Convert 3D dose distribution to DICOM RT dose

Operating system: windows 7 64bit
Slicer version: 4.8.0
Expected behavior: DICOM dose distribution
Actual behavior:

I got 3D dose distribution from Monte Carlo simulation. I want to know if 3D slicer can convert the 3D dose distribution to DICOM RT dose file in order to compare the DVHs.
Thanks in advance.

What format is it in? What do you use for MC simulation?

You can generally do this with the Slicer RT extension, but you need to also output the geometry, I.e. “region” or “cell” or however your code calls it, as a voxel type labelmap. Then you can use the DVH functionality of Slicer RT.

Note: Uncheck “show dose volumes only” because even though your volume is a dose volume, it’s probably not RT dose volume so it won’t immediately show up. The results will be displayed as “intensity volume histogram” but it’s equivalent to DVH.

SlicerRT only supports a few RT application specific formats, so what you write is not quite true. I need to know what format it is in.

The dose distribution is in text format, I use Penelope for MC simulation.

The DICOM files are RT format (.dcm). I got the DVH from this file.
My problem is the monte carlo dose. How to do to plot the DVH of the monte carlo dose simulated with Penelope?

How to output the geometry? (my geometry is a voxel phantom)
My idea is to convert the 3D dose distribution to DICOM format and with the help of the DVH functionality of Sliser RT i plot the DVH.

Can I see such a file please? It might be quite simple to add a reader plugin for it, similarly to this optical CT file format for example.

Text format is for the 3D dose distribution result from MC simulation and not CT file.

How can I send it to you, please?

  • You can use the Dose Volume Histogram module to calculate and plot DVHs
  • You don’t need to convert the dose to DICOM for DVH calculation, but you can if you want. You can export RT dose from the Data module, if the dose is under a study and is converted to dose volume

Any file sharing service will do. We usually use Dropbox, OneDrive, or similar.

To another of your questions: the geometry will probably be in the header of the text file, same as in the case of the other importer I used as example above.

For the first option: As far as I know, the dose volume (RT dose) and segmentation (RT structure) files are requered for the DVH to calculate and plot the DVHs, and these files can only be obtained from DICOM files.
Please, tell me how can i plot the DVH with 3D dose distribution file.
Thanks in advance.

The dose does not need to come from DICOM. However, we need to read it from your file, for which probably we’ll need to add a new file loader. Please refer to my explanations above.

Here is the file:

I wonder how can this be done without volumes! the dose distribution file does not contain any geometry or volumes.

You usually have to run a separate tally, or calculation mode to output the geometry from your MC program. I haven’t used the PENELOPE code, but for example in many particle transport
codes, there is an option to sample the material number (integer) , or region ID (integer) number in the voxel mesh (instead, or at the same time as, the dose tally) – there should be a description of how to do this within
PENELOPE’s documentation. Not sure if this helps, but how I usually make DVHs in Slicer is to:

a) run the dose simulation with the MC code to get 3D dose distribution which is imported into Slicer as a ‘volume’ (a reader may need to be made for it as cpinter mentioned)

b) run the geometry option with the MC code to get a voxel representation of the geometry, and import that into Slicer as a segmentation, or as a ‘labelmap’ which can be immediately converted to segmentation within Slicer

c) then calculate DVH within the DVH module of the slicer RT add-on

(Attachment mg_info.txt is missing)

1 Like

Dose distribution is typically a 3D image which we call volume in medical image computing. Is your data not a 3D image?

My data is 3D image.

I don’t have access to the data you shared. I clicked on Request access, please let me know once you granted it and I can download it.