Hello FreeSurfer users,

 

I may be asking a stupid question but it really troubled me a while.

I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it displayed in RAS coordinates, but template of FSL are in LAS coordinates. Should I filp L-R before doing any further analysis? 
Besides, my structrual imagews were scanned in sagittal view, and after  dcm2niigui transforation, it's in PIL coordinates in fslview. Should I reorient the image to LAS coordinates too?
But the letters L R I S A P are labled correctly (at least A-P and I－S are correct), which means FSL can read in orientation information correctly. So I am confused whether I should reorient my data or not.
I then processed strucutre images with Freesurfer, and the results from reoriented and not-reoriented images are different, so which one is correct?

Any help is appreciated,
Thanks!
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Chunhui Chen