Here is my pro file:

# hugin project file
#hugin_ptoversion 2
p f0 w821 h1258 v32  E0 R0 S25,780,0,1141 n"TIFF_m c:LZW r:CROP"
m g1 i0 f0 m2 p0.00784314

# image lines
#-hugin  cropFactor=1
i w4181 h6305 f0 v30 Ra0 Rb0 Rc0 Rd0 Re0 Eev0 Er1 Eb1 r-1.99893914018634e-12 
p2.25706389628805 y-0.274849518695532 TrX0 TrY0 TrZ0 Tpy0 Tpp0 j0 a0 b0 c0 d0 
e0 g0 t0 Va1 Vb0 Vc0 Vd0 Vx0 Vy0  Vm5 n"14560002.JPG"
#-hugin  cropFactor=1
i w1024 h1545 f0 v30 Ra0 Rb0 Rc0 Rd0 Re0 Eev0 Er1 Eb1 r1.99920544152276e-12 
p2.44304473111548 y-0.369857668322311 TrX0 TrY0 TrZ0 Tpy0 Tpp0 j0 a0 b0 c0 d0 
e0 g0 t0 Va1 Vb0 Vc0 Vd0 Vx0 Vy0  Vm5 n"14560014.JPG"


# specify variables that should be optimized
v Ra0
v Rb0
v Rc0
v Rd0
v Re0
v Vb0
v Vc0
v Vd0
v Ra1
v Rb1
v Rc1
v Rd1
v Re1
v Eev1
v r1
v p1
v y1
v Vb1
v Vc1
v Vd1
v


# control points
c n0 N1 x825.022286862588 y3455.78480877144 X205.954875194407 Y852.051352033934 
t0
c n0 N1 x812.682486620123 y5089.81361881057 X200.546508727828 Y1253.34676477777 
t0
c n0 N1 x213.547305515808 y6086.97914150293 X55.4847453011067 Y1500.49028923902 
t0
c n0 N1 x1433.63840050291 y1299.74012527778 X354.367433452982 Y323.763156452695 
t0
c n0 N1 x1054.17909401605 y2681.43290303793 X261.805254863911 Y663.767997000226 
t0
c n0 N1 x1374.07491623692 y3462.52104956626 X340.657401107209 Y852.95687169241 
t0
c n0 N1 x1207.94085236359 y5200.61428599698 X298.51655908337 Y1281.32448495085 
t0
c n0 N1 x2030.4189279187 y1842.35722234585 X500.175307460152 Y458.101827799735 
t0
c n0 N1 x1959.99616026983 y2300.85544457984 X482.912925257133 Y569.069518211624 
t0
c n0 N1 x1733.59593362952 y3793.43628996955 X428.049368920136 Y935.355939282536 
t0
c n0 N1 x2058.56801947459 y5062.38065435841 X506.670430297875 Y1247.10861810857 
t0
c n0 N1 x1775.39916703776 y5174.03197131337 X438.159124342456 Y1274.2739042156 
t0
c n0 N1 x2384.72596537744 y1365.43420147429 X587.500012016446 Y340.52131109056 
t0
c n0 N1 x2597.58555661418 y2833.86209026929 X638.302322573718 Y700.575003700678 
t0
c n0 N1 x2858.77820527546 y4104.65993747657 X700.785247448063 Y1012.60910369741 
t0
c n0 N1 x2574.15866172809 y4948.22543251576 X634.367133836147 Y1218.94772280914 
t0
c n0 N1 x2313.07537427925 y5206.09873147636 X569.094568199993 Y1281.32297034091 
t0
c n0 N1 x3024.37125319911 y1719.49936055248 X742.512209670846 Y426.399208846189 
t0
c n0 N1 x3301.76105109094 y3034.48487114456 X809.709584154192 Y750.443305172942 
t0
c n0 N1 x3002.63383924115 y3850.15416724066 X737.928849744098 Y949.506947440259 
t0
c n0 N1 x3038.51216607222 y4326.18929721218 X747.594730459521 Y1065.19635729627 
t0
c n0 N1 x3173.22088039004 y5153.17463060511 X779.157263435366 Y1268.35440833639 
t0

