The code now works, thank you very much.

However, when viewing the output file in fslview, the orientation labels are still wrong (anterior/posterior has been switched) and the angle of the brain in the sagittal view is very slanted. Is there something wrong or missing with my code??

$SlicerNew --launch DWIConvert --inputVolume ${nrrdraw}_QCed_unu.nrrd --conversionMode NrrdToFSL --outputBValues ${bval}_QCed_corr.txt --outputBVectors ${bvec}_QCed_corr.txt --outputVolume ${nrrdraw}_QCed_corr.nii.gz

Or is it that FSL is incorrectly reading the header? Have you seen this problem before?

In the past, I've "fixed" it with the code below (taken from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/O...), but this drastically changes the sform/qform header info and gives me severe problems when trying to use this output for registrations (e.g. moving to T1 space, using ANTs)

fslorient -deleteorient filename.nii.gz
fslorient -setsformcode 1 filename.nii.gz

Do you know of any solution to this problem? (this would be a huge help for me, I've been stuck on this problem for a long time)