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 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.

Note that options can be specified in abbreviated form (as long as they are unique) and can be given anywhere on the command line.

-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.

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.

-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.

-opts <value>

This is a private option intended only for debugging purposes. Please avoid using it.

-help

Print summary of command-line options and abort

-version

Print the program and library versions and abort

Peter Neelin Rich Hoge

Please direct all complaints and inquiries to Robert Vincent (bert@bic.mni.mcgill.ca)

Probably many. For best results, output files should be checked by a compenent 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 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 1993-2005 by Peter Neelin for the Montreal Neurological Institute.