Provided by: minc-tools_2.3.00+dfsg-2_amd64 
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 ´´ 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)