If the data is very oblique, then the grid of the input anatomical dataset may not show any voxels once it is moved to the EPI grid. You may want to use -giant_move or provide a -master_anat dataset. For -master_anat, you can provide special strings like MIN_DXYZ, BASE or the name of a dataset that is approximately on the grid of the EPI dataset with the anatomical resolution. One way to do this is with :

3dWarp -card2oblique myEPIdset.nii.gz -prefix myAnatOb.nii.gz myAnat.nii.gz

then use -master_anat myAnatOb.nii.gz

Another way is to throw out all the obliquity altogether with 3drefit -deoblique on the datasets. So there are at least three approaches. Let me know which one works for you.