dcm2mnc(1)dcm2mnc(1)NAMEdcm2mnc - convert sets of DICOM files to one or more MINC format files.
SYNOPSISdcm2mnc [<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
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 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
Institute.
$Revision: 1.5 $ May 03 2005 dcm2mnc(1)
