Elastix 101

[Ivana Mihalek]

Dear Elastix community,

After a day of fumbling around, I am ready to throw in the towel.

How exactly do you use Elastix?

My question boils down to this. I have a fixed image

And a moving image:

The parameters file, basically a copy from the Zoo collection (affine transformation) is attached.

I use the command line that reads:
elastix -f circleF.png  -m circleM.png  -p Parameters_Affine.txt  -out elastix_output

and I get this as a result

What am I missing?

Thanks

Ivana

[Chitresh Bhushan]

Result looks okay to me in terms of spatial alignment. 

If your question is about interpolation/typecasting/ringing issues in results (bright pixels around the circle), then that can perhaps be addressed by changing FinalBSplineInterpolationOrder to 1 or 0 as following:

(FinalBSplineInterpolationOrder 1)

OR 

(FinalBSplineInterpolationOrder 0)

[Ivana Mihalek]

Thank you, this might help, but my question is  dumber - why isn't the moving image moved?

Is the image file called "result" not supposed to be showing the resulting image moved to the fixed image?

(I tried using transformix, but got the same output.)

[Soren Christensen]

Hi Ivana,

 I am guessing it's moved just slightly and you see the interpolated result of a near identity transform.

Your shapes have no overlap. If an initial guess fails to provide some overlap then the similarity metrics may not be helpful.

Try positioning them with overlap.

Soren

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[Ivana Mihalek]

Hi Soren,

in that case, the suggestion sounds  very reasonable, what is this option in the parameters  doing:

[Soren Christensen]

I believe there's a sub option to thatbfæag. Geometric or center of mass. If you use center of mass they should align I guess - depending on how center of mass is calculated they may align perfectly just with that initialization, i am not sure.

I guess if you do a 1 iteration run you can see what the initialization did for you.

Soren

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[Ivana Mihalek]

ok, thank you!