[Elastix] µCT population average

Coert Metz coert.metz at gmail.com
Wed Feb 18 09:34:17 CET 2015


Hi Fabien,

When you average, do you include one identity transform for Tii (so
transformation from subject to itself)? This might be the reason it's not
working.
See, for example also section 2.2 of
http://bigr.nl/website/index.php?page=publications&subpage=publication&id=547

Regards,
Coert Metz


On Wed, Feb 18, 2015 at 9:21 AM, Fabien PERTUY <pertuy at igbmc.fr> wrote:

>  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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