Provided by: cmtk_3.0.0-1ubuntu1_amd64
dcm2image - DICOM to Image
Combine sets of DICOM slices to 3D image stacks
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) [Default: 1e-05]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
Report bugs at http://nitrc.org/projects/cmtk/
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.