I hav understood now how to calculate…but only one problem… the calculation comes in volume cm3 not in area cm2…
“Segment cross section area” is only available in recent Slicer Preview Releases, in Sandbox extension.
Hello, I recently segmented over 200 DICOM files of MRI enterographies where I segmented one mask of the psoas muscle and another mask of the paraspinal muscle. I then ask slicer to determine the 2D area of that one slice I segmented and divided by 2 as instructed. However, it seems like slicer takes account for the thickness of the slice (1mm, 3mm, 5mm, etc.) into the area output, so dividing the output by 2 would still have half the amount of that thickness. Is there a way to ONLY get the true 2D area without any thickness?
If you segmented a single slice and the slice is so thick that the area of the side wall is not negligible (this should be very rare) then you can compute the circumference and cross-section area from the known volume, surface area, and slice thickness with a simple formula (because you have two unknowns cross_section_area and circumference and two equations: volume = cross_section_area * slice_thickness and surface_area = 2 * cross_section_area + circumference * slice_thickness).
Alternatively, you can also use Segment Cross-Section Area module as described above (this is mostly useful if you have segmented on many slices).
In the future, you can measure 2D surface area directly using Closed curve markups:
When you segment an area on a single slice, calculate the volume for the segmented area. Then multiply the volume in cm3 x (10/slice thickness in mm). This will give you the area in cm2.
This is because the volume is calculated by multiplying the area x slice thickness which is usually less than 1 cm (10mm).
If you do not know the slice thickness, go to DICOM from the drop down menu, then right-click to get DICOM metadata and search for slice thickness.
Hello! Sir. I used this algorithm to find the area of a closed curve in a 2D film plane, but the result I get is wrong. Is it because the algorithm does not support this situation?
3D Slicer can measure cross-sectional area, surface area, volume, etc. various ways. They are all correct, but they may be used improperly (e.g., you measure surface area and you interpret it as cross-sectional area).
Above we discussed many different methods. Which one did you use? What kind of data you measured on? How the image was acquired (provided as a DICOM file by a medical device, captured using a flatbed scanner and saved as TIFF, captured using a digital camera and saved as JPEG,…)? What result did you get? What result did you expect?
Dear Professor:
Thanks for your reply!
I used 3D slicer 5.2.2. I have two formats for my images: provided as a DICOM file by a medical device (Eclipse treatment planning system, Varian), captured using a flatbed scanner and saved as TIFF (EBT3 film scanned by Epson V850 pro). The film mhd file is obtained through the dose curve.
I want to generate isodose lines in these images and use them as the outer contour to calculate the area inside the contour.
Hope your guidance!
Best wishes!