Dear FreeSurfer experts,

I find that mri_convert will convert DICOM of structural scan to neurological orientation by default. 

For example, mri_convert --in_type dicom --out_type mii <first file in the DICOM directory> <output.nii.gz>

Thus, the NII may need to be swapped in x for use in FSL.

In this the case?

Many thanks,

Daniel