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.

CMTK 3.3.1p2                                       Apr  1 2024                                      dcm2image(1)