Implementation: FLIRT and MCFLIRT

The registration and motion correction methods described in the previous sections have been implemented in C++ and are called FLIRT (FMRIB's² Linear Image Registration Tool) and MCFLIRT (Motion Correction FLIRT). In each case several implementation choices needed to be made to obtain a robust, working method. The more important choices are: (1) the use of Centre of Mass as the centre of transformation (also used for initial alignment); (2) the parameterisation of the transformations as three Euler angles, three translations, three scales and three skews; and (3) the number of intensity histogram bins set to 256 divided by the scale size (i.e. 256 for 1mm scaling but only 32 for 8mm scaling) since the number of voxels (samples) is small for large scalings and so fewer bins must be used in order to get reliable statistics [10]. Each of these choices is detailed more fully in [12].