Registration within FDT

If tractography results are to be stored in any space other than diffusion space then registration must be run.

Registration within Fdt uses flirt. Registration can only be applied after Bedpost has been run. Typically, registration will be run between three spaces:

• Diffusion space (using the nodif_brain.{hdr,img} file stored in the Bedpost directory)
• Structural space (using the struct.{hdr,img} file stored in the Bedpost directory, e.g., the space of a high resolution T1-weighted image of the same subject)
• Standard space (by default, the MNI152 brain stored within the fsldirectory).

Note that struct must have had bet applied. The nodif_brain image should be the brain extracted version of the nodif image that is automatically stored in the Bedpost directory. The user will have to manually apply bet to this image after running bedpost and before running registration. (it is important that the user check the qualtiy of bet results on these images and adjust the settings in bet where appropriate)

Transformation matrices, and their inverses, will be dervied from diffusion to structural space and from structural to standard space. Relevant matrices will be concatenated to produce transformation matrices between diffusion and standard space. The resulting matrices are stored within the 'xfms' subdirectory of the bedpost directory and named as follows:

• diff2str.mat - from diffusion to structural space
• str2diff.mat - from structural to diffusion space
• diff2standard.mat - from diffusion to standard space
• standard2diff.mat - from standard to diffusion space
• str2standard.mat - from structural to standard space
• standard2str.mat - from standard to structural space

By default, transformation matrices between diffusion and structural space are derived using 6 degrees of fredom, the mutual information cost function and normal search; transformations matrices between structural and standard space are derived using 12 degrees of freedom, the correlation ratio cost function and normal search. These parameters may be adjusted if required using the drop down menus in the reigistration panel.