nii2mnc

convert a NIfTI-1 or Analyze 7.5 format file to a MINC format file. nii2mnc <options> <infile> <outfile.mnc> nii2mnc -help

DESCRIPTION

The nii2mnc command is used to convert “NIfTI-1” format files to MINC format. The NIfTI-1 format was developed by the members 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 formats, 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.

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 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

Analyze 7.5 specific options

-transverse
Assume data is in ZYX dimension order.

-sagittal
Assume data is in XZY dimension order.

-coronal
Assume data is in YZX dimension order.

-xyz
Assume data is in XYZ dimension order.

-zxy
Assume data is in ZXY dimension order.

-yxz
Assume data is in YXZ dimension order.

-flipx, -flipy, -flipz
Invert the samples along the given axis.

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

mnc2nii

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.