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Hi All, I have a question regarding image orientation using fsl for an fMRI analyses. Both structural image and functional image has been unpacked using unpacksdcmdir script from Freesurfer (both images were acquired in the same scanner and in the same session). When I read both images' orientation using fslorient -getorient command, it gives me radiological orientation for the structural image and neurological orientation for the functional image. However, when actually look at both images in fslview, they seem to have same orientations. Even though, structural and functional image looked to have the same orientation visually, I did applied fslorient - swaporient command on the functional image to make the functional orientation to radiological. Then, I applied fslswapdim <input> RL PA IS <output> command for both structural and functional images (This was so that I can view the images in more standard viewing fashion in fslview). The resulting structural and functional images seemed to have flipped (only in Right - Left flip) to each other (as I suspect it would). I would be grateful if anyone can offer me some advice regarding my image orientation problem. Thanks in advance! -Sang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.