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nii2mnc

NAME

nii2mnc - convert a NIfTI-1 or Analyze 7.5 format file to a MINC format file.

SYNOPSIS

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 AT bic DOT mni DOT mcgill DOT 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.

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