Orient3D Overview: Difference between revisions
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Regions of interest (ROIs) are portions of an object's surface model that have been labelled as belonging to a particular group. They are used to calculate distance maps for articulating bones by finding the shortest distance from each point in one ROI to the corresponding ROI on a neighboring bone. For example, on the distal femur it is common to define an ROI on the lateral condyle and another one on the medial condyle. On the proximal tibia, an ROI would cover the medial half of the plateau, and a second ROI would cover the lateral half. After both bones have been tracked for a motion trial, distance maps between the medial femur and medial tibia ROIs could be calculated, and the same for the lateral side. In Visual3D these maps can be displayed as color tables on the articulating bones, and used to graph shortest bone-to-bone distances during the trial. Before defining ROIs on an object, it is important to define the LCS first. When ROIs are created, they are aligned with the LCS so that it is easier to interpret distance calculations, and to ensure that all ROIs on an object align with each other. Like the LCS algorithms, the ROIs are implemented in a dll plugin framework, allowing you to integrate your own ROI types. <!--There are currently three types of ROIs:--> | Regions of interest (ROIs) are portions of an object's surface model that have been labelled as belonging to a particular group. They are used to calculate distance maps for articulating bones by finding the shortest distance from each point in one ROI to the corresponding ROI on a neighboring bone. For example, on the distal femur it is common to define an ROI on the lateral condyle and another one on the medial condyle. On the proximal tibia, an ROI would cover the medial half of the plateau, and a second ROI would cover the lateral half. After both bones have been tracked for a motion trial, distance maps between the medial femur and medial tibia ROIs could be calculated, and the same for the lateral side. In Visual3D these maps can be displayed as color tables on the articulating bones, and used to graph shortest bone-to-bone distances during the trial. Before defining ROIs on an object, it is important to define the LCS first. When ROIs are created, they are aligned with the LCS so that it is easier to interpret distance calculations, and to ensure that all ROIs on an object align with each other. Like the LCS algorithms, the ROIs are implemented in a dll plugin framework, allowing you to integrate your own ROI types. <!--There are currently three types of ROIs:--> | ||
{| class="mw-collapsible mw-collapsed wikitable" width=" | {| class="mw-collapsible mw-collapsed wikitable" width="100%" | ||
! style="text-align:left;" | Currently implemented types | ! style="text-align:left;" | Currently implemented ROI types | ||
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{| class=" | {| class="wikitable" width="70%" | ||
! style="text-align:left;" | | ! style="text-align:left;" | Commands | ||
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<ul> | |||
<li> | |||
'''Add''': creates a new ROI and adds it to the table. | |||
</li> | |||
<li> | |||
'''Remove''': deletes the selected ROI, even if it has been placed (but not projected) on the surface model. However, if the ROI has already been projected, it does not remove it from the model. | |||
</li> | |||
<li> | |||
'''Place''': displays the ROI floating above the surface model, based on the landmarks. You can then check and modify its positioning before actually projecting it onto the model. To assist with the positioning of the ROI, a yellow wire frame search box is displayed as well. The ROI is projected onto the portion of the surface model that is within this search box. The size of the search box can be adjusted using the parameters in the Parameters section. | |||
</li> | |||
<li> | |||
'''Adjust''': enters and exits manual ROI adjustment mode. In this mode the placed ROI can be moved manually using the mouse buttons. The following interactions are defined: | |||
<ol> | <ol> | ||
<li> | <li> | ||
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Note that the yellow search box adjusts itself with the ROI. | Note that the yellow search box adjusts itself with the ROI. | ||
Pressing the <i>Adjust</i> button a second time exists adjustment mode. | Pressing the <i>Adjust</i> button a second time exists adjustment mode. | ||
</li> | |||
<li> | |||
'''Project''': projects the placed ROI onto the surface model. Each ROI subregion is projected along its normal to determine the polygons of the surface that it intersects. These polygons are labelled with that subregion's label. | |||
</li> | |||
<li> | |||
'''Clear Surface''': clears all of the ROI labels from the surface model. | |||
</li> | |||
</ul> | |||
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{| class=" | {| class="wikitable" width="70%" | ||
! style="text-align:left;" | | ! style="text-align:left;" | Parameters | ||
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The < | |||
<ul> | |||
<li> | |||
'''ROI Offset Factor''': the amount to offset the ROI surface along the principal axis, specified as a percentage (0.0 to 1.0) of the maximum dimension of the object. The default value is 0.03. The principal axis depends on the type of ROI, but is roughly equal to the direction of projection. | |||
</li> | |||
<li> | |||
'''Principal ROI Expand''': the scale factor for the search box in the principal direction of the ROI. The principal axis depends on the type of ROI, but is roughly equal to the direction of projection. | |||
</li> | |||
<li> | |||
'''Secondary ROI Expand''': the scale factor for the search box along the width of the ROI. | |||
</li> | |||
<li> | |||
'''Tertiary ROI Expand''': the scale factor for the search box along the length of the ROI. | |||
</li> | |||
</ul> | |||
|} | |} | ||
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Revision as of 20:26, 25 June 2020
Language: | English • français • italiano • português • español |
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Orient3D prepares surface models created by Surface3D (or third-party software such as Mimics and ScanIP) for use in kinematic analyses after they have been tracked in X4D or Locate3D. With it you can define a local coordinate system (LCS) for each object, landmarks, such as ligament attachment sites, and regions of interest (ROIs), which are used in the calculation of distance maps. The local coordinate system of an object is usually, but not necessarily, its “anatomical” reference frame. When a local coordinate system is defined for an object, it is stored in the subject file as a transform from the frame of the object’s segmented image data to the local coordinate system. To analyze tracking results from X4D in Visual3D, the surface model, landmarks, and regions of interest must be saved in the local coordinate system. Even if you are not exporting your data for kinematic analysis in Visual3D, it is still recommended to define the anatomical coordinate system in Orient3D. X4D's tracking results are output using this coordinate system, and it is easier to manipulate the bone in X4D when an anatomical coordinate system is defined.
