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I'm visualizing structural data in FSLVIEW, but the sagittal and coronal planes are both upside-down / not in the conventional orientation, i.e. rotated by 90º and 180º. I understand that this upside-down view is due to the images being displayed in the order that they are stored on disk, but as I need to anatomically define ROIs on my structural, it would be more convenient if the brain were correctly oriented.

Any ideas on how to rotate these two views? The actual orientation labels themselves (S/I, A/P) are correct. Thanks!

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Totally out of my league here, but judging from a quick Google search, this seems to be a common problem in FSL. Might this YouTube video help at all? Here's the summary: "FSL image_flip/check is an applescript that written to flip left and right orientation of group of brain images. It can be used as well for checking image orientation of group of images in sequence where presentation of each image lasts for a proper time (defined by user; 10 seconds as an example)." If that does the trick, let me know and I'll repost this as an answer. –  Nick Stauner Feb 20 at 1:52
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Thanks for your suggestion, Nick! I wasn't able to try out image_flip/check because I'm working on a Linux OS but it seems like a viable solution, and the Youtube video is very helpful. I just learned that Freesurfer's mri_convert does the trick: mri_convert --in_orientation [file's current storage order, e.g. LAS] --out_orientation [desired storage order] <in volume> <out volume>. Either one works, so feel free to repost your comment as an answer. –  14Gpc Feb 20 at 4:18
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Totally out of my league here, but judging from a quick Google search, this seems to be a common problem in FSL. You've said this YouTube video helps, so that's good...but since it uses an applescript, I suppose it requires the Mac OS.

You say Freesurfer's mri_convert works in Linux using this code:

mri_convert 
--in_orientation [file's current storage order, e.g. LAS]
--out_orientation [desired storage order] 
<in volume>
<out volume>
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