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

Einstein, Daniel R Daniel.Einstein at pnnl.gov
Thu Feb 12 21:42:21 CET 2015


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





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