Conform fieldmap images?

[mattcieslak]

Question for FSL experts: is it worth conforming the fieldmap images to the same voxel orientation as the data that is to be corrected? I know FSL uses voxel coordinates for a lot of its algorithms so I'm concerned that not conforming the fieldmap images might cause problems. I have no evidence this is the case though.

[oesteban]

I know FSL uses voxel coordinates for a lot of its algorithms

I guess the only problematic case here would be FUGUE, and I think it would choke when passed a fieldmap with different matrix size.

However, in SDCflows we stopped using FUGUE and things are done in physical coordinates space. This means that you can keep the accuracy of your fieldmap (it is not going to give you substantially better results, except for edge cases where a spike is present and it makes it to the final, resampled map).

[mattcieslak]

Ok this is really good to know. If sdcflows revisits topup we should be careful about orientations when making the 4D inputs