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other:dsx:xmanager:tutorials:how_to_create_a_subject [2024/07/16 19:21] – created sgrangerother:dsx:xmanager:tutorials:how_to_create_a_subject [2024/12/20 14:14] (current) – Added section headers as sign posts. wikisysop
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-====== How_to_Create_a_Subject ======+===== How to Create a Subject =====
  
-||+This tutorial walks through the steps of creating a subject in xManager for use in the DSX Suite. 
 + 
 +==== Set File Paths ====
  
 1) Select //New Subject// from the //File// menu. Use the file browser to create a new .dsx file to hold this subject's information. 1) Select //New Subject// from the //File// menu. Use the file browser to create a new .dsx file to hold this subject's information.
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 2) Click on the default //ID// (0000) in the tree view in the left panel. The right panel will display the subject information. 2) Click on the default //ID// (0000) in the tree view in the left panel. The right panel will display the subject information.
  
-{{xManNewSubjectPanel.png}}+{{:xManNewSubjectPanel.png}}
  
 3) Specify the ID, subject name, and study description. //Time Precision// is the number of digits after the decimal point for all time stamps in DSX. This is the precision used to store times in the subject file and to compare times to each other. For //Units//, it is recommended that you leave it at the default of millimeters. 3) Specify the ID, subject name, and study description. //Time Precision// is the number of digits after the decimal point for all time stamps in DSX. This is the precision used to store times in the subject file and to compare times to each other. For //Units//, it is recommended that you leave it at the default of millimeters.
  
-{{xManJohnDoePanel.png}}+{{:xManJohnDoePanel.png}}
  
 4) Right-click on //Sessions// in the tree view and select //Add Session// from the menu. 4) Right-click on //Sessions// in the tree view and select //Add Session// from the menu.
  
-{{xManAddSession.png}}+{{:xManAddSession.png}}
  
 5) Click on the default name of "newsession" to display the session information in the right panel. 5) Click on the default name of "newsession" to display the session information in the right panel.
  
-{{xManNewSessionPanel.png}}+{{:xManNewSessionPanel.png}}
  
 6) Specify the session name and subject metrics. 6) Specify the session name and subject metrics.
  
-{{xManSessionDetails.png}}+{{:xManSessionDetails.png}}
  
 7) Click on the //Paths// checkbox. Paths are shortcuts that are used to make data file locations relative to the path value. When a new file path is added to the subject file, xManager will replace part of the file path with a path shortcut if it can find a matching one. The DSX applications use these path shortcuts to keep the data directory structure organized. If you define path shortcuts for all of the data folders for a subject, and make all of them relative to the subject file, you will be able to move an entire subject data folder to a new location on your computer (or another computer) and not have to change any file paths. 7) Click on the //Paths// checkbox. Paths are shortcuts that are used to make data file locations relative to the path value. When a new file path is added to the subject file, xManager will replace part of the file path with a path shortcut if it can find a matching one. The DSX applications use these path shortcuts to keep the data directory structure organized. If you define path shortcuts for all of the data folders for a subject, and make all of them relative to the subject file, you will be able to move an entire subject data folder to a new location on your computer (or another computer) and not have to change any file paths.
  
-{{xManPaths.png}}+{{:xManPaths.png}}
  
 8) Right-click on the empty part of the path list and select //Add Path// from the menu. 8) Right-click on the empty part of the path list and select //Add Path// from the menu.
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 13) You do not need to specify the //CMO File Name//. You will be prompted for a name in one of the other applications when this file is created. 13) You do not need to specify the //CMO File Name//. You will be prompted for a name in one of the other applications when this file is created.
 +
 +==== Scan Data ====
  
 14) Click on the //Scan Data// checkbox to display the scan data information. 14) Click on the //Scan Data// checkbox to display the scan data information.
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 17) Repeat steps 15 - 16 for all 3D image data sets for this session. 17) Repeat steps 15 - 16 for all 3D image data sets for this session.
 +
 +==== Trackable Objects ====
  
 18) Click on the arrow next to the session name in the tree to reveal //Trackable Objects//, //Calibration Devices//, //Grid Devices//, and //Configurations//. Trackable Objects are the bones or implants that you will be tracking in the X-ray images. Calibration Devices are objects with embedded beads and are used to calculate the 3D configuration of the X-ray equipment. Grid Devices are sheets with a matrix of beads or holes and are used for distortion correction. Configurations are the different configurations of the X-ray equipment during data collection. 18) Click on the arrow next to the session name in the tree to reveal //Trackable Objects//, //Calibration Devices//, //Grid Devices//, and //Configurations//. Trackable Objects are the bones or implants that you will be tracking in the X-ray images. Calibration Devices are objects with embedded beads and are used to calculate the 3D configuration of the X-ray equipment. Grid Devices are sheets with a matrix of beads or holes and are used for distortion correction. Configurations are the different configurations of the X-ray equipment during data collection.
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 19) Right-click on //Trackable Objects// and select //Add Trackable Object// from the menu. 19) Right-click on //Trackable Objects// and select //Add Trackable Object// from the menu.
  
