[Vv] clitkDicomRTStruct2Image issues

[Jonathan Martens]

Dear all,

I am trying to work with Elastix (http://elastix.isi.uu.nl) and therefore need to convert structure sets from DICOM RT-STRUCT files to the proper format accepted by Elastix. Elastix seems to require files with a metaimage format in .mhd/.raw format.

On my search on the internet I found an older thread in this e-mail list referencing a tool (part of vv) to convert RT-STRUCT files to the required format (https://www.creatis.insa-lyon.fr/pipermail/vv/2013-February/000285.html).

I got the Docker container running as suggested per https://www.creatis.insa-lyon.fr/rio/vv?action=show&redirect=VV#line-109 on Windows 7 using the following:

  docker pull tbaudier/vv
  docker run -name vv -e DISPLAY= $(docker-machine ip):0 -v $(pwd):/home tbaudier/vv

in combination with XMing running with the following command line (had to add the -ac switch to the default command line)

  Xming.exe :0 -ac -clipboard -multiwindow

After that I am able to start the container and run vv in a X11 terminal on Windows 7. Besides I am able to attach a shell:

  docker exec -it vv /bin/bash

>From that I can run the command line tools. But when I try to extract data from my RT-STRUCT file like this:

p=P0162C0006I13345846;
rtstruct=RTSTRUCT/1.2.246.352.71.2.78480665410.4114624.20161221081018/RTSTRUCT.1.2.246.352.71.4.78480665410.142535.20161221114758.dcm;
ct=CT/1.3.6.1.4.1.32722.162.6.55613550350070884234080940853841385982/CT.1.3.6.1.4.1.32722.162.6.98938198109550082302924371538367888818.dcm;
d=/home/DICOM;
params=-v

clitkDicomRTStruct2Image $params \
-i $d/$p/$rtstruct \
-j $d/$p/$ct \
-o $d/$p/test.mhd

I seem to run into issues, as clitkDicomRTStruct2Image seems to, consequently, return correct .mhd files, but .raw with a size of 256kB that contain only NULL values (512 * 512 * 1 = 262144).

I would have expected to have some data in it as the RT-STRUCT file does contain contours. Even if I extract a specific contour for all slices of the CT set referenced from the RT-STRUCT I seem to get no data in any file.

Am I doing something wrong? Am I expecting something wrong?

Kind regards,

Jonathan
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