How to threshold only one slice in the DICOM Module

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1

Hi all,

I have loaded a 3D- CT scan into Slicer using the DICOM module. How can I apply thresholding to only one slice?

Thanks

2

There are many ways to do it. What would you like to achieve?

3

Hi Andras,

Thanks for the reply. I want to achieve accurate segmentation of muscle, SAT and VAT of the entire thoracolumbar region from T1 - L5. The method I was planning was to threshold 17 mid-vertebra slices and manually correcting them, then using the Fill between slice effect to propagate to the other slices and finally manually correcting them again. Is this a solid method to achieve the highest accuracy segmentation for a high resolution CT-volume? I am open to other suggestions :).

Thanks

4

Manual correction typically takes much longer time than specifying a region from scratch. So, I would definitely not recommend to create an initial “segmentation” with simple thresholding.

Instead, I would recommend to try these options:

  • Paint effect with appropriate “Editable intensity range”. You can find the correct threshold range in Threshold effect and then click “Use for masking”.
  • Draw effect, potentially with “Editable intensity range”.
  • Level tracing effect.

You may try to pre-process the image to reduce noise and make regions more homogeneous. For example, try Anisotropic Diffusion filters (in Filtering / Denoising category), or various other filters in Simple Filters module.

5

Great thanks for the suggestions! I still want to experiment thresholding at a single slice. You mentioned there are many ways to do this for a CT scan loaded using the DICOM module?

6

The easiest to see how bad the result is if you use simple thresholding is to threshold the entire volume, using Threshold effect. If you really want to threshold only a handful of slices, then you can set editable intensity range in Threshold effect, click Use for masking, then use Paint effect with a huge brush (so that you can easily cover the entire slice with a single click or a short paintstroke).

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7

Hi Andras,

Your fast responses are always much appreciated! Thanks.

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