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Why do Analyze format images appear upside down in MRIcro relative to ImageJ?

April 26, 2017analyze appear format imagej images mricro relative upside

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Why do Analyze format images appear upside down in MRIcro relative to ImageJ?

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Most image formats (e.g. DICOM) describe data starting from the top-left corner and move from the top of the image to the bottom (much as English readers start at the top-left corner, reading each line from left to right). On the other hand, SPM96/SPM99/FSL expect image to be in RAS format (lines going from left to right, then posterior to anterior and finally inferior to superior). MRIcro automatically rotates Analyze images so they appear in the correct orientation. ImageJ (and several other programs) do not take this into account, so Analyze images appear upside down. If you rename MRIcro ‘mr.exe’, it will also (incorrectly) load Analyze images upside down, matching the output of programs like ImageJ.