A new module - “Segment cross-section area” - has been added to Slicer. It can compute cross-sectional area of segmented structures along a chosen axis direction. Results are available both as a table and can be shown in a plot, too. Short demo video:
For now, the module is available by installing “Sandbox” extension in the extension manager in a recent 3D Slicer Preview Release.
If you have any comments and suggestions then please post it here.
Hello Professor Lasso, I want to calculate the cross-sectional area of the area of interest, how can I calculate
Follow the steps that are shown in the video above and let us know if you encounter any problems.
I have tried the method following instructions, but I do not get area. I get positions, not even sure what this means. Your instruction video also shows volume (cm^3), not area (cm^2). Is this an error? Or do I need to divide by slice thickness? Is there a way to convert when I am not exactly sure of slice thickness (varies by scanners in real life patients)? Also, how is this different from segment statistics?
Please watch the whole video, the table you want is at the end. The initial table is the output from segment statistics which reports volumes (so in cm3).
CA of segments reports cross-sectional area in a slice-by-slice manner. Positions you refer to can be the slice number (but see below). And the other value is the cross-sectional area.
If you want to get a more in-depth understanding of what the module does, I suggest experimenting with the module more. For example, segment a structure of interest in one slice. Then run the CA module and I think you will find it fairly easy to interpret results (every other slice apart from your segmentation will have 0s, and you will a single spike in the plot). The only confusion you may have is that volume axis is referred as row, column and slice (as oppose to axial, sagittal, or coronal, or X, Y or Z). But if you do the exercise I suggest, you will quickly find out which one corresponds to your segmentation plane.
Thank you for the reply. Now I understand. I was very confused on the position column. I need to scroll down to the correct slice number to see my measurement. Are the units in mm2 if I used DICOM files?
Default units in Slicer is mm. So I reported values should in mm2. But again, when in doubt, the best thing is to test with something know. For example, you can segment a 10mm radius circle (with the paint tool) and be certain about what units its being reported at…
Thank you for the suggestion!
Also note that in the table you get RAS position of the center of the slicing plane. Anatomical orientations (axial, sagittal, coronal) are not used because cross-section axes are not aligned with anatomical planes but with volume axes (which may or may not coincide with anatomical directions).
I want to calculate area and volume´s segments with 3D slice. I have installed Sandbox extension with the extension manager but I still can see the “segment cross-section area” in the Quantification part in modules.
How could I fix it?
Many thanks in advance.
It is available for recent Slicer Preview Releases.
Thank you for your response.
I tried with 4.11.10 version and it is not available this module.
You can follow these steps:
- Install latest Slicer Preview Release (if you do it between 12am-11am EST then you can download the release created the day before, to make sure that all extension builds are completed).
- Install Sandbox extension (you may need to choose Examples category to see it)
- Wait for the “Restart” button to become active and click it to restart the application
- Find “Segment cross-section area module” using the module finder
I am working with Slicer 4.11.20200930 but there is not Sandbox in extension?!!
You can find it in the “Examples” category. However, you need to use at least the latest stable release (currently Slicer 4.11.20210226).
Thank you so much.
1-Where is the “Example” category?
2- I want to get the cross section area of a cannula tube which is not circle? does it work for me?
Many thanks Lassoan. Found it
I get the plot. What is the slice index in the plot? How can I find the desired cross section area of my volume? is there any connection between the plot and views?
The cross-sectional area works for any cross-section shape.
Slice index is the voxel index of the selected “Volume” node (). You can get physical (RAS coordinate system, unit in mm) coordinates of the cross-sections in the “Position” column of the table.
Hello - I would also like to determine the cross-sectional area of the region I identified using Segment Editor. I can’t find the Sandbox extension - has it been renamed?