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 stor

ing 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 ANA

LYZE 7.5 format. The goals of this modified data format are (1)

to add information to the header that will be useful for func

tional neuroimaging data analysis and display. These additions

include:

- More basic data types.
- Two affine transformations to specify voxel coor

dinates.
- "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 AN

ALYZE 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 three 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 manip

ulate the header field information, including orientation matri

ces. Volume-wise, timecourse-wise, access to image data.

fsliolib -- i/o routines for reading and writing nifti-1

format files, higher level than niftilib, includes routines for

reading the data blob by volume, timecourse, etc., and addresses

image orientation issues. This is still work in progress and sub

ject to significant revision.

TOOLS

The libraries are accompanied by a number of tools. Please

run each tools with --help to see a usage summary and available

options:

nifti_tool - nifti file perusal, manipulation and copying

- copy a set of volumes (sub-bricks) from one

dataset to another
- copy a dataset, restricting some dimensions to

given indices
- display the contents of a nifti_image (or various

fields)
- display the contents of a nifti1_header (or vari

ous fields)
- display AFNI extensions (they are text)
- display the time series at coordinates i,j,k
- display the data from any collapsed image
- do a diff on two nifti_image structs (or various

fields)
- do a diff on two nifti1_header structs (or vari

ous fields)
- add an AFNI extension
- remove any extension
- modify any field(s) of a nifti_image
- modify any field(s) of a nifti1_struct

nifti_stats - compute NIfTI statistical functions

Supports several distributions (normal, uniform,

logistic, chi, etc.) and calculates density or cummulative dis

tribution function (and many more). Values are printed to stdout

and can be piped to other tools.

nifti_test - NIfTI file conversion

Converts NIfTI files from and to ANALYZE 7.5 for

mat, compressed or uncompressed NIfTI files (pair or single

file). Additionally one can convert NIfTI headers into ASCII for

mat for convenient manipulation of header data.

SEE ALSO

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)