Hey. I am new to slicer segmentation. I try to segment lung nodules with the help of CIP lesion analyser, but unfortunately after the first successful nodule segmentation, I select the second nodule but I am unable to proceed with the segmentation button. Is there any way around? It is very useful in order to do a semi-automatic segmentation like that.
Hi,
This seems to be an outdated module that needs servicing.
I can not get it running either even not in 4.10.2
Please describe what you would expect to have in your clinical workflow.
I am not the creator of that package.
Best regards
rudolf
In the meantime, you could try to use the “Local threshold” effect of the “Segment Editor” with the following parameters:
CTRL+left click into the nodule you want to segment - done.
Please use Slicer preview 4.13. You need to install “Segment Editor Extra Effects” to have that effect available.
Thank you so much for the help. I used the CIP plug-in as it seemed more specific to lung nodule analysis. I will try your suggested method. I will use the MIP viewer from CIP extension and segment the nodules as you suggested. Tried installing the “segment editor extra effects” with no luck. I will use the latest slicer preview and try again.
Thanks again for your help
Tried a lot of tricks in order to instal the “segment editor extra effects”. Just couldn’t. Could you please suggest a way? Thanks in advance.
Install Slicer 4.13. (important)
Go extension manager:
Enter “extra” in the input box at the upper right edge of the window:
Install and restart Slicer.
After that, you should find “Local threshold” in the Segment Editor.
I am grateful to you for your guidance. Followed your screenshots and installed the extra effects extension. However, I don’t think I can do the segmentation. I followed the instructions but when I ctlr + left click, the whole are of the image flashes and I cannot continue with the segmentation. Are there some additional options I need to select?
Thanks again for the help
I produced a short clip, hope that helps.
Did exactly what you didi but the nodule just doesn’t want to get segmentated. I add a video of my try.
You are using “Watershed” in your Local threshold dropdown field, I am using “GrowCut”
I did it with grow cut. The output is the same as I presented in the video
Are you able to share an anonymized dataset?
Try to use grow from seeds.
Please try to adjust the “Local threshold” threshold slider in a way that the nodule gets completely filled, even gets a bit “overfilled”. Then CTRL+Left Click into the nodule again.
Make sure that “Editable intensity range” is unchecked.
sorry to bother you again, but unfortunately I couldn’t manage to do it. Tried everything you said, experimented with other suggestions found online, but I couldn’t.
The CIP plugin is a more user friendly way of doing the segmentations. Is there a way to install an older version of Slicer 3D that worked well with that?
Thanks in advance
No, I am not aware of such a version.
The Slicer version that is recommended on the Chest Imaging Platform homepage and linked there for download does not include a fully working Lung Lesion Analyzer extension. I am not prepared to go further back in time for testing.
