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dcm2nii(1) [debian man page]

DCM2NII(1)							   User Commands							DCM2NII(1)

dcm2nii - convert DICOM or PAR/REC image into the NIfTI format SYNOPSIS
dcm2nii <options> <sourcenames> OPTIONS
-a Anonymize [remove identifying information]: Y,N = Y -b load settings from specified inifile, e.g. '-b /etc/mricron.ini' -c Collapse input folders: Y,N = N -d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y -e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y -f Source filename [e.g. filename.par -> filename.nii]: Y,N = Y -g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = Y -i ID in filename [filename.dcm -> johndoe.nii]: Y,N = Y -n output .nii file [if no, create .hdr/.img pair]: Y,N = Y -o Output Directory, e.g. '/tmp' (if unspecified, source directory is used) -p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y -r Reorient image to nearest orthogonal: Y,N -s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = N -v Convert every image in the directory: Y,N = Y -x Reorient and crop 3D NIfTI images: Y,N = N You can also set defaults by editing /home/michael/.dcm2nii/dcm2nii.ini EXAMPLES
dcm2nii -a y /home/joe/Documents/dcm/IM_0116 AUTHOR
dcm2nii was written by Chris Rorden. This manual page was written by Michael Hanke <>, for the Debian project (but may be used by others). SEE ALSO
mricron(1) MRIcron Homepage: Michael Hanke April 2010 DCM2NII(1)

Check Out this Related Man Page

mnc2mnc(1)																mnc2mnc(1)

mnc2nii - convert a MINC format file to a NIfTI-1 or Analyze format file. SYNOPSIS
mnc2nii [<options>] <infile.mnc> <outfile.mnc> mnc2nii -help DESCRIPTION
The mnc2nii command is used to convert MINC format files to either NIfTI-1 or Analyze format. The NIfTI-1 format was developed by the mem- bers of the Neuroinformatics Technology Initiative's Data Format Working Group (DFWG). The NIfTI-1 format is based upon the Mayo Clinic's Analyze 7.5 format. The name of the program is derived from the common filename suffixes used for NIfTI-1 and MINC files. NIfTI-1 defines two possible for- mats, a "header plus raw image" 2-file format, and a single-file format that includes both header information and the image data. As with Analyze 7.5, the 2-file format consists of one file with the suffix ".hdr" and another file with the extension ".img". In NIfTI-1 single- file format, the two files may be combined into a single file with a ".nii" filename suffix. In addition to the NIfTI-1 formats, mnc2nii can convert MINC files to the Analyze 7.5 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 format -dual Save file in NIfTI-1 two-file format (.hdr and .img) -ASCII Save file in non-standard NIfTI-1 ASCII file format -nii Save file in NIfTI-1 single-file format (.nii) -analyze Save file in Analyze 7.5 compatible format Output voxel format -float Save voxels in 32-bit floating point format -double Save voxels in 64-bit floating point format -byte Save voxels in 8-bit integer format -short Save voxels in 16-bit integer format -int Save voxels in 32-bit integer format -signed Save voxels in signed (2's complement) integer format -unsigned Save voxels in unsigned integer format Other options -noscanrange Don't scan data to determine valid range. -quiet Quiet operation - do not print progress or debugging information. Generic options for all commands -help Print summary of command-line options and abort -version Print the program and library versions and abort KNOWN BUGS
Current handling of NIfTI-1 qform and sform coordinate transforms should probably be revised as the NIfTI group clarifies the correct usage of these fields. SEE ALSO
nii2mnc AUTHOR
Robert Vincent ( with assistance from the NIfTI-1 library authored by Robert Cox et al. COPYRIGHTS
Copyrights 2005 by Robert Vincent for the Montreal Neurological Institute. $Revision: 1.3 $ Apr 22 2005 mnc2mnc(1)

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