Hi Yi-Fen,

If you supply nifti as inputs the orientation of the parameter maps shouldn't change. Is this occurring? If you supply dicoms then they they will be converted to LAS by spm dcm2nii functions. If you do tractography after calculating the parameter maps then the tracts will be converted to LPS. This is because DSI studio expects LPS and the .fib file has no orientation info other than dimension and voxel size. Consequently if you try to load in other images like t1 or any of the parameter maps, it puts them in LPS. I realize this may be frustrating for other applications. In the future we will add an option not to do this.

Sincerely,

Russell