Convert image and segmentation to DICOM

Support
1

Andras,
I am now trying to convert nrrd files to DICOM. The main image is
converting just fine, but I am not able to figure out how to convert just
the contour, as it does not show up when using “Create a DICOM series.” How
can I also convert this file?

2

You are trying to convert nrrd files into a RT Structure Set using 3D Slicer? By coincidence, I documented this procedure earlier today.

  1. Load all images. At time of load, click “Labelmap” checkbox for each structure
  2. Go to Segmentation module
  3. For “Active segmentation”, choose “Create new segmentation”
  4. For each structure, repeat:
    4a) In “Export/Import segments”, choose structure, and import as labelmap
  5. Click on one of the segments, and then click “Edit selected”
  6. Set the “Master volume” to your CT
  7. Go to Data module.
  8. On background, right click choose “Create new subject”
  9. On subject, right click choose “Create child study”
  10. Drag the CT and segmentation node onto the child study
  11. Right click on study, choose “Export to DICOM”
  12. Enjoy your newly created DICOM-RT file
1 Like
3

When I am loading the images, I am not seeing a “Labelmap” checkbox.

4

Click “Show options” in the Add data dialog.

If you already have your contours as segmentation you can start at step 7.

5

I am not seeing a “create new subject” option once I am in the data module,
or any of the steps past 7.

6

You should see this when you right-click in the big white empty area in the Subject hierarchy tab of Data module:

7

That is not what I have. I have version 4.6.2, so I’m not sure if that is
where the difference is.

8

4.6.2 is very old (almost a year). Use the latest nightly build.

9

When I click on export on the final step, nothing happens. Nothing shows up in the folder which I have selected, and the export window doesn’t change or go away.

10

Please copy the complete application log (menu: Help / Report a bug). Scrub any patient info from the logs before posting.

11

There are very different ways to do this, and the approach will be different depending on your specific needs.

Can you explain why you want to convert these nrrd files to DICOM? What do you want to do next with those DICOM files?

12

It is to test if the files from pyradiomics will be able to run on some new
code we have created. We are trying to verify that our code will correctly
read the images.

13

I do not understand what you are trying to do. The output from pyradiomics is a table with numbers. pyradiomics does not produce any images.

14

There is a plugin in Slicer called “Create a DICOM Series”

15

I am trying to get another system to output the same numbers as
pyradiomics. However, that other system can only use DICOM images. This is
to check that the other system is outputting the correct numbers.

16

Ok, now I understand I think.

The simplest would be to just start with an image dataset that is already in DICOM and compute radiomics features using both tools.

17

A post was split to a new topic: Export segmentation as DICOM

18

A post was split to a new topic: Use segmentation for radiomics