you don't need to reorient your data for FreeSurfer. Check the FSL site/list to see what there orientation requirements are
doug
chenchunhuichina wrote:
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! -- Chunhui Chen 2010-05-04 Chunhui Chen _________________ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875
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