Dear List, <br><br>I have a question regarding using .img in Freesurfer. <br><br>We only have analyze images, but we can tell the orientation of the images through the patient&#39;s lesion location. Because freesurfer sometimes flips these image after recon-all, I&#39;m now flipping the &quot;problematic&quot; ones using  mri_convert &lt;input&gt; --out_orientation RAS &lt;output&gt; before running them again. <br>
<br>Could someone please explain why if we use analyze images, some of them would be flipped by Freesurfer but not others? Does that only apply to lesioned/patient brains and not normal brains?  <br><br>Many thanks!<br>Catherine<br>