plastimatch convert --input CT/ --output-img ct.nrrd
plastimatch convert --input rtdose.dcm --output-dose-img rd.nrrd --fixed ct.nrrd
The size between rd.nrrd and ct.nrrd is not same.
I'm not sure if this is a bug or not. For example, if you did:
plastimatch convert --input DICOM/ --output-dose-img dose.nrrd --output-img ct.nrrd --fixed other.nrrd
would you expect both the dose and ct to be resampled? I could be convinced either way, but it's not completely clear.
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Subject: [Plastimatch] plastimatch convert --fixed option is not work with rtdose
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I thought about your question about resampling the dose. It's not always what you want, but it seems a useful option. So I added "--resize-dose" to force this to happen. Use it like this:
plastimatch convert --input DICOM/ --output-img image.nrrd --output-dose-img dose.nrrd --fixed reference.nrrd --resize-dose
If you update your plastimatch from source you can use this. Now you can do it in a single command (as above) if rtdose.dcm is in the same directory as the image.
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Wow, great idea. I just tried it, and it works!
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The plastimatch-build is the latest plastimatch code build directory.
There was a RTSTRUCT.dcm file under ~/rs_dcm_dir/, And I ran the following command:
foo@bar:~/plastimatch-build$ ./plastimatch convert --input ~/rs_dcm_dir/ --output-prefix ~/rs_nii_dir/ --prefix-format nii.gz --xor-contours --referenced-ct ~/ct_dcm_dir/
Loading RDD complete
Sorry, could not load input as any known type.
For some reason plastimatch is not reading your RTSTRUCT. I am getting something like this:
Loading RDD complete
Found RTSTUCT, UID=1.2.8184.108.40.20680043.8.2220.127.116.1123329.23364.1600463281.956502RTSTRUCT
Trying to load rt structure set.
Adding structure (1), Body
Adding structure (2), Tumor
I wonder if DCMTK is not being properly linked. What is the value of DCMTK_DIR in your CMakeCache.txt? I use Debian's DCMTK, and have the below.
//The directory containing a CMake configuration file for DCMTK.
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I checked CMakeCache.txt and found that DCMTK_DIR was DCMTK_DIR-NOTFOUND, and ITK_DIR was also ITK_DIR-NOTFOUND.But there were DCMTK-build and ITK-build directory generated in the plastimatch build directory, and they all seemed to build successfully.