Oh so that first (cyan tinted) image is a gap between two individual 
images? I thought it was on a larger scale gap on a multi image mosaic. I 
was thinking it might be from an errant mask, Hugin bug, or some other 
esoteric problem.

What scale is this thing at? How large an area does each image and the 
finished mosaic cover? Is there a curved surface to flat surface mapping 
problem that is cropping up because of the scale of the mosaic?

Please excuse me if this is stupid. Just offering my thoughts. :-)
Can 2 points on each image be tied to a specific latitude (or any 
theoretical straight line on the base map) if so they could be designated 
as line control points. Obviously you want a line that is along the axis of 
the plane track (it goes through all the images in a row or strip.) Even 
better if that line lies within the overlap with the next line of images. 
Perhaps this is the same thought Terry suggested earlier with the GIS 
software which you abandoned? Sorry if this is useless or redundant.
John

On Friday, January 25, 2013 10:58:40 AM UTC-6, Julien Schroder wrote:
>
> It could be perfect indeed, but I have no idea how to do that with Hugin.
> It might as well fix the first problem which appear I suspect when I try 
> to straight the stripes.
> I have the Gps tracks but I don't know how to use them in Hugin
> Thanks for your comment
>

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