-{{xManAddTrackableObject.png}}+{{:xManAddTrackableObject.png}}
  
 20) Click on "newobject" in the tree to show the object information in the panel on the right. 20) Click on "newobject" in the tree to show the object information in the panel on the right.
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 22) //Color// is the color of the object's DRR in [[Other:DSX:X4D:X4D_Overview|X4D]]. It is a good idea to make each object a unique color that is relatively bright so that it shows up well over the white X-ray images. 22) //Color// is the color of the object's DRR in [[Other:DSX:X4D:X4D_Overview|X4D]]. It is a good idea to make each object a unique color that is relatively bright so that it shows up well over the white X-ray images.
  
-{{xManRightFemur.png}}+{{:xManRightFemur.png}}
  
 23) //File Data// for an object contains: 23) //File Data// for an object contains:
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   - //Inner Surface File//: the polygonal file (OBJ) representing the inner boundary of the cortical bone of an object, defined in the CT reference frame. This file is used when tracking bones derived from MRI data. If you create a Surface file representing the outer boundary of the cortical bone, and an Inner Surface File representing the inner boundary, you can create simulated CT data from them using the [[Other:DSX:Orient3D:Image_Data_Generator|Image Data Generator]] widget in Orient3D.   - //Inner Surface File//: the polygonal file (OBJ) representing the inner boundary of the cortical bone of an object, defined in the CT reference frame. This file is used when tracking bones derived from MRI data. If you create a Surface file representing the outer boundary of the cortical bone, and an Inner Surface File representing the inner boundary, you can create simulated CT data from them using the [[Other:DSX:Orient3D:Image_Data_Generator|Image Data Generator]] widget in Orient3D.
  
-{{xManFileData.png}}+{{:xManFileData.png}}
  
 24) //Reference Frame// is the 4x4 transform from the object's CT frame to its local, anatomical reference frame. If you will be computing this frame in [[Other:DSX:Orient3D:Orient3D_Overview|Orient3D]], you do not need to specify it now. 24) //Reference Frame// is the 4x4 transform from the object's CT frame to its local, anatomical reference frame. If you will be computing this frame in [[Other:DSX:Orient3D:Orient3D_Overview|Orient3D]], you do not need to specify it now.
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 26) //Points of Interest// are points on the object that can be tracked in the X-ray images, such as beads implanted in bones or beads in a calibration object. To add a POI, right-click on the empty part of the POI list and select //Add POI// from the menu. For the calibration object, create a POI for each bead in the object. The //Radius// should be the radius of the physical bead, which is usually specified in millimeters. 26) //Points of Interest// are points on the object that can be tracked in the X-ray images, such as beads implanted in bones or beads in a calibration object. To add a POI, right-click on the empty part of the POI list and select //Add POI// from the menu. For the calibration object, create a POI for each bead in the object. The //Radius// should be the radius of the physical bead, which is usually specified in millimeters.
  
-{{xManPOITable.png}}+{{:xManPOITable.png}}
  
 27) Repeat steps 19 - 26 for all objects in this session. 27) Repeat steps 19 - 26 for all objects in this session.
 +
 +==== Calibration Devices ====
  
 28) Right-click on //Calibration Devices// and select //Add Calibration Device// from the menu. 28) Right-click on //Calibration Devices// and select //Add Calibration Device// from the menu.
  
-{{xManAddCalDevice.png}}+{{:xManAddCalDevice.png}}
  
 29) Click on "newcal" in the tree to show the calibration device information in the panel on the right. 29) Click on "newcal" in the tree to show the calibration device information in the panel on the right.
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 If you want to synchronize your dynamic X-ray images with motion capture data, you need to put at least three motion capture markers on the calibration device and specify their locations and radii. The coordinates of these mocap markers are specified in the X-ray lab reference frame. Once they are tracked by the motion capture system during collection of the X-ray images of the calibration device, the transform from the X-ray lab frame to the motion capture frame can be computed by [[Other:DSX:CalibrateDSX:CalibrateDSX_Overview|CalibrateDSX]]. If you want to synchronize your dynamic X-ray images with motion capture data, you need to put at least three motion capture markers on the calibration device and specify their locations and radii. The coordinates of these mocap markers are specified in the X-ray lab reference frame. Once they are tracked by the motion capture system during collection of the X-ray images of the calibration device, the transform from the X-ray lab frame to the motion capture frame can be computed by [[Other:DSX:CalibrateDSX:CalibrateDSX_Overview|CalibrateDSX]].
  
