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==Module Segment Editor== | ==Module Segment Editor== | ||
| − | + | This is the advanced version of the editor module, in this the tools have been improved and the workflow varies as there are more possibilities in the interaction with the data. (<xr id="fig:ModuleSegmentEditor" />) | |
<figure id="fig:ModuleSegmentEditor"> | <figure id="fig:ModuleSegmentEditor"> | ||
| Línea 82: | Línea 82: | ||
</figure> | </figure> | ||
| − | *Mask volume: | + | *Mask volume: Use the selected segment as a mask. The mask is applied to the default master volume. |
| − | + | The inner and outer filling operation creates a binary label map volume as output, with the inner and outer filling values modifiable. (from the tool description) | |
| − | *Surface cut: Use | + | *Surface cut: Use reference marks to fill in a segment. The surface is generated from the placed points. (from the tool description) |
| − | *Watershed: | + | *Watershed: Grows segments to create a complete segmentation. The location, size and shape of the initial segments and the content of the master volume are taken into account. The final segment limits will be set where the master volume brightness changes sharply. (from the tool description) |
| − | == | + | ==Documentation in Slicer.org== |
[[http://slicer.readthedocs.io/en/latest/user_guide/module_segmenteditor.html Segment Editor]] | [[http://slicer.readthedocs.io/en/latest/user_guide/module_segmenteditor.html Segment Editor]] | ||
| − | == | + | == Workflow == |
Before the segmentation | Before the segmentation | ||
| − | * | + | *With the '''Crop Volume''' module check that the resolution in the three dimensions is the same |
| − | * | + | *In the same module, adjust the ROI to the area to be worked on, in order to reduce the processing load. |
| − | + | Procedure | |
| − | * | + | *Create a new segmentation for each anatomical structure |
| − | * | + | *Delimit it roughly with the tool '''Paint'''. |
| − | * | + | *Repeat the previous two steps with each of the segmentations to be created |
| − | * | + | *Apply the '''Grow from seeds''' effect to automatically generate the segmentations |
| − | + | Reffination | |
| − | * | + | *Using the effects of the second row of tools, adjust the automatically generated segmentations to match the desired anatomical reality |
| + | |||
| + | === Examples === | ||
| + | The video examples serve to show you how the editor's tools work, in a dynamic and convenient way. | ||
| + | ======Language subtitles======= | ||
| + | The videos are presented without audio, with the texts in English, French and Spanish subtitles. To change the language of the displayed subtitles, follow the steps below: | ||
| + | |||
| + | '''1.''' Click on ''settings'' on the lower bar on the video window | ||
| + | [[File:Sub1.png|center|frame]] | ||
| + | |||
| + | '''2.''' Click on ''Subtitles/CC'' | ||
| + | [[File:Sub2.png|center|frame]] | ||
| + | |||
| + | '''3.''' Choose the desired language | ||
| + | [[File:Sub3.png|center|frame]] | ||
| + | |||
| + | ===Bone segmentation=== | ||
| + | Introduction of the tools ''Scissors'', ''Threshold'', ''Logical operators'' and ''Islands'' on a segmentation example of foot bones. | ||
| + | <youtube>https://youtu.be/kZ5-krQcRNQ?cc_load_policy=1&hl=fr</youtube> | ||
| + | |||
| + | <hr> | ||
| + | [[Clínicos 3D Slicer/en| MENU]] | ||
Revisión actual del 12:43 3 sep 2018
Module Segment Editor
This is the advanced version of the editor module, in this the tools have been improved and the workflow varies as there are more possibilities in the interaction with the data. (Figure 1)
Figure 1: Module Segment Editor
Interface
The module now allows you to work with different sets of segmentations, depending on the volume you are interacting with, as you can see in the first two drop-down menus of the interface.
