[Vv] clitkDicomRTStruct2Image issues

[Thomas BAUDIER]

Hi Jonathan,

Thank you to report this problem.

I just want to be sure you use the clitkDicomRTStruct2Image tool 
correctly:
The tool takes a RTStruct file in input (-i) with 1 or more structures 
and a CT image (-j). Be sure to have a complete CT image with all slices 
(I saw you just take a .dcm file, but I don't know if it's just a slice 
or not). I prefer to use an mhd image for the CT. You can convert a 
DicomSerie into a .mhd file with clitkDicom2Image -o output.mhd *.dcm
And the outputs are each structures in a different .mhd file. The name 
of these files are VARnbStruct.mhd with Var the output -o and nbStruct 
the number of your structure.

The Docker image isn't very suitable for command line tools, we did for 
vv exclusively. So we didn't test the command line tools with Docker. 
The best is to use the git version to be sure to have the newest running 
version.

Thomas

On 2017-01-23 12:55, Jonathan Martens wrote:
> 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
> [1] 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
> 
> Links:
> ------
> [1] 
> https://www.creatis.insa-lyon.fr/rio/vv?action=show&redirect=VV#line-109
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