Man page - cmtk-dcm2image(1)

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Manual

dcm2image

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Global Toolkit Options (these are shared by all CMTK tools)
Main Options
Input Options
Output Options
Filtering Options
Sorting Options
Stacking Options
AUTHORS
LICENSE
BUGS
ACKNOWLEDGMENTS

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).

Main Options

--no-progress

Disable progress reporting.

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.

--include-identifiers

Include potentially protected identifying information (e.g., UIDs, device serial numbers, dates) in the created XML sidecar files.

--embed

Embed DICOM information into output images as ’description’ (if supported by output file format). Supported values: "StudyID_StudyDate", "PatientName", "SeriesDescription", "None", where the default is "None", 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 digits only and will repeat sooner or later.

--PatientName

Patient name, tag (0010,0010)

--SeriesDescription

Series description, tag (0008,103e)

--None

Embed no information - leave ’description’ field empty. [This is the default]

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

--write-single-slices

Also write output images for single-slice DICOM files that could not be assigned to any 3D stacks. By default, these are skipped.

--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). If one or more volumes cannot be stacked because of non-uniform slice spacing that exceeds this threshold, dcm2image will return an exit code of 3. [Default: 1e-05]

AUTHORS

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

BUGS

Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.