dcm2image(1) The Computational Morphometry Toolkit dcm2image(1)
NAME
dcm2image - DICOM to Image
SYNOPSIS
dcm2image SearchDirList
DESCRIPTION
Combine sets of DICOM slices to 3D image stacks
OPTIONS
Global Toolkit Options (these are shared by all CMTK tools)
--help
Write list of basic command line options to standard output.
--help-all
Write complete list of basic and advanced command line options to standard output.
--wiki
Write list of command line options to standard output in MediaWiki markup.
--man
Write man page source in 'nroff' markup to standard output.
--version
Write toolkit version to standard output.
--echo
Write the current command line to standard output.
--verbose-level <integer>
Set verbosity level.
--verbose, -v
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
--threads <integer>
Set maximum number of parallel threads (for POSIX threads and OpenMP).
Input Options
--recurse, -r
Recurse into directories
Output Options
--out-pattern <string>, -O <string>
Output image path pattern. Use the following substitutions: printf-style %d variante (image number); %n (image number with automatic
number of digits); %N (like %n, but with a hyphen '-' before number if there is more than one image); %D (DICOM SeriesDescription); %R
(DICOM RepetitionTime - MRI only); %E (DICOM EchoTime - MRI only); %T (RawDataType - vendor-specific, currently GE MRI only) [Default:
image%n.nii ]
--xml, -x
Write XML sidecar file for each created image.
--embed
Embed DICOM information into output images as 'description' (if supported by output file format). Supported values: "StudyID_Study-
Date", "PatientName", "SeriesDescription", "None", where the default is "StudyID_StudyDate", or use one of the following:
--StudyID_StudyDate
StudyID, tag (0020,0010), then underscore, followed by StudyDate, tag (0008,0020). Date is appended because StudyID is four dig-
its only and will repeat sooner or later. [This is the default]
--PatientName
Patient name, tag (0010,0010)
--SeriesDescription
Series description, tag (0008,103e)
--None
Embed no information - leave 'description' field empty.
Filtering Options
--filter <string>
Filter DICOM files and include only those matching the given pattern of the form 'TagName=text', such that the value of the DICOM tag
with the given name contains the given text. If multiple filter patterns are provided via repeated use of this option, only files that
match ALL patterns are included.
--exclude <string>
Exclude all DICOM files matching the given pattern of the form 'TagName=text', such that the value of the DICOM tag with the given
name contains the given text. If multiple exclusion patterns are provided, all files are excluded that match ANY of the patterns.
Sorting Options
--no-sort
Do NOT sort files by file name (sorting determines image stack order when resolving spatial collisions)
--sort-by-name
Sort files lexicographically by file name. Use this when instance numbers are non-unique.
--sort-by-instance
Sort files by image instance number. Use this when file names are different lengths, etc. [This is the default]
Stacking Options
--ignore-acq-number
Ignore 'AcquisitionNumber' tag for image grouping, i.e., do not separate stacks based on this tag.
--no-orientation-check
Disable checking of image orientations (to avoid rounding issues)
--tolerance <double>
Tolerance for floating-point comparisons (must be >= 0; 0 = exact matches only; default: 1e-5) [Default: 1e-05]
AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, and Daniel B. Russakoff
LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
BUGS
Report bugs at http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS
From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and
Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).
CMTK 2.2.2 Jul 20 2012 dcm2image(1)