Hi, 

The outputs generated by WhyD_preproc.m do not appear to be in either the FLAIR or T1 space. Since the defaults do not save a transformation matrix we are unable to decipher what inputs generate this 'warped' space. Could you please advise where specifically in the script one would need to alter the default spm jobman settings to allow transforms to be saved so that we can warp the outputs back to the original native space, please? 

Thanks very much, 

Cheers, 

Will