BitsStored	  :16
       HighBit		  :15
       PixelRepresentation:1
       Orientation Label: CORONAL

   Davie Clunie datasets:
       Using data from David Clunie datasets:

       $ gdcminfo BRTUM001.dcm

       MediaStorage is 1.2.840.10008.5.1.4.1.1.4.1 [Enhanced MR Image Storage]
       NumberOfDimensions: 3
       Dimensions: (256,256,15)
       Origin: (40,-105,105)
       Spacing: (0.820312,0.820312,6)
       DirectionCosines: (0,1,0,0,0,-1)
       Rescale Intercept/Slope: (0,1)
       SamplesPerPixel	  :1
       BitsAllocated	  :16
       BitsStored	  :16
       HighBit		  :15
       PixelRepresentation:1
       Orientation Label: SAGITTAL

   Checking the md5sum of the Pixel Data
       After compressing a DICOM file (see gdcmconv) using a lossless compression algorithm, it is fairly easy to compare the two files for
       differences at DICOM attribute level. However one operation is slightly easier to do: how to make sure the compression was actually
       lossless ? In this case one could use the --md5sum operation.

       Take an uncompressed DICOM image file:

       $ gdcminfo --md5sum SIEMENS_ImageLocationUN.dcm

       The tool return: 0621954acd5815e0b4f7b65fcc6506b1

       Now compress this file:

       $ gdcmconv --jpegls SIEMENS_ImageLocationUN.dcm lossless_compressed.dcm

       and then check again the md5sum:

       $ gdcminfo --md5sum lossless_compressed.dcm

       The tool return: 0621954acd5815e0b4f7b65fcc6506b1

   Checking if Pixel Data is lossless
       In come environment one wish to check whether or not the DICOM file is lossless or not. It is fairly easy to do that in most cases. Only in
       two occasion this is not clear from the sole DICOM Attribute. When the Transfer Syntax is JPEG 2000 Image Compression
       (1.2.840.10008.1.2.4.91) and when the Transfer Syntax is JPEG-LS Lossy (Near-Lossless) Image Compression (1.2.840.10008.1.2.4.81).

       In this case, the only solution is to open the Pixel Data element, read the specific JPEG header and check whether or not the JPEG
       transformation was lossless or not:

       $ gdcminfo --check-compression gdcmData/MAROTECH_CT_JP2Lossy.dcm

       The tool returns: 'Encapsulated Stream was found to be: lossy'

SEE ALSO

       gdcmdump(1), gdcmraw(1), gdcmconv(1)

COPYRIGHT

       Copyright (c) 2006-2011 Mathieu Malaterre

Version 2.2.0							  Tue Feb 5 2013						       gdcminfo(1)