Scissors Not Working

Sandy1 · February 7, 2022, 5:50am

I am in the segment editor, and I am attempting to remove jewelry and bone from my image. I have selected the erase inside option. Nothing happens once I’ve circled the areas with the scissors that I want to remove. Please help.

DIV · February 7, 2022, 6:36am

Hello, Sandra.
Sorry to hear that it didn’t work.
From my experience what commonly happens is that the segment you were tying to erase wasn’t selected in the panel on the side.
See below.

In the example, only Segment_2 is visible; Segment_3 and Segment_4 are hidden. So the user will often expect to be editing Segment_2*. (Alternatively, the other segments might be visible, but located outside of the current field of view**, say.) But none of that matters. the only thing that matters is that Segment_3 is highlighted, so the Scissors effect will be applied to it. Nothing in Segment_2 will be erased.

—DIV

*There’s actually a warning that is displayed in this situation in recent versions of 3D Slicer.
**No warning about this, AFAIK.

Sandy1 · February 9, 2022, 6:31pm

This still did NOT work for me. Getting this tool to work is critical for me at the moment as I am working on my dissertation project and am on a strict timeline. Is there anyone willing to virtually meet with me to help figure this out? One thing I did notice in your example is that underneath the flag you have a pencil icon marking the segment you plan to edit and circles for the others. I do not have a pencil icon. I only have a flag and a check mark icon. Could this be another clue to what is causing this issue? I am available any time in the mornings before noon. Please help. Id be so grateful.
Sandy

muratmaga · February 9, 2022, 7:00pm

Without screenshots of what you have done so far, it is not possible for us to guide you. Please provide a screen capture of what is not working at the stage you are using the scissor tool.

Sandy1 · February 9, 2022, 7:12pm

Understood. Currently at work but will do tomorrow morning. Thank you!!

Sandy1 · February 10, 2022, 5:21pm

OK, SO I have set up the image I want to edit.

My GOAL is to remove everything from this image because all I need to see is the skull. I want to delete the earrings, nose ring, vertebrae, etc… So, I open up the Segment Editor to use the scissors tool…

I use the scissors as directed and absolutely NOTHING happens. Please Help.

hherhold · February 10, 2022, 5:23pm

It looks like you are viewing the volume rendering of the data. Scissors works on the segmentation, not the volume data. You need to create a segment from the volume data, and then cut it with the scissors.

Sandy1 · February 10, 2022, 5:30pm

Thank you for your response. Can you explain how to create a segment from the volume data?

hherhold · February 10, 2022, 5:35pm

Image segmentation is a vast subject area. If this is a medical CT scan and you’re concentrating on bones, you can probably use the thresholding tool and pick the right Houndsfield unit range for bones (I’m an entomologist, so I’ve no idea what that would be). You can also use the paint tool, or local thresholding tool, etc. There are a LOT of tools for image segmentation.

muratmaga · February 10, 2022, 5:55pm

Please review these tutorials. You will find them helpful:
https://slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html

github.com

SlicerMorph/Spr_2021/blob/main/Day_2/Segmentation/Segmentation.md

## IMAGE SEGMENTATION with 3D Slicer

This is the big enchilada. Segmentation is what most people begin learning Slicer for and it is one of the first steps acquiring data towards a morphometric study. Careful extraction of anatomy and constructing an accurate 3D representation will have direct downstream impact on some of the analytical procedures, particularly for various semi-landmarking approaches and other morphometric techniques that require dense-correspondence. 

In Slicer, there two complementary modules that are used hand-in-hand for segmentation tasks.

1. `Segment Editor: ` is the actual module for segmentation of volumes. Segmentation (also known as contouring) delineate structures of interest. Some of the tools in `Segment Editor` mimic a painting interface like photoshop, but work on 3D arrays of voxels rather than on 2D pixels. In addition to the core segmentation tools (such threshold, paint, logical operations etc) provided, **SegmentEditorExtraEffects** extension (already bundled with SlicerMorph) provides additional segmentation tools (such as Mask/Split Volume by segments etc).   
2. `Segmentations:` is the module that allows you to manipulate the segmentations generated by `Segment Editor`. Some of the key functionality is to import/export segmentations into **Label Map** or **3D Model** representation, adjust and edit display properties, copy/move segments across different segmentations, and so forth. 

In addition there are couple supporting modules such as:

3. `Segment Statistics`, which allows you to extract quantitative information (such as volumes, moments of interia, centroid positions, etc) from the segmentations and tabulate them.
4. `Segment Comparison` allows you calculate various similarity indices for two different segmentations (e.g., compare segmentation results from one expert to the other). 
5. `Segment Registration` allows you to linearly and/or deformably register segments from two different datasets using the Elastix registration framework. 
6. `Segment cross-section area` module allows you to calculate, plot and tabulate the cross-sectional area of any segment as a function of slice number. 

If you are new to image segmentation, probably you should read the [official **Image Segmentation** documentation from Slicer.](https://slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html)

Even if you have previous experience with other 3D segmentation programs, it might be good to take a minute to read the Slicer specific functionalities and how different types of data types relate to each other (see figure below).

This file has been truncated. show original

Peto · September 8, 2022, 1:51am

Step 1.
Go to Segmentation Editor.

Select Threshold and adjust the sliders so that the bones are green.

This usually means adjusting the first slider up the scale (from a negative value to a positive value) to exclude soft tissue structures.

Once you are happy select Apply. You have now segmented the data set. Click on the “Show 3D” button to see the model.

Step 2.
Now you can use the Scissors on the 3D model to remove sections.

dav · November 1, 2022, 11:01pm

Yeah is this a bug? I’m in the segment editor. You can see the green volume (Segment_12) I created that I’m trying to cut. I’m only trying to cut the volume Segment_12 itself so I’ve selected . The settings are set below:

snipping_pic

(I also tried with and without the “Editable intensity range” on)

Here’s a video of me cutting it in the 3D view:

gif1_spine

Same happens if I try in the other views. It doesn’t remove the volumes. The only time I see it remove is if the “Editable area” is set to any of the options above the individual segment line. When I tried the “Outside Visible Segments” or others, it works, but it removes the segments selected (the green section (and maybe the other segments not visible)?

What’s going on?

muratmaga · November 1, 2022, 11:27pm

Can you try with the latest stable (5.0.3) and report back?

dav · November 2, 2022, 12:46am

Yes I was using 4.11… It works great with 5.03. Thanks.

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Scissors Not Working

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