What cost function and/or degrees of freedom (DOF) should I use in FLIRT?
There are two main types of cost function: intra-modal (least squares and normalised correlation) and inter-modal (correlation ratio and mutual information-based options). If you are registering two images of different modality then you must use an inter-modal cost function, whereas for images of the same modality either can be used, although the intra-modal options may be more accurate. Within each category there is not much to choose from – it is a practical, experience-based decision. The recommended options (to try first) are: correlation ratio (which is the default) for inter-modal and normalised correlation for intra-modal. The choice of DOF (Degrees of Freedom) depends largely on whether the images to be registered are intra/inter-subject and small/large FOV. When the images are of the same subject then 6 DOF is appropriate for large FOV and 3 DOF is appropriate for small FOV/single slice. If the scanner voxel size may have changed (due to calibration shifts) then it is appropri
