I ran into this issue a few months ago. I found it only affects images in Neurological orientation, so one workaround would be to have everything in radiological orientation before beginning processing with FSL.
Here's the thread where I tested images with Neurological / Radiological orientation as described by fslorient:
> On Aug 1, 2017, at 3:34 PM, Cheryl McCreary <[log in to unmask]> wrote:
> I am having some issues with editing masks in fslview. When I use the "Save As" command on a mask, the mask gets right-left flipped. I can correct this with fslreorient2std, however, reorienting every save doesn't seem like a good solution. Is this possibly a bug in FSLview?
> I am working with brain masks extracted from saggitally acquired T1 data. The data was reoriented2std after conversion to nifti format. I am working on Mac OS X 10.11.6 (El Captian) with FSL version 5.0.10 and fslview version 6. The brain mask generated from BET command line is saved in the correct orientation. It is only after "Save As" from FSLview that the orientation is flipped.
> Are there any suggestions as to how to deal with this effieciently or prevent it?
> Thanks in advance for any help you can offer.