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>DESCRIPTION¶
The dcm2mnc command is used to convert DICOM format files to MINC format.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
-
- -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:%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
AUTHORS¶
Peter Neelin and Richard D. HogeBUGS¶
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.comCOPYRIGHTS¶
Copyrights 1993-2005 by Peter Neelin for the Montreal Neurological Institute.May 03 2005 | $Revision: 1.5 $ |