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Input Mag_dist_est params to MotionCor2

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Crick_user
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Joined: 19 Nov 2016

Good morning,

I have run mag_dist_est program and I got two sets of params (original Apix is 0.889):

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The following distortion parameters were found :-

Major Scale = 1.002
Minor Scale = 0.998
Distortion Angle = 109.1

Stretch only parameters would be as follows :-

Major Scale = 1.005
Minor Scale = 1.000
Distortion Angle = 109.1

Corrected Pixel Size = 0.887

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My question is: when running MotionCor2, should I use the first set of params in -Mag option or the second? Also, should I change the pixel size to the new value only if I am adopting the second set of params (while I should keep unaltered apix when adopting the first set)?

Thank you very much!

timgrant
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Joined: 16 Jul 2010
Hi, I'm not all that familiar

Hi,

I'm not all that familiar with MotionCor2, but I can tell you generally and that will probably apply to MotionCor2, but you may want to check with Shawn or post on CCPEM to double check.

The difference between the normal and stretch only parameters, is that the normal parameters will leave an edge in the image, which may cause problems for future processing steps. The stretch only parameters leave no edge, but change the pixel size. I therefore generally recommend using the stretch only parameters. If you were using mag_distortion_correct, then the pixel size of the corrected images would be the "Corrected pixel size", and you would use that in the future processing. If you are using cisTEM, then the pixel size calculations are done for you, you should enter the distortion amount, and the original pixel size, you will see that the pixel size of the aligned image is corrected for you.

Hope that helps.

Tim