Dear Afni people,

We are currently using 3dAllineate to warp EPI data on reference anatomical scans and it is doing a great job in general !

1) However, as far as we understand, the –EPI option only performs shearing and scaling in the phase-encoded direction.
For our EPI data, the phase-encoded direction has y-orientation but we would like to make sure that AFNI has access to that piece of information.

=> Q1: Where and how should the information about the phase encoded direction be properly stored ? In the .hdr file ?

2) Since our imaging slices are spaced away pretty far in the z-direction, we would like to avoid any transformations in z-direction.

=> Q2: Could you help us confirm that we fixed the parameters correctly? For –EPI, the help offers a good example. Is this the way to do it for DICOM coordinates? :

3dAllineate -warp affine_general -replacebase -warpfreeze -parfix 2 0 -parfix 4 0 -parfix 5 0 -parfix 8 1 -parfix 10 0 -parfix 12 0 \
-master EPI+orig -base Anatomical+orig -prefix EPItr -input EPI+orig

=> Q3: Is there a similar way we can fix parameters in 3dvolreg?

Thank you so much for the very helpful support !

Walther