3. Apply nonlinear transform to generate a mean FA volume of all participants using the FSL script "tbss_3_postreg"
The "tbss_3_postreg" script applies the nonlinear transform found in step 2 to all subjects to bring them into standard space. This generates a mean FA volume of all participants. This mean FA volume is thinned to generate a mean FA skeleton representing the centers of all common tracts. This results in a standard-space version of each subject's FA image. These are merged into a 4D image file called all_FA. The 4th dimension is "participant" (e.g. the 1 in the fourth dimension is participant 1). This script also created a subdirectory called stats, wherein all the of the statistical analyses for group comparisons will be stored.The mean of all FA images is created in a file called mean_FA. Mean_FA is fed into the FA skeletonization program to create mean_FA_skeleton. The -S flag in the code below indicates that the mean FA and its derived skeleton is from the mean of the subjects in this study (as opposed to the FMRIB58_FA mean FA image).