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.