libnifti(1) [debian man page]

NIFTI(1)																  NIFTI(1)

NAME

       nifti - IO libraries and tools for the NIFTI-1 data format

DESCRIPTION

       The  NIfTI-1  data  format  is  a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI
       (fMRI) brain images.

       The NIfTI format is an extension of the widely used ANALYZE 7.5 format. The goals of this modified data format are (1) to  add  information
       to the header that will be useful for functional neuroimaging data analysis and display. These additions include:

	      - More basic data types.
	      - Two affine transformations to specify voxel coordinates.
	      - "Intent" codes and parameters to describe the meaning of the data.
	      - Affine scaling of the stored data values to their "true" values.
	      - Optional storage of the header and image data in one file (.nii).

       And (2) To maintain compatibility with non-NIFTI-aware ANALYZE 7.5 compatible software (i.e., such a program should be able to do something
       useful with a NIFTI-1 dataset -- at least, with one stored in a traditional .img/.hdr file pair).

       The NIfTI library package consists of two libraries:

       znzlib -- low level library for handling read/write of compressed files.

       niftilib -- core i/o routines for reading and writing nifti-1 format files. Primarily routines to  read/write  and  manipulate  the  header
       field information, including orientation matrices.  Volume-wise, timecourse-wise, access to image data.

SEE ALSO

       nifti_tool(1), nifti1_test(1), nifti_stats(1).

       Homepage: http://niftilib.sourceforge.net

AUTHOR

       The NIfTI libraries were written by the NIfTI Data Format Working Group (DFWG, http://nifti.nimh.nih.gov/ ).

       This manual page was written by Michael Hanke <michael.hanke@gmail.com>, for the Debian project (but may be used by others).

Michael Hanke							    August 2006 							  NIFTI(1)

nii2mnc(1)																nii2mnc(1)

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 Neu-
       roinformatics 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.

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.

$Revision: 1.4 $						    Apr 22 2005 							nii2mnc(1)