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 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 manipulate the header field information, including orientation matrices. 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 subject 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 various 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 various 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 distribution 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 format, compressed or uncompressed NIfTI files (pair or single file). Additionally one can convert NIfTI headers into ASCII format 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 <[email protected]>, for the Debian project (but may be used by others).