[Elastix] Groupwise nD+t B-splines for 4DCT of lungs

Floris Berendsen floris at isi.uu.nl
Fri Feb 13 14:01:59 CET 2015

Hi Dan,

That is an interesting application. I was not involved in the works you
mention, however I can give my view based on experiences with these methods
and the elastix framework.

Answer 1):
Unfortunately, a set of 3d images must be provided as a 4D volume with its
last dimension the image number or time index. In the current framework of
elastix the groupwise registration is sort of hacked in, therefore it has
these restrictions.

Asnwer 2):
I think my answer is threefold.
2a): I would assume that more (independent) image data can provide a better
registration (estimate) in general. A higher SNR is a bonus as well.
2b): In the current groupwise registration framework the resulting
transformation is defined to point from a floating 'spatial average' image
domain to each time frame domain. Since you would like to model all
deformations in the space of the TLC image you would need to chain the
resulting transformations to each time frame with the inverse
transformation of the TLC. This can be done with some scripting.
As a downside of including the TLC image in the time stack you  probably
should not use any time domain smoothness for the registration, since that
doesn't make sense for such a hybrid stack.
2c): Ultimately, you might want to adapt the groupwise framework such that
you have a the TLC image as fixed image and the time stack as moving image.
In that way you have the TLC image as a reference domain for modelling and
the image similarity metric is still calculated in a groupwise fashion. You
would need to write an adapted metric and possibly transformation for that,
but the current framework allows this, I think.

Answer 3):
Not sure about the details in the paper. I would say that the lung mask
needs to be 4D (and possibly different for each 3d sub volume), such that
the sampler knows what the valid samples are.

Answer 4):
External tools/labour are needed to generate these label images. Delmon et
al. use "Automated Segmentation of a Motion Mask to Preserve Sliding Motion
in Deformable Registration of Thoracic CT" for that. I worked on an
approach similar to that of Delmon et al. My souce code is not yet part of
elastix, but the method is published so far is as:

Registration of organs with sliding interfaces and changing topologies

Combining sliding organs with a groupwise approach has come to my mind as
well. I think it can be done, but requires bigger adaptations of the code
and might be limited to certain setups. Both our slidng organ methods
require a label image that is defined in the fixed domain. In principle
this conflicts with the floating spatial domain, but 2c) would solve this.


On Thu, Feb 12, 2015 at 9:42 PM, Einstein, Daniel R <
Daniel.Einstein at pnnl.gov> wrote:

>  Hello,
>  I am interested in applying a number of ElastiX 4D lung registration
> approaches to 11 dynamic rat lung images that are described in:
>  http://www.ncbi.nlm.nih.gov/pubmed/22087338
>  and
>  http://www.ncbi.nlm.nih.gov/pubmed/23799057
>  The parameter file (Par0012) available at
> http://elastix.bigr.nl/wiki/index.php/Par0012 seems to be what I am
> after.
>  Question 1): do the images input to the elastic command line need to be
> truly 4D, or can they be multiple 3D images?
>  elastix -f <dynamic nD+t image> -m <dynamic nD+t image> -p <par
> filename> -out <output dir>
>  Question 2): We have a higher-resolution, higher SNR static TLC image
> from the same animal upon which we would like to base a model geometry.
> Assuming both sets of images (4D + TLC) are up/down sampled to be equal, do
> you think there is any benefit to including the TLC image in the groupwise
> registration?
>  Question 3): The text of the Metz et al 2011 paper mentions that "the
> proposed method, registration was always performed on the complete 4D image
> and using a lung mask". The command line above does not call for a mask.
> Were different settings used in the Metz et al paper and was a single mask
> used for all images or was a 4D mask image used?
>  Question 4): Later work with ElastiX described in Delmon et al 2013,
> describes the use of direction dependent B-splines for relative motion
> between the lung and the thorax (
> http://elastix.bigr.nl/wiki/index.php/Par0016). This exercise requires a
> label image, that appears not to be readily available. Has any attempt been
> made to combine the methods in Par0012 and Par0016?
>  Thank you for your patience as I get my feet wet with your code.
>  Kind Regards,
> Dan
>   ___________________________________________
> Daniel R Einstein, PhD
> Computational Biology & Bioinformatics
> Pacific Northwest National Laboratory
> www.pnnl.gov
>  and
>  Department of Mechanical Engineering
> University of Washington, Seattle
> https://www.me.washington.edu
> _______________________________________________
> Elastix mailing list
> Elastix at bigr.nl
> http://lists.bigr.nl/cgi-bin/mailman/listinfo/elastix
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