A similar issue has been previously reported:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1208&L=FSL&P=R72695&1=FSL
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1401&L=FSL&P=R2954&1=FSL
I just wanted to update because I have encountered this problem in the latest release. I'm running FSL 5.0.9 on CentOS 6.6.
The flipping happens after saving a mask that is in neurological orientation. Further editing flips the mask - if you are paying attention or the asymmetry is large, you'll see it flip.
However, if you simply save the image twice, the display is not refreshed and the second copy is flipped on disk.
Here's a minimal example I made using c3d (http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.C3D).
---
# Make the images in Neuro or Rad orientation
$ c3d -create 128x128x64 1x1x1mm -orient RPI -o testR.nii.gz
$ c3d -create 128x128x64 1x1x1mm -orient RAI -o testN.nii.gz
$ fslorient -getorient testN.nii.gz
NEUROLOGICAL
$ fslorient -getorient testR.nii.gz
RADIOLOGICAL
---
$ fslview testN.nii.gz testN.nii.gz
# Now unlock the overlay and draw an L and R on the axial slice
# Click File -> Save As, save as testN2
# Click File -> Save As, save as testN3
# Click File -> Save As, save as testN4
---
# View results
$ fslview testN.nii.gz testN2.nii.gz # Mask is correct
$ fslview testN2.nii.gz # Still correct when viewed as main image
$ fslview testN3.nii.gz # Flipped L-R
$ fslview testN.nii.gz testN3.nii.gz # Mask is flipped L-R
$ fslview testN.nii.gz testN4.nii.gz # Mask is correct
---
# Try creating a mask within fslview
$ fslview testN.nii.gz
# Click File -> Create Mask
# Draw an L and R on the axial slice
# Click File -> Save As, save as testN-mask
# Click File -> Save As, save as testN-mask2
$ fslview testN.nii.gz testN-mask.nii.gz # Mask is correct
$ fslview testN.nii.gz testN-mask2.nii.gz # Mask is flipped L-R
---
Repeating the same procedure with the radiological image testR does not produce a flip. testR2, testR3, testR4 etc are correct.
I think a boolean variable is being inverted on each save, but only for neurological images. The first save operation is correct, but the second is flipped, the third is correct again, and so on.
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