Sometimes after stitching a stereo panorama there is vertical parallax between the left and right spheres, uniform all around. This is basically due to uncorrected (or improperly corrected) camera misalignment, and can happen with any stitching method, even PT3D. Fortunately it is easy to fix with PTGui.
With all images of both spheres loaded you can see the vertical offsets in the panorama editor (or detail viewer) window — easiest with seam lines enabled.
Open the lens settings tab and mark one set of images (left or right) as having individual shifts. Then you can offset the other set by typing in a vertical shift for the global lens. In PTGui version 10 this is displayed in pixels, in version 11, as a percentage of the long image axis. As you enter new values you will see the vertical realignment in the pano editor and can quickly arrive at a good correction. Then stitch both spheres again — the vertical parallax should be gone, or at least greatly reduced.
If you have the desire, you can actually correct vertical parallax image by image by typing vertical shifts into the image parameters tab.
These pictures illustrate the method on a single-row, 8-around stereo stitch in PTGui 10. Pic 1 is a detail of pano editor window showing vertical misalignment between left and right spheres. Pic2 is the lens settings tab set up for correction. Changing global vert shift from 80.6 to 0 aligned the spheres as shown in pic 3.
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