Match registered MR to RT Struct

[Ramón Emiliani]

Hi! I was trying to import some data to XNAT using an MR registered to a CT that has an associated RT Struct with some annotations. The upload for the RT Struct failed most probably because the Referenced SOP Instance UID point to the DICOM files of the CT and not the MR.

Assume I have an `input` folder with the MR (registered) DICOM series and the RT Struct that was created using the CT as reference. What I did was to first convert the RT-Struct to masks using plastimatch:

`plastimatch convert --input /input --output-prefix /output/mask`

After this I reconverted the masks generated to a DICOM series using:

`plastimatch convert --input /input/  --input-prefix /output/mask --output-dicom /output`

For this newly created DICOM series I had no problem and could upload to XNAT with the also created RT Struct. Could someone give me a good insight of what is happening under the hood? What would be the best way to associate the registered MR to the RT Struct without access to the CT.

[Sharp, Gregory C.]

Hi Ramon,

Good question. Is /input the directory containing the DICOM MR? If so, I would think that should work. If it does not work, is there a data set you can share?

Nevertheless, there are options. To attach a structure set to an existing DICOM image, one would normally do something like this:

plastimatch convert --input-prefix prefix/ --output-dicom output-structs/ --referenced-ct mr-dicom/

The input-prefix directory should be in the same (or similar) geometry as the referenced-ct directory. Does this do as expected?

Greg

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From: plast...@googlegroups.com <plast...@googlegroups.com> on behalf of Ramón Emiliani <ra...@afxmedical.com>
Sent: Wednesday, May 18, 2022 4:09 PM
To: Plastimatch
Subject: [Plastimatch] Match registered MR to RT Struct

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[Ramón Emiliani]

Hi Greg, I appreciate your quick response.

Yes, the DICOM MR is inside the directory and the commands work. The only thing is that converting to mask and back makes the contours lose some quality on the process. The naive approach I tried was to overwrite the RT Structure file and match the tags to the registered image (for example `Referenced SOP Class UID` on the contour data). I was able to load the annotations and no quality was lost, though I am not sure if it is the best approach, seems a bit arbitrary. Would the best way be to construct a new RT Struct file? Does the plastimatch convert command cover this case? I feel more than conversion is just reconstructing the RT.

Sorry if the question feels a bit out of scope and I am grateful for your help.

Ramón

[Sharp, Gregory C.]

Hi Ramon,

I'd have to take a look more deeply to see if this can be done directly from DICOM. I suspect it might work if you just dump the RTSTRUCT into the same directory as the MR and convert DICOM -> DICOM.

There is another option. There is a lossless contour-based text format called CXT. If you convert the RTSTRUCT to CXT (using --output-cxt option), then you convert back to DICOM as --input-cxt option with --referenced-ct set to the DICOM MR directory.

I hope that explanation was clear.

Greg

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From: plast...@googlegroups.com <plast...@googlegroups.com> on behalf of Ramón Emiliani <ra...@afxmedical.com>

Sent: Friday, May 20, 2022 11:15 AM
To: Plastimatch
Subject: Re: [Plastimatch] Match registered MR to RT Struct

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