Dear Matt,
before doing any manual reorientation, there are at least two things to check for each subject:
- coregistration between T1 and EPI
- normalisation of T1
Coregistration should print some output by default. If you are keeping the T1 as reference image fixed, make sure you move all your 3D-EPI images (as "other images"). Moving only the first one (even in a 4D file) is not sufficient. If Coregistration is fine, look at normalisation.
Best,
Volkmar
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