MRI images upside-down in FSLVIEW I'm visualizing structural data in FSLVIEW, but the sagittal and coronal planes are both upside-down / not in the conventional orientation, i.e. rotated by 90º and 180º. I understand that this upside-down view is due to the images being displayed in the order that they are stored on disk, but as I need to anatomically define ROIs on my structural, it would be more convenient if the brain were correctly oriented.

Any ideas on how to rotate these two views? The actual orientation labels themselves (S/I, A/P) are correct. Thanks!
Totally out of my league here, but judging from a quick Google search, this seems to be a common problem in FSL. You've said this YouTube video helps, so that's good...but since it uses an applescript, I suppose it requires the Mac OS.

You say Freesurfer's mri_convert works in Linux using this code:

mri_convert 
--in_orientation [file's current storage order, e.g. LAS]
--out_orientation [desired storage order] 
&lt;in volume&gt;
&lt;out volume&gt;