I saw in a previous thread that T2-images can be used in TOPUP if you have not sampled the DTI 0-images with reversed phasencoding.
I suppose that implies registering the T2 to the 0-image before using them in TOPUP. Do you have to resample the T2 to the 0-image before you do
the registration or will the registration solve this? And will the resampled T2-image be affected by the intensities in the T2-image while doing this?
I do not quite follow the instructions on the FSL-page.
Best
Nick
Niklas Lenfeldt, PhD, MSc, MAJ SWE A
Clinical Neuroscience, Umeå university
Phone: +46 70 609 66 87