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


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

       dcm2mnc -help


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

       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.


       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

              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.

              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".

              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

              The mosaic image is stored in descending order.

              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

       -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.


              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  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.

              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

       -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

              Print the program and library versions and abort


       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


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


       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


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


       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 ´´ filenames...


       Peter Neelin and Richard D. Hoge

       Please  direct  all  complaints  and  inquiries   to   Robert   Vincent


       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.


       For  more  information  on  DICOM,  visit the NEMA (National Electrical
       Manufacturer’s Association) website at  and  also
       see  David  Clunie’s  excellent  website  on  medical  image formats at

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


       Copyrights 1993-2005 by Peter  Neelin  for  the  Montreal  Neurological

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