Dear Catherine
I think freesurfer uses the voxel space not world space (hdr file). some other programs use hdr file too which means world space like spm.
if you want to have same world space and voxel space you have to have re-slice your img file in spm if you use spm. then everything would be same in every program.

Best
Rouhi  

On Thu, Aug 11, 2011 at 4:34 PM, Catherine Wan <cycwan@gmail.com> wrote:
Dear List,

I have a question regarding using .img in Freesurfer.

We only have analyze images, but we can tell the orientation of the images through the patient's lesion location. Because freesurfer sometimes flips these image after recon-all, I'm now flipping the "problematic" ones using  mri_convert <input> --out_orientation RAS <output> before running them again.

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? 

Many thanks!
Catherine

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