A couple of things:

If these input images are cylindrical, Hugin won't detect this automatically, 
you need to set the input projection to cylindrical (in addition to the output 
projection).

Cylindrical images are often cropped, meaning that the horizon doesn't run 
through the middle of the image, in this case you need to optimise the 'e' 
parameter in addition to 'v, r, p & y'. This itself would explain the 
dislocation you are seeing.

How are you extracting the images from the MOV files? Somewhere we have a Hugin 
tool for parsing QTVR data and reassembling a panorama automatically - would 
this be useful?

-- 
Bruno


On 29 April 2019 00:34:44 BST, James Proctor wrote:
>Greetings -- I'm using Hugin to stitch together some old digital images
>
>taken from a Nikon Coolpix atop a tripod/pano mount (14 total per pano). 
>There was plenty of overlap btw all images, including the first and last 
>image. The stitching process seems to work great, but when I export and
>
>view the pano the vertical position of elements at the left and right ends 
>is off, resulting in a jagged transition...see e.g. attached. 
>
>The settings I used are as follows:
>
>   1. Load Images: Lens type rectilinear, 3.8mm/13.7 multiplier 
>   (automatically detected?)
>   2. Projection switched from default Rectilinear to Cylindrical
>3. I've played a bit with Center/Fit/Straighten buttons, but they don't
>
>   seem to do the trick
>
>There must be an easy explanation as to why the stitching process doesn't 
>align the two ends of the pano, given the original images overlap 
>substantially. It just doesn't seem to recognize that these 14 images are 
>from a quasi-cylindrical (vs. e.g. planar) source.
>
>If you could please point me to a ready solution I'd sure appreciate! The 
>app is proving useful for me to re-stitch circa 2000 digital panos 
>previously saved in now-extinct QTVR format.

-- 
A list of frequently asked questions is available at: 
http://wiki.panotools.org/Hugin_FAQ
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