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.