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dcm2mnc(1)							    dcm2mnc(1)

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 for-
       mat.

       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 in-
       cludes 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 se-
       ries and	attempts to determine the correct geometry and	ancillary  in-
       formation 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 pa-
       tient's name, the acquisition date, acquisition	time,  series  identi-
       fier, 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 identify-
	      ing 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 conver-
	      sion 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	debug-
	      ging problems with dcm2mnc.

       -verbose
	      Verbose operation.  Prints a large amount	of additional informa-
	      tion  about the program's	operation. This	information can	proba-
	      bly only be interpreted by someone familiar with both this  pro-
	      gram 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 coor-
	      dinates  rather  than the	standard DICOM fields for slice	thick-
	      ness 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 gen-
       erates 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 identifer,	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 fol-
       lowed 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 '' 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 encoun-
       tered.  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 Man-
       ufacturer'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 soft-
       ware 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 In-
       stitute.

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

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | Output file options | Siemens mosaic specific options | Other options | Generic options for all commands | FILENAMES | AUTHORS | BUGS | SEE ALSO | COPYRIGHTS

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