xManager Overview

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xManager is the central DSX application that manages the subject information, data files, data collection parameters, and analysis parameters.

The application is launched with an empty workspace.

When a subject is loaded or created, the workspace contains all information related to a subject (including all sessions).

xManager.png

     How To: Create a Subject

1) Select New Subject from the File menu. Browse for a new .dsx file to hold this subject's information.

2) Click on the default ID (0000) in the tree view in the left panel. The right panel will display the subject information.

DSX New Subject.jpg

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.

DSX John Doe.jpg

4) Right-click on Sessions in the tree view and select Add Session from the menu.

DSX Add Session.jpg

5) Click on the default name of "newsession" to display the session information in the right panel.

DSX New Session.jpg

6) Specify the session name and subject metrics.

DSX Session.jpg

7) Click on the Paths checkbox. Paths are shortcuts... Define them before specifying any other files for this subject so that the files will use the shortcuts.

8) Right-click on the empty part of the path list and select Add Path from the menu.

9) Click on the browse button on the right to browse for a folder.

10) Double-click on the path's name and enter an appropriate name.

11) Click on the Relative checkbox if you want this shortcut path to be relative to the folder containing the subject file. This makes it easier to move the subject file and data folder to different places on your hard drive.

12) Repeat steps 8 - 11 for all paths you want to define. You might want one for the X-ray files, one for the CT files, one for the surface model files, and one for the motion capture files. Or you might want one for each trial and/or each X-ray configuration.

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.

14) Click on the Scan Data checkbox to display the scan data information.

15) Right-click on the empty part of the list and select Add Scan Data from the menu.

16) Click on the edit icon on the right to display the scan data dialog. Use it to select the 3D image data. If the data is a set of 2D images, choose the first image in the file browser.

17) Repeat steps 15 - 16 for all 3D image data sets for this session.

18) Click on the arrow next to the session name in the tree to reveal Object and Configurations. Objects are the bones or implants that you will be tracking in the X-ray images. Configurations are the different configurations of the X-ray equipment during data collection.

19) Right-click on Object and select Add Object from the menu.

DSX Add Object.jpg

20) Click on "newobject" in the tree to show the object information in the panel on the right.

21) Fill in the object information. The Mocap Segment Name is the name of the segment in the Visual3D kinematic model that corresponds to this object. You do not need to specify the Weighted Center; this will be calculated automatically when the object's image data is loaded into X4D. Select the type of object from the pull-down menu. Calibration should be used for your calibration object. CalibrateDSX will automatically select an object of this type when you select the calibration trial. You can then digitize the POIs on the object and compute the X-ray configuration. The other types (bone, prosthesis, and device) are for your reference only; the DSX software does not distinguish between these types.

DSX Type Combo.jpg

22) Color is the color of the object's DRR in 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.

DSX Right Thigh.jpg

23) File Data for an object contains:

  1. Image File: the segmented 3D image data (CT) representing the object. If use use Surface3D to segment the object from the image data, you do not need to specify the file now. If you create it using a third-party program such as Mimics or ScanIP, specify the file here.
  2. Surface File: the polygonal file (OBJ) representing the surface of the object, defined in the CT reference frame. You do not need to specify this file now, as it will be generated by Orient3D later.
  3. ROI Surface File: the same surface model of the object, but with regions of interest and defined in the object's local anatomical reference frame. This file will also be generated by Orient3D.

DSX File Data.jpg

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 Orient3D, you do not need to specify it now.

25) Landmarks are landmarks created in the 3D image data by Surface3D or on the surface model by Orient3D.

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.

DSX Points of Interest.jpg

27) Repeat steps 19 - 26 for all objects in this session.

28) Right-click on Configurations and select Add Configuration from the menu.

DSX Add Configuration.jpg

29) Click on "newconfig" in the tree to display the configuration information in the panel on the right.

30) Set the name and date. The Lab to Mocap Transformation will be calculated by CalibrateDSX when you calibrate the system.

31) Click on the arrow next to the configuration name in the tree to reveal Setup, Calibration, and Trials.

32) Click on the arrow next to Setup to reveal Views, then click on the arrow next to Views to reveal the two default X-ray views.

33) Click on each view and set its name. The other parameters are calculated in CalibrateDSX when you compute the 3D X-ray configuration.

DSX View1.jpg

34) 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.

DSX Calibration.jpg

35) 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.

36) For each of the three calibration trials:

  1. Click on it in the tree to display its information in the panel on the right.
  2. Click on the Views checkbox to reveal the views.
  3. Click on the first view in the list. Specify the Raw File containing the uncorrected X-ray data for this view.
  4. Click on the second view in the list. Specify the Raw File containing the uncorrected X-ray data for this view.

37) Right-click on Trials (not Calibration->Trial) in the tree and select Add Trial from the menu.

38) Click on "newtrial" in the tree to display the trial information in the panel on the right.

