Is the data already warped to MNI space through the FSL FEAT pipeline? 3drefit doesn't actually do a transformation, it just modifies the file header. Use it only when you believe you know the data should be a particular way (similar to changing the file extension). If you data is in subject space, then you probably want to:
1) Align the anatomical to TLRC using @auto_tlrc
2) Apply that warp to your pe.nii.gz file using @auto_tlrc (usage 2)
If your data was warped to MNI space as part of FSL, then you could try the -mni2tta option of 3dWarp. More information on how you processed your data could be helpful to the debugging process.
Is there a particular reason you're using FSL for this particular data?
