NAME¶
dcm2image - DICOM to Image
SYNOPSIS¶
dcm2image SearchDirList
DESCRIPTION¶
Combine sets of DICOM slices to 3D image stacks
OPTIONS¶
- --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).
- --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_StudyDate", "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
digits 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).