NIfTI1

NIfTI-1 is a widely used file format for storing neuroimaging data, such as MRI, fMRI, and diffusion imaging. It was designed to improve upon the older Analyze 7.5 format by providing a more robust header with clear spatial orientation information and a flexible data type system. The format is standardized by the Neuroimaging Informatics Technology Initiative (NIfTI) and commonly used in both single-file (.nii) and paired header/image (.hdr/.img) forms, as well as in compressed form (.nii.gz).

A NIfTI-1 file comprises a 348-byte header followed by the image data, with the possibility of an offset to the data indicated in the header. The header stores dimension information (dim[8]), voxel sizes (pixdim[8]), the data type (datatype) and bit depth (bitpix), and the data offset (vox_offset). It also includes intent fields for additional data interpretation, scaling factors (scl_slope, scl_inter), and descriptive text (descrip). Orientation and spatial mapping are provided by qform and sform transforms, along with corresponding codes. The header ends with a magic string that identifies the file type, typically "n+1" for a single-file .nii and "ni1" for paired header/image formats.

Data within a NIfTI-1 file can use several numeric datatypes, defined by datatype codes, with bitpix indicating the bits per voxel. The format thus supports 3D volumes and 4D datasets, where the extra dimension often represents time or different modalities. Endianness is handled in the header, and the file’s structure enables consistent interpretation across software tools.

NIfTI-1 is widely supported by major neuroimaging software such as FSL, SPM, AFNI, FreeSurfer, and NiBabel. It remains a common standard due to its balance of simplicity and rich metadata, with common usage including compression into .nii.gz and eventual evolution to newer formats like NIfTI-2.