Operating system: Windows 10
Slicer version: 4.10.2
Hi, how to do a mammographic density segmentation in order to show automatic identification of breast density?
Thank you,
Paola
Slicer has many tools for this kind of analysis. If you can write a bit more about what you would like to achieve (or provide reference to a paper that describes a workflow that is similar to what you would like to implement) then we can give more specific advice.
I would like to achieve an automated brest density assessement. In the work I mention below the software automatically identified on the mammogram the pixel with higher intensities. The density was measured in percentage. It’s what I am willing to reproduce.
Thank you
DOI 10.25259/JCIS_70_2019
You can segment the ROI(the white area and green area in your picture) and then get the each area statistic in segment statistic module.
Thank you. I am wondering if there is a way to segment automatically the ROI and to let the software calculate the pixel with higher density within that ROI.
If simple thresholding can segment the high-density area then the process can be made fully automatic very easily by writing a short Python script. See examples here: https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#How_to_run_segment_editor_effects_from_a_script
You may find “create fat/muscle/bone segment by thresholding and report volume of each segment” example particularly relevant. If the script works well then you can make a Python scripted module out of it.
By thresholding the segmentation seems suboptimal. In the picture I posted the author could “colour” just the fibroglandular breast parenchyma.
Thank you
The screenshot in the image indicates that the authors used “Level tracing” effect in Editor module (which correspongs to “Segment Editor” module in current Slicer version).
I had the same intuition but selecting “Level tracing”, the program don’t let me do any operation on the DICOM file. I thought there was the need of doing something else before but can’t find it.
Thank you
Once you have your segment highlighting the region of interest, you can follow the steps described above to get the density. Would you expect to do any other operation on the DICOM file?
Hi, i want to know how to make dense tissue segmentation from tomosynthesis images?
thank you
If dense tissue appears bright then you can segment it using Threshold effect in Segment Editor module.
Ok but i will have to do that on every slice, i’m guessing ?
Thresholding is performed for the entire 3D volume. No need to do it for every slice.
In general, in 3D Slicer all data is specified in 3D and all operations (with very few exceptions) are performed in 3D.
Ok. And how do i make a 3D volume from the tomosynthesis images? I’m starting to use 3D slicer for the first time, so if you could post a screenshot of the steps i have to do, i’d be very grateful.