The preprocessing is handled by WhyD_preproc.m
Although main processing files are stored, this particular transformation map is not. Spm8 however allows one to store them. You can change the storing variables in the above script file, or better, simply run spm8 warp routine on T1 and FLAIR native spaces and get the transformations. After that you can apply them one at a time to your manual segmentations. This is easier. See spm8 warp and normalize modules.