Thanks Rachel,

  Unfortunately, I do not have PA and AP images from my acquisition to run topup. I just was wandering if there was any procedure in DTIPrep or Slice to run an equivalent procedure, such as warping b0 image to T2 images and then apply the wrap field to the DWI as other groups have done using ANTS.
 Otherwise, I guess I can always run this procedure before or after DTIPrep (always before computing the tensors).

Thanks.