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PROGRAM:

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

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