It only uses the example_func, so if that is affected, then the registration will be off. In general, you should not use freesurfer with data you have non-linearly registered with some template. The freesurfer intersubject registration itself is non-linear.
doug
Georg Homola wrote:
Hi Doug!
May be a very basic question for better understanding, but how much does reg-feat2anat care about the FSL preprocessing e.g. dewarping? And especially important for me, does it make a difference if you FNIRT or FLIRT on first level? Is it a good idea to process non-linearly registered subjects with reg-feat2anat? In other words: is anat2exf.register.dat actually affected by FEAT preprocessing output (warp field and transformation matrices), or not at all?
Many thanks in advance Georg