39) Set the trial name. Choose whether the trial type is reference or motion. Reference trials are usually short, static trials that are used to define a reference pose for multiple motion trials. Motion trials are all other trials (usually ones in which the subject is in motion).

40) If the type is reference and there is motion capture data for this trial, specify the Visual3D model and script files and define the generalized coordinates. See the Motion Capture Data section of the X4D documentation for details on these parameters.

41) If the type is motion, specify the corresponding C3D file, if any. Also choose the reference trial for this trial. For both types of trials, specify the Time Offset, which is the start time of the X-ray data collection minus the start time of the motion capture data collection.

42) Click on Tracked Bodies to reveal the list of objects that are defined in the Objects section of the tree. For each of the objects in the list that can be tracked in this trial, check its box. If you click on the object name, the object's data files will be shown on the right. All of these files will be generated later, when the object is tracked in the X-ray images.

43) Click on the Views checkbox at the bottom of the right panel to reveal the views.

44) Click on the first view in the list. Specify the Raw File containing the X-ray data for this view.

45) Click on the second view in the list. Specify the Raw File containing the X-ray data for this view.

46) Repeat steps 37 - 45 for all trials in this configuration.

47) Repeat steps 28 - 46 for all configurations in this session.

48) Repeat steps 4 - 47 for all sessions in this subject.

xManDataFields.png

     Menus
     File Menu
     xManLoadSubject.png
The Load Subject command loads a subject file.
This command can also be accessed with the Ctrl + O shortcut.
     xManNewSubject.png
Creates a new, empty subject.
This command can also be accessed with the Ctrl + N shortcut.
     xManSaveSubject.png
The Save Subject command saves the currently loaded subject to its existing subject file.
This command can also be accessed with the Ctrl + S shortcut.
     xManSaveSubjectAs.png
The Save Subject As command saves the currently loaded subject to a new subject file.
     xManShowSettings.png
The Show Settings command opens a dialog with the paths to the executable files in the DSX Suite. If the executable file for any of these programs has been moved, the path can be updated using the browse button to the right of the file path. If an executable path is incorrect you will not be able to open the associated program by clicking on the program button at the bottom of the xManager screen. Changes to the paths can be saved by clicking on the Done button at the bottom of the dialog.

DSX Settings.jpg

     xManExit.png
The Exit command exits the program and all unsaved data will be lost. The program can also be closed by using the X in the top right corner of the program window.
     Help Menu
     S3DHelpButton.png
The Help command opens the xManager wiki page in the default browser. The F1 shortcut can also be used.
     S3DAboutButton.png
The About option displays a dialog with information about xManager, including the installed version number. It also contains the Deactivate button, for deactivating your xManager license.
     Applications

The Applications that belong to the DSX Suite can be accessed by clicking on the application buttons that are listed at the bottom of the DSX Manager screen.

Whenever one of the applications is opened from the DSX Manager it will be automatically loaded with the subject file that is open in the DSX Manager.

     CalibrateDSX calibrates the system.

CalibrateDSX calculates the 3D configuration of the x-ray hardware (the pose of the x-ray sources and image planes) from images of the calibration object.

The primary purpose of the CalibrateDSX program is to correct the uniformity, correct any distortions, and resize the x-ray images. CalibrateDSX also allows the following functions:

  • Digitizing the beads in the calibration cube,
  • Calculating the 3D configuration parameters for each view, and
  • Calculating the transformation matrix between the x-ray frame defined by the calibration cube and the motion capture reference frame.

Note: The transform matrix between the x-ray frame and the motion capture reference frame is needed if you want to use motion capture data to seed the pose optimization in X4D.

     Surface3D creates tracking bones and surface models.

Surface3D creates tracking bones (RAW files or stacked TIFFs) and surface models (OBJs) from CT and MRI data. Surface3D (S3D) is used to create triangulated surface models from 3D image data using the Marching Cubes algorithm. Currently, Surface3D can only use CT data. Surface3D can also export CT data that has been cropped to an individual object of interest. This cropping is required to enable the creation of Digitally Reconstructed Radiographs (DRRs) for each individual object. This in turn enables the optimization of the 3D position and orientation for each object individually.

     Orient3D works with the surface models created
Orient3D works with the surface models created with Surface3D or another 3rd party application (e.g., Mimics).
It allows you to define anatomically meaningful reference frames, add landmarks, and define regions of interest, which are used to calculate distance maps.
     Locate3D tracks beads in x-ray trials.

Locate3D tracks beads in x-ray trials.

     X4D tracks bones in x-ray trials, using single-frame or 4D optimization.

X4D tracks bones in x-ray trials, using single-frame or 4D optimization.

     PlanDSX can be used to design x-ray configurations when planning a new study.

PlanDSX can be used to design x-ray configurations when planning a new study.

Subject Data

     Subjects

Subjects

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