#hugin_optimizeReferenceImage 0
#hugin_blender enblend
#hugin_remapper nona
#hugin_enblendOptions 
#hugin_enfuseOptions 
#hugin_hdrmergeOptions -m avg -c
#hugin_outputLDRBlended false
#hugin_outputLDRLayers false
#hugin_outputLDRExposureRemapped false
#hugin_outputLDRExposureLayers false
#hugin_outputLDRExposureBlended true
#hugin_outputLDRStacks false
#hugin_outputLDRExposureLayersFused false
#hugin_outputHDRBlended false
#hugin_outputHDRLayers false
#hugin_outputHDRStacks false
#hugin_outputLayersCompression LZW
#hugin_outputImageType jpg
#hugin_outputImageTypeCompression LZW
#hugin_outputJPEGQuality 30
#hugin_outputImageTypeHDR exr
#hugin_outputImageTypeHDRCompression LZW
#hugin_outputStacksMinOverlap 0.7
#hugin_outputLayersExposureDiff 0.5
#hugin_optimizerMasterSwitch 1
#hugin_optimizerPhotoMasterSwitch 21


> On Apr 6, 2015, at 3:57 PM, Pell Emanuelsson <p_emanuels...@gmx.net> wrote:
> 
> Yo'av,
> 
> You didn't send the message to the list, I think - just to me personally, so 
> Donald and Terry probably didn't see your answer.
> In any case I believe there is no Hugin mystery here.
> First, as I wrote, if you scan the same photo twice, even with different 
> resolutions, it should be enough to translate, rotate and scale one image in 
> order to have a perfect fit. (I'm ignoring shear here.)
> There's no use for the full Hugin camera model. If you don't get a good fit, 
> then there's something else wrong with your scanning process, something Hugin 
> can't compensate for.
> 
> Just looking at the two source images in an image viewer gives the impression 
> that the shrouded tree has the same width, but has a larger height in 
> 14560014.jpg. Comparing width and height of this object gives:
> 
> 14560002.jpg W: 803-3205=2402  H: 1200-5271=4071 Aspect: 1.6948
> 14560014.jpg W: 201-787=586 H: 300-1298=998 Aspect: 1.7031
> 
> Difference: 1.7031-1.6948=0.0083  At 4000 px: 4000*0.0083=33 px
> 
> So the two images don't have the same resolution proportions in X and Y. 
> Keeping the width the same, the height differs by 0.8% which at around 4000 
> pixels gives an error of 33 pixels. So this is why Hugin can't optimize. If 
> it lines up the X values of the control points perfectly, the Y values can 
> differ by up to 33 pixels due to the different Y resolutions of the images. 
> And Hugin can't just scale one dimension of a photo, as far as I know (though 
> I'm still at the 2012 version, so something might have changed).
> 
> To check if this is the only problem, I scaled down the hi-res image from 
> 4181x6305 to 4160x6305 and then tried to optimize again.
> I now get almost a perfect fit.
> However, it's still not quite perfect. Since the images are now so close to 
> eachother, visual comparison is possible. I get the impression that the 
> resolution varies a little over the whole image, i.e. some pixel rows are 
> closer together, some are further apart and I don't see this in the X 
> direction. This indicates that the scanning sled motion is not perfectly 
> linear. This is also probably never the case and I can't say if this scanner 
> is better or worse than any other.
> 
> I placed my project and input/output images here:
> https://dl.dropboxusercontent.com/u/95455644/hugin.zip 
> <https://dl.dropboxusercontent.com/u/95455644/hugin.zip>
> 
> Regards, 
> Pell
> 
> On 2015-04-05 09:43, Yo'av Moshe wrote:
>> Hi,
>> 
>> Donald - could you include your pto file? As for the distortion I'm seeing, 
>> it's quite easy to notice on my output - I'm aligning image B on top of 
>> image A, matching the the top left corner of the tree, and then when 
>> checking the bottom right corner I can see it's off by about 15px-20px . 
>> That's the distortion I mean.
>> 
>> Terry - I've tried both pto and they both still seem to include some 
>> distortion when aligning the images. I can't really tell how good the fused 
>> image on your screenshot is because it's quite zoomed out :-/ 
>> 
>> Pell - The noise doesn't have to do with the quality of the scanning AFAIK. 
>> It's a scanned film from a quite good lab over here, and the noise is 
