Applying segmentation/thresholding to cropped area only

(Tom) #1

Operating system: Window
Slicer version: 4.10.0

I have a DICOM image of the thigh, and I want to crop the image so I am left with a single “slice” from which I will then use segmentation to calculate CSA of the quadriceps. I thought I had cropped the image to my single slice of interest, but when I use thresholding to segment, it applies it to the whole stack of images.

How can I isolating my segmentation to the single slice I am interested in? Im not sure my cropping has applied to the sagittal and conronal views, despite me dragging the ROI box accordingly to just the area of the single slice I wanted to segment.

Thanks for your help

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(Andras Lasso) #2

You don’t need to crop the image, just use Segment Editor’s paint or draw effect to segment a single slice. You can then get surface are by using Segment Statistics module. Both sides of the surface is included, so divide the result by 2.

In recent nightly versions of Slicer, we added “closed curve” markup, which will allow cross-section area computation directly from the closed curve, without segmentation. You can already define the curve but it’s area is not reported yet - the area display is expected to be ready within a few weeks.

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(Tom) #3

Ok, thank you. So I assume I can’t use the thresholding function on a single slice, I have to paint or draw?

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(Andras Lasso) #4

If you want to fill the entire slice then you can set a large brush size and paint the entire image slice with a single click.

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