Convert RT struct to a label map volume

Operating system: Ubuntu 16.04 LTS
Slicer version: 4.7.0-2017-06-03 r26072
Expected behavior: Conversion from RT Struct to a label map in segmentation module producing label map volume with nonzero entries
Actual behavior: Output label map volume is zero everywhere

Dear all,
I have RT structs with a contouring in it, after installing SlicerRT I can import these from DICOM files. I would like to convert the RT struct to a binary labelmap. This is what I tried:
Segmentations module -> Representations: Create binary labelmap -> Export/import models and labelmaps: select export, label map and an output node. This produces a labelmap volume with no nonzero entries.
Can you point me to a solution?

Best and thank you,
Yannick

1 Like

Are the structure sets displayed correctly?
If you go to Segment Editor and select a master volume, can you edit segments (for example, paint in it)?

Hi Lassoan, I can display correctly and be able to paint in it. And the file format of contours is changed from .seg.vtm to .seg.nrrd. However, I still need to convert the contours to label cause I assume the label can be deformed with the image during the deformable image registration. Please advice 1. if my assumption is correct and 2. if correct, how I can convert the contours to label. Thanks a lot.

You can apply rigid or deformable transforms directly to segmentation nodes, even in real-time (change the transform and you immediately see how the segments change). No need to export it to other node type.

If you want to edit a deformed segmentation then you need to go to Transforms module and “harden” the transform on the segmentation by clicking image button.

Thanks Lassoan. Please see the screen shot:image. Q1: The structure is not deformed by BSpine. Because pink contour represents heart, and it is not following heart. How to make BSpine applied on RTSTRUCT? Q2: RTSTRUCT stays at the original location. How to change its original location to the same as CBCT (the fixed image) in the work? Thanks a lot.

I’ve just checked and Transforms are applied correctly to Segmentations nodes. See this example video: https://1drv.ms/v/s!Arm_AFxB9yqHsJ8NLVWOX6tvTNHtpw

If you still have problems, then please reproduce the problem with a data set that you can share (for example, data sets from Slicer’s Sample Data module), save the scene, upload to dropbox/onedrive, and paste the link here.