Hi!
 
I have just tried out the program for the first time. Our output map does not seem to line up with either the BRAVO or the FLAIR. Which image are the output maps supposed to line up with and do you know what the source of this issue might be?
 
Hannah

Hello.

All the images are in the native space i.e., the T2 registered to the T1 space. Please check WhyD_preproc.m for the defaults options of SPM preprocessing.
I am not sure where the problem would come from. If you go through the intermediate images may be the mis-match can be spotted (which should not happen if defaults are used).

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