-{{xManCalDeviceDetails.png}}+{{:xManCalDeviceDetails.png}}
  
 30) Right-click on //Grid Devices// and select //Add Grid Device// from the menu. 30) Right-click on //Grid Devices// and select //Add Grid Device// from the menu.
  
-{{xManAddGridDevice.png}}+{{:xManAddGridDevice.png}}
  
 31) Click on "newgrid" in the tree to show the calibration device information in the panel on the right. 31) Click on "newgrid" in the tree to show the calibration device information in the panel on the right.
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 XY Angle - the angle between the X and Y axes of beads/holes in the grid object. For hex grids, this parameter can be set to 60.0 or 120.0. The default value is 90.0. XY Angle - the angle between the X and Y axes of beads/holes in the grid object. For hex grids, this parameter can be set to 60.0 or 120.0. The default value is 90.0.
 X Angle - the angle between the X axis of grid beads/holes and the X axis of the grid image. If the grid X axis is supposed to be aligned with the image intensifiers, set this parameter to 0.0. If the alignment of the grid X axis is unknown (common with hex grids of holes), set this parameter to a value outside the range -360.0 to 360.0, which tells CalibrateDSX to calculate the alignment. The default value is 999.9. X Angle - the angle between the X axis of grid beads/holes and the X axis of the grid image. If the grid X axis is supposed to be aligned with the image intensifiers, set this parameter to 0.0. If the alignment of the grid X axis is unknown (common with hex grids of holes), set this parameter to a value outside the range -360.0 to 360.0, which tells CalibrateDSX to calculate the alignment. The default value is 999.9.
-{{xManGridDetails.png}}+{{:xManGridDetails.png}}
  
 32) Right-click on //Configurations// and select //Add Configuration// from the menu. 32) Right-click on //Configurations// and select //Add Configuration// from the menu.
  
-{{xManAddConfiguration.png}}+{{:xManAddConfiguration.png}}
  
 33) Click on "newconfig" in the tree to display the configuration information in the panel on the right. 33) Click on "newconfig" in the tree to display the configuration information in the panel on the right.
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 37) Click on each view and set its name. The other parameters are calculated in [[Other:DSX:CalibrateDSX:CalibrateDSX_Overview|CalibrateDSX]] when you compute the 3D X-ray configuration. 37) Click on each view and set its name. The other parameters are calculated in [[Other:DSX:CalibrateDSX:CalibrateDSX_Overview|CalibrateDSX]] when you compute the 3D X-ray configuration.
  
-{{xManViewDetails.png}}+{{:xManViewDetails.png}}
  
 38) Click on //Calibration// in the tree to reveal the source-to-image distances for the two views in the right panel. Enter these distances, in millimeters, as measured on the physical X-ray components (X-ray source to plane containing the grid object). It is important to measure these distance accurately, as the calculation of the 3D configuration is fairly sensitive to their values. 38) Click on //Calibration// in the tree to reveal the source-to-image distances for the two views in the right panel. Enter these distances, in millimeters, as measured on the physical X-ray components (X-ray source to plane containing the grid object). It is important to measure these distance accurately, as the calculation of the 3D configuration is fairly sensitive to their values.
  
-{{xManSourceToImage.png}}+{{:xManSourceToImage.png}}
  
 39) Click on the arrow next to //Calibration// to reveal //Trials//, then click on the arrow next to //Trials// to reveal the three [required] calibration trials. 39) Click on the arrow next to //Calibration// to reveal //Trials//, then click on the arrow next to //Trials// to reveal the three [required] calibration trials.
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 41) For the Distortion trial, select the grid device that you created in steps 30 and 31. 41) For the Distortion trial, select the grid device that you created in steps 30 and 31.
  
-{{xManDistortionGrid.png}}+{{:xManDistortionGrid.png}}
  
 42) Right-click on //Trials// (not //Calibration->Trial//) in the tree and select //Add Trial// from the menu. 42) Right-click on //Trials// (not //Calibration->Trial//) in the tree and select //Add Trial// from the menu.
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 50) Click on the second view in the list. Specify the //Raw File// containing the X-ray data for this view. 50) Click on the second view in the list. Specify the //Raw File// containing the X-ray data for this view.
 +
 +==== Trials, Configurations, and Sbujects ====
 +
 +You have now set up a specific trial for a given configuration. In order to finish creating your subject:
  
 51) Repeat steps 37 - 45 for all trials in this configuration. 51) Repeat steps 37 - 45 for all trials in this configuration.
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 53) Repeat steps 4 - 47 for all sessions in this subject. 53) Repeat steps 4 - 47 for all sessions in this subject.
  
-{{xManCompleteSubject.png}}+{{:xManCompleteSubject.png}}
  
  
  
other/dsx/xmanager/tutorials/how_to_create_a_subject.1721157710.txt.gz · Last modified: 2024/07/16 19:21 by sgranger