I am trying to run topup/eddy on a single shell dMRI sequence with dual phase encoding (AP and PA). I'm also working with a multi-shell sequence but let's start with the basics. I first ran the data on server A and everything looked great - bvecs rotated, tractography is beautiful. But I decided to do denoising first so I transferred the raw niftis to server B and now running eddy after topup I am not getting rotated bvecs. I get the *.eddy_parameters file and unwarped volumes, but no bvecs.
I've tried several versions of fsl, and fsl 5.0.10 does give rotated bvecs, but they aren't right - V1 file looks flipped in the X direction, but even when I try to manually correct that, the tractography is a mess. I've read about issues with radiological/neurological convention, but I must be having a different issue.
I'm nearly positive that server A has fsl 5.0 installed, but I've tried several different ones on server B and having the issue of either no rotated or incorrectly rotated bvecs output. Sorry if I've missed a thread that answers this, but any advice you can offer is appreciated.