Diffusion MRI

Software

• Brainapp
• Diffusion Processing Pipeline

File Formats

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. You can test for the format by using the is_nifti_file() function in the I/O wrapper library.

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 in $G/lib/nifti and $G/include/nifti. You might also try snooping around $G/doc/nifti to see what they have to say in their documentation. $G/src/nifti2mriimage/nifti2mriimage.cpp demonstrates reading the header and extracting information from it, as well as reading the image data.

To use the NIfTI I/O wrapper library, simply #include <nifti1_io.h> in your code and add the following to the library list in your makefile: niftiio znz m z.

From the command line or shell scripts, the nifti_tool utility is pretty powerful and can read the header in a structured way.

The online documentation for NIfTI is also pretty sweet:

• NIfTI-1 Header Field Description
• NIfTI FAQ

MRIimage

MRIimage is our in-house format for storing MRI data. It is manipulated by the gg/mri_g++-* library and its header is <gg/mri/image.H>.