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NAME

       dcm2mnc - convert sets of DICOM files to one or more MINC format files.

SYNOPSIS

       dcm2mnc [<options>] <input-list> <output-dir>

       dcm2mnc -help

DESCRIPTION

       The dcm2mnc command is used to convert DICOM format files to MINC format.

       DICOM  (Digital  Imaging and Communications in Medicine) format is used by many vendors of
       medical  imaging  equipment  as  a  standard  means  of  data  interchange.    The   DICOM
       specification  is  extremely  complex  and  includes  protocols  for  data interchange and
       communications as well as the specifics of the data format.  In most cases, tens  or  even
       hundreds of DICOM files must be combined to produce a single MINC file.

       In  normal  operation,  the  input-list  will consist of the names of one or more files or
       directories.  The program scans all specified input files and directories and attempts  to
       identify  groups  of  files  that  should be combined into a single MINC file.  Once these
       groups (or "series") of DICOM files are identified, the program analyzes the data for each
       series  and  attempts  to  determine  the correct geometry and ancillary information to be
       incorporated into the MINC file.

       If all goes well, one or more MINC files will be created in  one  or  more  subdirectories
       created  in  the  specified  directory  output-dir.   These  directories and files will be
       automatically named according to the patient's name,  the  acquisition  date,  acquisition
       time, series identifier, and modality.

       For  a variety of reasons, medical imaging manufacturers have chosen to implement a number
       of proprietary extensions to the DICOM format. This program attempts to be  very  general,
       but it does some extra checking for specific proprietary fields where useful or necessary.
       However, as device settings change and software is updated, the  precise  details  of  the
       DICOM  output  for a given device may shift.  Different devices from the same manufacturer
       may produce substantially different DICOM output.

OPTIONS

       Note that options can be specified in abbreviated form (as long as they  are  unique)  and
       can be given anywhere on the command line.

Output file options

       -clobber
              Overwrite  existing  files.   By  default,  dcm2mnc will not write over an existing
              file.

       -anon  Do not store the patient name in the MINC file.  The  string  "anonymous"  will  be
              used  instead.  Note that all other identifying information will still be stored in
              the file.

       -nosplitecho
              Do not split echoes into separate files.  If  multiple  echoes  are  present  in  a
              series,  they  will  all  be  stored  in  a single MINC file with a dimension named
              "echo".

       -splitdynamic
              Split dynamic scans into separate files. Normally dynamic scans  are  stored  in  a
              single  MINC  file with a "time" dimension.  If this option is specified, each time
              slice will be saved in a separate file.

       -fname <format-spec>
              Set the format of the output file name. See FILENAMES section for details  on  this
              option.

       -dname <format-spec>
              Set  the  format of the output subdirectory name. See FILENAMES section for details
              on this option. Set this to the empty string to avoid creating a subdirectory.

Siemens mosaic specific options

       These two options control the manner in which Siemens mosaic data is  converted.   Siemens
       scanners  commonly  represent  fMRI data as a "mosaic" of subimages combined into a single
       large image.  Normally these are in what we call "ascending" order, but if your functional
       image  is not converted properly, you may need to specify one of these options.  NOTE that
       the mosaic order is often not the same as the slice acquisition order.

       -descending
              The mosaic image is stored in descending order.

       -interleaved
              The mosaic image is stored in alternating (odd/even) order.

Other options

       -stdin This option tells dcm2mnc to read a list of input files from the standard input  in
              addition to any files specified on the command line.

       -cmd <string>
              This  option  will  apply  the given command string to each output file after it is
              created.  Can be used to run gzip or compress on each output file, for example.

       -minmax

              Use the values for the largest and smallest pixel value  as  stored  in  the  DICOM
              file.  This  is  useful  especially  with  GE  PET data, but may be needed to get a
              quantitatively accurate conversion with other manufacturers.  If this option is not
              specified.   .B  dcm2mnc  uses  the  full range of the datatype as specified by the
              number of bits  stored  per  voxel  (field  #  0028,0101).   When  this  option  is
              specified,  the  0028,0106  and  0028,0107  will  be used to set the valid range of
              pixels.

