nii

nii refers primarily to the NIfTI file format used for storing neuroimaging data. The file extension .nii (and the compressed form .nii.gz) identifies a NIfTI-1 file, a standard widely used in MRI, fMRI, and other brain imaging data. NIfTI was designed as an evolution of the Analyze 7.5 format, combining header metadata and image data into a single portable file and providing a more flexible data model.

A NIfTI-1 file contains a header with essential metadata such as the data dimensions, voxel sizes, data type, and orientation information, typically expressed through qform and sform affine matrices. The actual image data can be three-dimensional or four-dimensional (adding time as a dimension). This structure supports straightforward interpretation of spatial relationships and voxel values across imaging sessions and modalities. The compression format .nii.gz is common, reducing file size without changing the data content.

NIfTI is widely supported by major neuroimaging software packages, including FSL, AFNI, SPM, FreeSurfer, and MRIcron. It is favored for its relatively simple, self-contained single-file organization and its ability to store complex datasets with multiple time points or contrasts.

In addition to neuroscience use, the acronym NII can refer to the National Institute of Informatics, a research institution in Japan. Context typically makes clear whether nii means the neuroimaging file format or the organization. The term is sometimes encountered in discussions of data provenance, sharing, and reproducibility in brain imaging research.