rbumm
June 17, 2022, 5:26pm
1
During the preparation for the MONAILabel workshop, I noticed that in the public ML Task06_lung dataset there are several datasets with strange contrasts that display very “dark” initially.
These data are difficult for both manually assisted as well as AI segmentation. How do you guys handle these data? Could preprocessing help here?
lassoan
June 17, 2022, 6:13pm
2
This has been discussed here:
opened 11:49AM - 08 Oct 21 UTC
closed 02:33PM - 24 Apr 22 UTC
enhancement
backlog
We have had some feedback from clinical partners regarding setting of window for… highlighting different organs.
The window/levels are defined typically by window width (WW) and window level (WL). This is then used in the following formula to set the min/max levels for CT images.
w_min = WL - WW/2
w_max = WL+WW/2
More info about this can be found here: https://radiopaedia.org/articles/windowing-ct?lang=gb
There are known WL/WW values for different organs/tissues (as listed in the above link).
For example, a lung window is typically defined as WW=1500 and WL=-600. This has the following effect on visualizing the image volume:
Before applying lung window:
After applying lung window (WW=1500, WL=-600):
You can notice that it highlights tissues/lesions inside lung better. The above is just one example, the values for WW/WL can vary for different organs and institute.
In 3D Slicer, the above can be achieved as:
```
WL=-600; WW=1500
volumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
volumeNode.GetDisplayNode().SetAutoWindowLevel(False)
volumeNode.GetDisplayNode().SetWindowLevelMinMax(WL-WW/2, WL+WW/2)
```
Does this sound like something we can pass as argument from an app as default, given that we know the target organ/tissue and its WL/WW. In cases where these are not present, we can skip updating the above. In other cases where the user wants to change these, there is a window level button that can be used to adjust manually.
cc: @tvercaut
Add a comment there, describing why it is a problem for you.