       -list  List files in  series,  but  do  not  perform  conversion.   Sometimes  useful  for
              verifying the validity of a dataset, and for debugging problems with dcm2mnc.

       -verbose
              Verbose  operation.   Prints  a  large  amount  of additional information about the
              program's operation. This information can probably only be interpreted  by  someone
              familiar with both this program and the DICOM standard.

       -debug Extremely  verbose operation.  Prints a huge amount of additional information about
              the program's operation. This information  can  probably  only  be  interpreted  by
              someone familiar with both this program and the DICOM standard.

       -usecoordinates
              This  option requests that the conversion rely on the slice coordinates rather than
              the standard DICOM fields for slice thickness and spacing.  It  is  useful  if  for
              some  reason  the  standard  DICOM  fields  for  slice  thickness  and  spacing are
              incorrect.

       -opts <value>
              This is a private option intended only for debugging purposes.  Please avoid  using
              it.

Generic options for all commands

       -help  Print summary of command-line options and abort

       -version
              Print the program and library versions and abort

FILENAMES

       To  avoid  naming collisions when converting a large set of input DICOM files to a smaller
       set of MINC output files, dcm2mnc  automatically  generates  the  names  of  output  files
       according  to various parameters of the DICOM file information.  The normal behavior is to
       place all of the output files in a subdirectory of the given output  directory  which  has
       its name derived from the patient's name and the study date and time as follows:

       patientname_yyyymmdd_hhmmss/

       The  individual files are named according to the patient name, study date and time, series
       identifier, and modality information as follows:

       patientname_yyyymmdd_hhmmss_series_scan_modality.mnc

       The optional scan information includes the echo number ('e<n>'), slice  number  ('sl<n>'),
       time series position ('d<n>'), phase number ('p<n>'), or chemical shift ('cs<n>').

       The  optional  modality  information  consists  of either the string "_pet" or "_mri".  No
       suffix is added for unrecognized modalities.

       The -fname and -dname commands allow  the  user  to  override  the  standard  file  naming
       behavior  by  specifying  alternative output directory and file formats.  The arguments to
       these options are template strings that will be expanded to include information  from  the
       DICOM  sequences  in  specified  locations.  Replacements are specified by a '%' character
       followed by a single alphabetic character, as follows:

           %N - Name of patient
           %D - Date of scan
           %T - Time of scan
           %S - Study ID (typically 'yyyymmdd.hhmmss')
           %A - Acquisition or series ID
           %s - Optional slice label
           %e - Optional echo number
           %t - Optional dynamic scan number
           %p - Optional phase number
           %c - Optional chemical shift number
           %m - Optional modality

       The default file name convention is therefore given by the format string:

       %N_%D_%T_%A%s%e%t%p%c%m

       and the default directory name is given by the format string:

       %N_%D_%T

       If you wish to avoid creating a subdirectory, you may do so by giving a zero-length string
       as the argument to the -dname option:

       dcm2mnc -dname ยดยด filenames...

AUTHORS

       Peter Neelin and Richard D. Hoge

       Please direct all complaints and inquiries to Robert Vincent (bert@bic.mni.mcgill.ca)

BUGS

       Probably  many.  For  best results, output files should be checked by a competent human to
       verify that the conversion was performed properly.  DICOM is a very complex format, and it
       is  difficult to anticipate all of the possible combinations of fields and values that may
       be encountered.  If you have a  problem,  please  contact  the  maintainer.   It  will  be
       extremely  useful if you can provide an example dataset that exhibits the problem you have
       discovered.

SEE ALSO

       For more  information  on  DICOM,  visit  the  NEMA  (National  Electrical  Manufacturer's
       Association)  website  at  http://dicom.nema.org  and  also  see  David Clunie's excellent
       website on medical image formats at http://www.dclunie.com

       Many manufacturers  create  "DICOM  Conformance  Statements"  for  each  software  release
       associated   with  their  medical  imaging  products.  These  can  be  useful  sources  of
       information.

COPYRIGHTS

       Copyrights 1993-2005 by Peter Neelin for the Montreal Neurological Institute.

$Revision: 1.5 $                           May 03 2005                                 dcm2mnc(1)