[Elastix] Writing out a downsampled DVF with transformix

S. Klein s.klein at erasmusmc.nl
Wed Feb 4 23:30:15 CET 2015

Hi Matthew,
Before calling transformix -def all , you should edit the TransformParameters.txt file: fields Spacing, Size. (e.g. double the spacing, half the size). Then transformix will generate the deformation field on the domain specified.

On 4-2-2015 18:20, Matthew J. Riblett wrote:
Hello Elastix Users,

I’ve been working on using Elastix for CBCT motion compensation and ran into an issue downsampling the transform DVF image before applying it during image reconstruction.

Currently, I’m getting a ‘deformationField.mhd’ out that is approximately 4.2Gb in size, and when I try to apply it during reconstruction with RTKFDK, its causing a yet unknown issue that prompts the application to stall.  Just to make sure the file size is not responsible for the issue, I attempted to write a script that downsamples the DVF to a more manageable size, however, I’m not convinced that the script is handling this in an appropriate (or correct) way.

I was wondering if a method exists— I haven’t been able to find one in the documentation — to have transformix downsample the DVF during its production.

Just to be clear, I’m calling transformix with 'transformix -def all -out <directory> -tp TransformParameters.0.txt’ to get the full resolution DVF.


— Matt

Matthew J. Riblett
Virginia Commonwealth University
Department of Radiation Oncology
Medical Physics Graduate Program

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