[Elastix] µCT population average

Fabien PERTUY pertuy at igbmc.fr
Wed Feb 18 09:21:48 CET 2015

Hi ElastiX community,

I am a new user of ElastiX interested in registration of µCT scans to generate population average that could be used to create custom atlases.
I tried to reproduce described approaches (including Roy van Pelt's) based on computing the mean of several transforms. The results I got with these methods were not good at all, although I tried several parameters.
In the mean time I succeeded using multiImageRegistration, registering each image to all others at once.

My main concern is that I cannot figure why I won't get se same result with one image registration to multiple fixed images (moving_A to fixed_A, fixed_B, fixed_C) and with the mean of the transforms of the same moving image to each fixed images (mean of moving_A to fixed_A, moving_A to fixed_B and moving_A to fixed_C, performed using WeightedCombinationTransform) . Could anyone help me with that ?

The reason why I want to switch to the mean of 1 to 1 transforms instead of a single 1 to multi registration is RAM consumption. For now I work with 100Mo stacks, and I completely fill 32Go RAM with the registration of 1 moving and 20 fixed images. I will probably have to work with over 30 of these images at once and this will heavily use swap instead of my RAM, wasting a lot of time. Moreover I will also have to work with larger data (3-9Go images) and I will probably encounter similar memory problems.

I would also be interested if someone could give me any tip to lower RAM consumption.
You can find a typical parameter file attached, used to register 1 moving to 9 fixed images with bspline transform.

Kind regards,

Fabien Pertuy
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