FNIRT

FNIRT, short for FMRIB's Nonlinear Image Registration Tool, is a component of the FMRIB Software Library (FSL) used for nonlinear registration of brain images. It estimates a deformation field that warps a source image into the space of a reference image, enabling voxelwise comparisons across subjects or modalities. FNIRT is commonly employed to align individual MRI scans to standard templates (for example, the MNI152 template), facilitating group analyses and the use of regionally defined anatomical labels.

The deformation is modeled with a three-dimensional cubic B-spline grid, creating a smooth warp field defined by control points at a specified resolution. Registration proceeds in a coarse-to-fine fashion, starting with a low-resolution warp and progressively refining it. The objective combines an image similarity term that measures how well the warped source matches the reference with a regularization term that penalizes unrealistic, overly complex deformations, promoting smoothness and plausible anatomical mappings. The method supports intra- and inter-subject registration and can utilize different similarity metrics depending on modality and data characteristics.

FNIRT outputs include the nonlinear warp field and the resampled (warped) image, along with auxiliary files such as the inverse warp when available. It is typically used after an initial affine alignment and is integrated into broader pipelines for structural analyses, voxel-based morphometry, and functional MRI preprocessing to bring data into standard space. Limitations include computational cost and sensitivity to image quality; careful parameter selection is advised for robust results.