Hi Hamied,
There is some confusion as to what the three first columns in the acquisition parameter files are. They are NOT spatial directions, but image dimension. So, you will have 1/-1 in the fist column if the PE is along the first dimension of your image, in the second column if it is along the second dimension, etc.
To check along which dimension your PE is, just open your image in FSLview, and change the first voxel _index_ (the one labeled as "X"; note: not the position (in mm), but the index), and see along which dimension the crosshair in the image moves. If it is the same dimension along which the distortions happen, then you will have to enter the "1/-1" in the first column of the acquisition parameters file.
Most images have the slice direction along the third dimension (third index), so that is why you got your error message saying that "third element of pevec must be zero". It means that the PE distortions shouldn't be along the third dimension, because --almost always-- they will correspond to the slice direction (sagittal, in your case).
If, for whatever reason your PE direction happens to be along the third dimension of your images, you will have to re-orient your images before running topup on them.
I hope this helps,
-Pablo
|