AAPM Thoracic Auto-segmentation Challenge Forum

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> Convertion to DICOM RT

How can I convert single segmentation files (nii/mhd) to DICOM RT using 3D Slicer?

Posted by: Bruno @ June 19, 2017, 9:11 p.m.

You may need to use the SlicerRT module:
https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SlicerRT#Tutorials

Posted by: yangjinzhong @ June 20, 2017, 2:41 a.m.

You will want to use the nightly build. Here are the steps:

1) Load using DICOM module
2) Go to segmentations module, make the structure set as the active segmentation
3) In the "Export/Import" section, click "Export" to export as new labelmap
4) In the "Binary labelmap" section of "Representations", click "Make master" (then click "Yes" to acknowledge)
5) Click "Save". You can choose nifti or other formats in this dialog. The structures will be a 4D image (one plane per structure).

Posted by: gregsharp @ June 20, 2017, 3:04 p.m.

Ha, sorry I mis-read. You want the reverse process.

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

Posted by: gregsharp @ June 20, 2017, 3:30 p.m.

Thank you! I can already create the Dicom properly.

Posted by: Bruno @ June 21, 2017, 10:23 a.m.

Hi, I'm new to use 3D Slicer.
I'm trying to convert my .mhd segmentation file into required .dcm, but couldn't find the labelmap checkbox you mentioned when uploading the data. The following steps didn't work either....
Do I need to upload the data in .dcm file instead? Thanks!

Posted by: ttzhao @ July 12, 2017, 1:53 a.m.

Hi, when uploading the data, you need to select the show options checkbox in the upper right of the uploading window. Here you will find the labelmap checkbox.

Posted by: Bruno @ July 12, 2017, 10:51 a.m.

It seems that it creates a series of .dcm files... But the submission requires to generate one .dic for each case

Posted by: PXL @ May 18, 2018, 5:55 a.m.
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