Hi Robert,

You have entered the lovely realm of file format interpretation . . . FSL requires a specific orientation and is rather inflexible, which can cause problems such as you are encountering.

Personally, I convert from DICOM to nifti using MRtrix.  We use the FSL eddy tool and BET, and then feed into DKE after restructuring the nifti to have one leading B0, then each Bseries.

After DKE you can use fslreorient2std on the niftis to get them in the orientation that FSL likes, coregister to MNI via an FA atlas (using the FA out of DKE).  We first go FA atlas to MNI atlas (once) then FA(DKE) to FA(atlas), and then concatenate the matrices to go direct FA(DKE) to MNI.  Then we're good to go for TBSS.

If you want more details, I can ask one of my student's who's set up our TBSS analysis pipeline.

Cheers,

Kirk