dcm2nii(1) [debian man page]

DCM2NII(1)							   User Commands							DCM2NII(1)

NAME

       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 <michael.hanke@gmail.com>, for the Debian project (but may be used by others).

SEE ALSO

       mricron(1)

       MRIcron Homepage: http://www.cabiatl.com/mricro/mricron/

Michael Hanke							    April 2010								DCM2NII(1)

mnc2mnc(1)																mnc2mnc(1)

NAME

       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 (bert@bic.mni.mcgill.ca) 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)