---
name: "nii2mnc"
section: "1"
platform: "linux"
package: "minc-tools"
version: "2.3.00+dfsg-12"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/nii2mnc"
---

# nii2mnc(1)

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

## 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@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.