The segmentations are generated individually, by means of the button bar that appears next to these menus (Figure 2):
Figure 2: Segments bar
The functions of these buttons are quite intuitive:
- Add: creates a new segmentation
- Remove: removes the selected segmentation
- 3D show: shows active 3D segmentations
- Segmentations: leads to the module of that name
Effects
Figure 3: Effects
The first two rows of icons correspond to the Segment Editor module itself, but the third is the SegmentEditorExtraEffects' extension, which is recommended to be installed, as it complements this module.
first fow
Figure 4: Effects row1
- None: returns the pointer to its default behavior
- Paint: Paint (select) areas of the image
- Draw: draw contours for drawing
- Erase: erases the zones marked with the two previous tools
- Level tracing: traces areas of similar intensity
- Grow from seeds: create segmentations from areas marked with the paint tool
- Fill between slices: segmentation between different sections of the volume
- Threshold: threshold. Selects areas of related intensity throughout the image.
second row
Figure 5: Effects row2
- Margin: Enlarges or contracts the selection in a fixed increment
- Smoothing: smoothes the surface of the selection, eliminating bumps and holes. It has several application parameters:
- Medium: eliminates small details while preserving as much contour as possible.
- Opening: eliminates packages smaller than the specified size.
- Closing: fills holes smaller than the specified size.
- Gaussian: softens all the contours, at the cost of contracting the segment.
- Joint smoothing: applied to multiple segments simultaneously, to smooth them out and eliminate gaps between them.
- Scissors: cuts (removes) parts of the selection
- Islands: manipulates the independent surfaces within the segmentation. Its settings are listed below, and their effect will vary depending on the mask used: everywhere (everywhere), inside all segments (affects only the segmentations), inside all visible segments (affects only the visible segmentations), outside all segments (affects only what is not part of the segmentation) and outside all visible segments (affects only what is not part of the visible segmentation).
- Keep largest island: retains the largest island
- Remove small islands: removes all islands smaller than the specified size
- Split islands into segments: separates the islands into segments
- Keep selected island: keeps the selected island
- Remove selected island: removes the selected island
- Add selected island: adds the selected island to the segmentation you are working on
- Logical operators: operations with logical operators between segmentations
- Copy: replaces the selected segment with the modifier
- Add: adds the modifier segment to the selected one
- Substract: substracts the selected segment by the modifier
- Intersect: intersects the selected segment with the modifier
- Invert: inverts the selected segment
- Clear: Deletes the selected segment
- Fill in the selected segment
- Fast marching: Expands the selected segment to regions with similar intensity.
- Flood filling: filling of area byflooding through the voxels with similar intensity
third row: extra effects
Figure 6: Effects row3: extra effects
- Mask volume: Use the selected segment as a mask. The mask is applied to the default master volume.
The inner and outer filling operation creates a binary label map volume as output, with the inner and outer filling values modifiable. (from the tool description)
- Surface cut: Use reference marks to fill in a segment. The surface is generated from the placed points. (from the tool description)
- Watershed: Grows segments to create a complete segmentation. The location, size and shape of the initial segments and the content of the master volume are taken into account. The final segment limits will be set where the master volume brightness changes sharply. (from the tool description)
Documentation in Slicer.org
Workflow
Before the segmentation
- With the Crop Volume module check that the resolution in the three dimensions is the same
- In the same module, adjust the ROI to the area to be worked on, in order to reduce the processing load.
Procedure
- Create a new segmentation for each anatomical structure
- Delimit it roughly with the tool Paint.
- Repeat the previous two steps with each of the segmentations to be created
- Apply the Grow from seeds effect to automatically generate the segmentations
Reffination
- Using the effects of the second row of tools, adjust the automatically generated segmentations to match the desired anatomical reality
Examples
The video examples serve to show you how the editor's tools work, in a dynamic and convenient way.
Language subtitles=
The videos are presented without audio, with the texts in English, French and Spanish subtitles. To change the language of the displayed subtitles, follow the steps below:
1. Click on settings on the lower bar on the video window
2. Click on Subtitles/CC
3. Choose the desired language
Bone segmentation
Introduction of the tools Scissors, Threshold, Logical operators and Islands on a segmentation example of foot bones.