Tutorials
How To: Define the LCS of an Object
How To: Define Regions of Interest on an Object
Menus
File Menu |
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LCS Menu |
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Surface Menu |
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View Menu |
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Options Menu |
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Help Menu |
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Widgets
Object Configuration |
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Landmarks |
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Landmarks are 3D locations on a surface model, such as ligament attachment points, that you digitize for later use in other applications. Their coordinates are expressed in the reference frame of the object’s segmented image data (not the “local coordinate system”), and are stored in the subject file.
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Local Coordinate System (LCS) | ||||
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This widget lets you create a local coordinate system (LCS) for each object in your data set. Before tracking an object in X4D or Locate3D, you should define an LCS for it because the tracking output for each X-ray frame is the transform from the X-ray lab frame to the object's LCS. The LCS is stored in the subject file, and is expressed as the transform from the object's segmented image frame to its local coordinate system (as if you were traveling from the segmented frame to the LCS). There are three methods of defining an LCS, as described in How To: Define the LCS of an Object.
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Regions of Interest (ROIs) | ||||||||||||
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Regions of interest (ROIs) are portions of an object's surface model that have been labelled as belonging to a particular group. They are used to calculate distance maps for articulating bones by finding the shortest distance from each point in one ROI to the corresponding ROI on a neighboring bone. For example, on the distal femur it is common to define an ROI on the lateral condyle and another one on the medial condyle. On the proximal tibia, an ROI would cover the medial half of the plateau, and a second ROI would cover the lateral half. After both bones have been tracked for a motion trial, distance maps between the medial femur and medial tibia ROIs could be calculated, and the same for the lateral side. In Visual3D these maps can be displayed as color tables on the articulating bones, and used to graph shortest bone-to-bone distances during the trial. Before defining ROIs on an object, it is important to define the LCS first. When ROIs are created, they are aligned with the LCS so that it is easier to interpret distance calculations, and to ensure that all ROIs on an object align with each other. Like the LCS algorithms, the ROIs are implemented in a dll plugin framework, allowing you to integrate your own ROI types.
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Image/Surface Match | ||||||||||||||
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This widget lets you check if an object's surface model is in the same reference frame as its image data. This is important in X4D so that the surface models are aligned with the DRRs. It works by creating an image surface from the image data, and displaying it in the 3D view with the object's surface model. If they are not aligned, you can use the widget controls to scale, rotate, and translate the image surface so that it aligns with the surface model. Then you can apply the inverse of this transformation to the surface model, so that it aligns with the initial pose of the image surface.
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Image Data Generator | ||||||||
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This widget creates 3D image data from surface models of objects. X4D tracks objects in xray images by generating DRRs from 3D image data (usually CT) of the objects. In some cases CT data is not appropriate for a particular subject and only surface models are available. These surface models could be CAD files of metal implants, or surfaces made from MRI or some other imaging modality that does not represent bone density. This widget creates simulated CT data from the surface models so that the objects can be tracked in X4D. For implants you would typically start with a CAD model of the device, and create a solid object within the image data. For bones, it is recommended that you obtain an outer surface (the outer boundary of the cortical bone), and an inner surface (the inner boundary of the cortical bone), to create more realistic image data. If an inner surface is not available, you can specify the cortical thickness in order to create a shell of constant depth.
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3D View |
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The 3D View shows the surface model of the currently loaded object. It can also display the global and local coordinate systems. You can change the view camera using these commands:
R: Resets the view camera such that the surface model is centered in the window.
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Settings |
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