NIfTI
Files ending in .nii are in the NIfTI medical image format; it is becoming a standard export format for many different software packages, including FSL. .nii files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in .hdr/.img pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension .nii.gz. You can test for the format by using the is_nifti_file() function in the I/O library.
Paths
$G/src/nifti is the source code for the NIfTI I/O library, which installs to $G/lib/nifti and $G/include/nifti.
Use
Library
To use the NIfTI I/O library, simply #include <nifti1_io.h> in your code and add the following to the library list in your makefile: niftiio znz m z.
$G/src/nifti2mriimage/nifti2mriimage.cpp demonstrates reading the header and extracting information from it, as well as reading the image data.
Command-Line Utilities
The $G/bin/nifti_tool utility can read the header in a structured way and print out tons of metadata, as well as manipulating the actual data and doing a lot more. It's a good way to explore new data before deciding how to script with it.
Format Conversion
$G/bin/nifti2mriimage converts to MRIimage.
Documentation
make install puts some documentation in $G/doc/nifti. However, the online documentation for NIfTI is probably even better and more useful:
History
The format was created by the Neuroimaging Informatics Technology Initiative at NIH. It is a superset of Analyze 7.5, re-purposing empty fields in the Analyze format to support more features. Fortunately for us, the NIfTI reference library is available in the public domain, and $G/src/nifti is set up to download the latest version (with make download), build it, and install it. NIfTI is an actively developed format, but the NIfTI-1 specification is fixed; NIfTI-2 will be formulated and released at some point in the future.