>> because of the type of the film and the relatively high ISO/ASA level. 
>> However, while I understand why this can create false control points, I'm 
>> not really sure why it would matter when I'm setting the control points 
>> myself? I've tried putting the two images in your zip file one on top of the 
>> other and again there seem to be the same distortion I mentioned above.
>> 
>> Please note that I'm not trying to create the fused image using Hugin - I'm 
>> generating two different files specifically so I can tweak the final result 
>> of mixing the two later on using Photoshop/Gimp.
>> 
>> Anyway thank you all so much for your time. It really is appreciated a lot. 
>> I won't be available during the coming week (holiday over here!) so sorry in 
>> advance for the my delayed response.  
>> 
>> And again thank you.
>> 
>> Yo'av
>> 
>> 
>> 
>> 
>> 2015-04-05 3:50 GMT+03:00 Pell Emanuelsson <p_emanuels...@gmx.net 
>> <mailto:p_emanuels...@gmx.net>>:
>> Yo'av,
>> 
>> I'm not sure what you are trying to do. None of the images are scanned very 
>> well... Much noise.
>> 
>> Anyway, since it's the same photo scanned twice, there's no need to change 
>> any camera parameters.
>> They are the same for the two images. Due to repeatability issues it might 
>> make sense to optimize FOV for one of the photos.
>> Also no need to set many control points. I set only four points and they 
>> match quite well. At least well enough for optimizing exposure.
>> To transfer the exposure parameters from one photo to the other, I simply 
>> chose to optimize the high-res image for exposure, color and camera 
>> response. I chose to use 4000 points instead of the default 400, since the 
>> whole images overlap.
>> I still think it would be better to experiment with different settings while 
>> scanning.
>> If your scan program doesn't support this, check out VueScan.
>> http://www.hamrick.com/ <http://www.hamrick.com/>
>> 
>> I placed the two result images and a PTO here:
>> https://dl.dropboxusercontent.com/u/95455644/hugin.zip 
>> <https://dl.dropboxusercontent.com/u/95455644/hugin.zip>
>> 
>> The image 14560014-145600020001.jpg is the one you want (the high resolution 
>> with new exposure).
>> 
>> The PTO is for Hugin 2012.0.0. 
>> 
>> Regards,
>> Pell
>> 
>> 
>> 
>> On 2015-04-03 09:20, Yo'av Moshe wrote:
>>> Hi,
>>> Thank you again for your kind help!
>>> 
>>> Both jpegs and the .pto file can be downloaded here: 
>>> http://bit-else.com/hugin.zip <http://bit-else.com/hugin.zip> 
>>> 
>>> @panostar - I generally never touched any of the lens parameters, but I 
>>> noticed the focal length was set slightly differently for both images so I 
>>> set them both to 23.56 (the original setting of one them). It didn't seem 
>>> to change much when aligning them though :-( 
>>> 
>>> Yo'av
>>> 
>>> On Friday, 3 April 2015 01:04:14 UTC+3, Tduell wrote:
>>> Hello Yo'av, 
>>> 
>>> On Thu, 02 Apr 2015 19:06:44 +1100, Yo'av Moshe <bje...@gmail.com <>> 
>>> wrote: 
>>> 
>>> > 
>>> > Any ideas for why my control points doesn't seem to fix the distortion? I 
>>> > believe Hugin is giving them a really bad score (I had to take the 
>>> > threshold to 0.3 in the preferences panel) but I think it's because of   
>>> > the noise and the size difference. Do I need to add more maybe? 
>>> > 
>>> 
>>> It's not obvious what the problem is without seeing your project images. 
>>> Are you able to make them available so we can look more closely at the   
>>> problem? 
>>> If so, a good way to do that is put the images on Dropbox or similar,   
>>> along with your .pto file. 
>>> 
>>> Cheers, 
>>> -- 
>>> Regards, 
>>> Terry Duell 
>>> -- 
>>> A list of frequently asked questions is available at: 
>>> http://wiki.panotools.org/Hugin_FAQ <http://wiki.panotools.org/Hugin_FAQ>
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>> 
>> 
>> 
>> 
>> -- 
>> Yo'av Moshe
> 
> 
> -- 
> A list of frequently asked questions is available at: 
> http://wiki.panotools.org/Hugin_FAQ <http://wiki.panotools.org/Hugin_FAQ>
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