.TH nii2mnc 1 "Apr 22 2005" "$Revision: 1.4 $" ""
.SH NAME

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

.SH SYNOPSIS

.B nii2mnc 
.I [<options>] <infile> <outfile.mnc>

.B nii2mnc 
.I -help

.SH DESCRIPTION

The 
.B 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.

.SH "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.

.SH "Output voxel format"
.TP 
.BI -float
Save voxels in 32-bit floating point format
.TP 
.BI -double
Save voxels in 64-bit floating point format
.TP
.BI -byte
Save voxels in 8-bit integer format
.TP 
.BI -short
Save voxels in 16-bit integer format
.TP 
.BI -int
Save voxels in 32-bit integer format
.TP
.BI -signed
Save voxels in signed (2's complement) integer format
.TP 
.BI -unsigned
Save voxels in unsigned integer format
.SH Analyze 7.5 specific options
.TP
.B -transverse
Assume data is in ZYX dimension order.
.TP
.B -sagittal
Assume data is in XZY dimension order.
.TP
.B -coronal
Assume data is in YZX dimension order.
.TP
.B -xyz
Assume data is in XYZ dimension order.
.TP
.B -zxy
Assume data is in ZXY dimension order.
.TP
.B -yxz
Assume data is in YXZ dimension order.
.TP
.B -flipx, -flipy, -flipz
Invert the samples along the given axis.
.SH "Other options"
.TP
.BI -noscanrange
Don't scan data to determine valid range.
.TP
.BI -quiet
Quiet operation - do not print progress or debugging information.

.SH "Generic options for all commands"
.TP 
.BI -help
Print summary of command\-line options and abort
.TP
.BI -version
Print the program and library versions and abort

.SH "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.

.SH "SEE ALSO"
.IR mnc2nii

.SH AUTHOR
Robert Vincent (bert@bic.mni.mcgill.ca) with assistance from the NIfTI-1
library authored by Robert Cox et al.

.SH "COPYRIGHTS"
Copyrights 2005 by Robert Vincent for the Montreal Neurological Institute.
