[Insight-developers] Y axis inversion during slice extraction

[Dženan Zukić]

Hi everyone,

in the attached simple code for slice extraction. I am using similar code in
my segmentation tool. The problem is that 2D slices, which I display using
Qt, look flipped
(Y_axis_current.png<http://i274.photobucket.com/albums/jj262/dzenanz/OnlineImageHosting/Y_axis_current.png>).
Flipping slices either vertically or horizontally resolves the discrepancy
between 2D slices and 3D visualization
(Y_axis_inverted.png<http://i274.photobucket.com/albums/jj262/dzenanz/OnlineImageHosting/Y_axis_inverted.png>
).

I believe the problem arises somewhere due to origin of coordinate system
(lower left vs upper
left). \InsightToolkit-3.18.0\Code\BasicFilters\itkExtractImageFilter.txx,
line 206 clearly states that direction cosines are not taken care of. PNG
image writer does not take into account coordinate system conventions
(conclusion based on a glimpse into code).

Am I doing something wrong? If no, how do you deal with this?

Regards,
Dženan
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