Surface3D Overview: Difference between revisions
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'''Add Object Label''' (Ctrl + A): adds a segmentation label to the Segmentation widget. | |||
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'''Remove Object Label''' (Ctrl + R): deletes the currently selected segmentation label. | |||
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'''Undo''' (Ctrl + Z): undoes the last manual edit to the segmentation label. | |||
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'''Redo''' (Ctrl + Y): redoes the last undone manual edit to the segmentation label. | |||
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'''Select Thresholding Seed''': allows the user to pick a point(pixel) in any of the 2d render windows, which will then be used as a seed for 3d thresholding using the threshold values set in the Histogram widget. | |||
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'''Fill 3D Holes''' (Ctrl + H): first opens a dialog with some descriptive text and the opportunity to change the value of the ''3D Hole Threshold'' parameter (default: 2000). When the user decides to go ahead, the command automatically fills all 3D holes in the current segmentation. The algorithm finds each unlabelled voxel next to a labelled voxel and uses a flood-fill algorithm to find all unlabelled voxels that are connected to it. If the size of this region is less than the value of the ''3D Hole Threshold'' parameter, then the region is labelled with the current label. | |||
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'''Fill Gaps''': Still under development. | |||
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:Still under development. | |||
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'''Erode Label''': automatically erodes the segmentation. The basic effect is to erode away the boundaries of regions of the currently selected label. Thus areas of label pixels shrink in size, and holes within those areas become larger. | |||
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'''Dilate Label''': automatically dilates the segmentation. The basic effect is to gradually enlarge the boundaries of regions of the currently selected label. Thus areas of label pixels grow in size, and holes within those areas become smaller. | |||
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'''Unlabel Disconnected Regions''': unlabels all voxels that are not connected to the selected voxel. It is useful for unlabelling large sections of the image data after you have labelled the bone of interest. For example, when segmenting a vertebra from spine images, the appropriate threshold settings often label all of the vertebrae because of their close proximity. Rather than manually erase the label from all of these unwanted voxels, you can use this command. Start by completely labelling the bone of interest. Then erase the label from all unwanted voxels bordering this bone, so that the bone is not connected to any other labelled regions. Then choose this command and select any voxel in the bone of interest. | |||
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'''Manual Hole Filling''': fills a 2D hole in the segmentation, based on where you left-click on one of the 2D images. Selecting this command puts you in "hole-filling mode," so you can left-click on a series of holes in the 2D slices to fill them in. Press Esc to exit this mode. Alternatively, you can press and hold Ctrl + M and then left-click on holes to fill them. | |||
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'''Erase Object Labels''': erases a circular region of the segmentation in one 2D image slice, centered on the voxel on which you left-click. The radius of the circle, in voxels, is specified by the ''Paintbrush Radius'' parameter. Selecting this command puts you in "erase" mode, so you can left-click on a series of voxels to erase a circle of labels. Press Esc to exit this mode. Alternatively, you can press and hold Ctrl + E and then left-click on voxels. | |||
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'''Paint Object Labels''': paints the current label onto a circular region in one 2D image slice, centered on the voxel on which you left-click. The radius of the circle, in voxels, is specified by the ''Paintbrush Radius'' parameter. Selecting this command puts you in "paint" mode, so you can left-click on a series of voxels to paint a circle of labels. Press Esc to exit this mode. Alternatively, you can press and hold Ctrl + P and then left-click on voxels. | |||
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Revision as of 15:50, 18 June 2020
Language: | English • français • italiano • português • español |
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Surface3D segments objects (bones, implants, etc.) from CT data for use in model-based tracking, and it creates surface models of these objects for subsequent kinematic analysis of the tracking results. After segmenting an object from the CT data, the CT data can be cropped and masked, and then saved to a RAW or TIFF file. These cropped image files with just one object in them, are used by X4D to generate DRRs for model-based tracking. It can also generate a polygonal surface model from the currently segmented object using a marching cubes algorithm, and save it to an OBJ file. The surface models are used by Orient3D to define anatomical references and regions of interest (for distance map calculations), and by Visual3D for kinematic analysis. Surface3D also allows you to identify landmarks (e.g., ligament attachments) and points of interest (e.g., implanted beads) in the image data.
Tutorials
How To: Segment Image Data and Create Surface Models
Menus
File Menu |
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View Menu |
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Segmentation Menu |
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Model Menu | ||||||||
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Options Menu | ||||||||
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Help Menu | ||||
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Widgets
Object Configuration | ||||||
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The Object Configuration widget is available only if a subject file is currently loaded in Surface3D.
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Histogram of Image |
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The histogram of the image shows the range of voxel intensities in the currently loaded image data. If a label is selected in the Segmentation widget, the upper and lower thresholds of the label are represented in the histogram as red and green vertical lines, respectively. You can left-click and drag these lines to change the respective threshold values. |
Points of Interest | ||||||
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Landmarks | ||||||
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Segmentation |
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The Segmentation widget provides access to the labels that you use to identify and segment objects (bones, implants, etc.) in the image data. The labels are contained in a table with their name, color, and upper and lower threshold values. For most applications, it is recommended that you segment one object at a time, as described in How To: Segment Image Data and Create Surface Models. When you are finished with the first object, remove the label and create a new one for the next object. To create a label, use the command Segmentation -> Add Object Label. To remove a label, use the command Segmentation -> Remove Object Label. To change the name of a label, double-click on the name and type in a new one. To change its color, double-click on the color cell in the table and select a new color from the dialog. The upper and lower threshold values can be changed by dragging the vertical lines in the Histogram of Image widget, or by double-clicking on the cells in the table and typing in new values. |
Image Data Windows
2D Views |
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The three 2D views show cross sections of the image data along the X, Y, and Z axes. The upper-left view, with the red border around the image data, shows a slice perpendicular to the X axis. The lower-right view (green) shows a slice perpendicular to the Y axis, and the upper-right view (blue) shows a Z slice. When the mouse cursor hovers over a 2D view, its border turns yellow indicating the window has become active. The following interaction is possible in an active 2D view:
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3D View |
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The 3D view in the lower-right shows the image slices from the 2D views as well as the current object's surface model, if one exists. It also shows the reference frame of the image data, with its origin in the lower-left corner of the first image slice in the data file. When the mouse cursor hovers over the 3D view, its border turns yellow indicating the window has become active. The following interaction is possible in an active 3D view:
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