XManager: Basics: Difference between revisions
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:'''Surface File''' - This file is the polygonal mesh representing the surface of the object. This file is generated in [[Surface3D_Overview|Surface3D]] (or a third-party application). If you use Surface3D to create this file, you do not need to enter the ''File Path'', the ''Units'', or ''Use Mocap Time'' checkbox; Surface3D will create them and automatically add them to the subject. If you use a third-party application to create this file you will need to enter this information manually. | :'''Surface File''' - This file is the polygonal mesh representing the surface of the object. This file is generated in [[Surface3D_Overview|Surface3D]] (or a third-party application). If you use Surface3D to create this file, you do not need to enter the ''File Path'', the ''Units'', or ''Use Mocap Time'' checkbox; Surface3D will create them and automatically add them to the subject. If you use a third-party application to create this file you will need to enter this information manually. | ||
:'''ROI Surface File''' - This file is the Surface File after regions of interest have been defined on it, and it has been transformed into its local (anatomical) reference frame. It is generated by [[Orient3D_Overview|Orient3D]] so you do not need to specify the ''File Path'', ''Units'' or ''Use Mocap Time''. If you export tracked DSX trials to a CMZ file for analysis in Visual3D, the ROI Surface File for each tracked object will be added to the CMZ. Visual3D expects these object surfaces to be defined in meters, so that is the default unit for these files. | :'''ROI Surface File''' - This file is the Surface File after regions of interest have been defined on it, and it has been transformed into its local (anatomical) reference frame. It is generated by [[Orient3D_Overview|Orient3D]] so you do not need to specify the ''File Path'', ''Units'' or ''Use Mocap Time''. If you export tracked DSX trials to a CMZ file for analysis in Visual3D, the ROI Surface File for each tracked object will be added to the CMZ. Visual3D expects these object surfaces to be defined in meters, so that is the default unit for these files. | ||
:'''Inner Surface File''' - This optional file is used only by the [[Orient3D: Image Data Generator|Image Data Generator]] widget in Orient3D to make 3D image data (Image Files) from surface models. This widget is primarily used for generating simulated CT data from surface models created from MRI. If the object has an Inner Surface File when the Image Data Generator is used, voxels between the outer surface and the inner surface will be given the specified cortical density, and voxels inside the inner surface will be given the specified cancellous density. This creates more realistic simulated CT data then using only the Surface File and a constant cortical thickness. The Inner Surface File must be in the same units and reference frame as the Surface File. It should be a closed polygonal surface without holes, and it should not connect to or intersect with the outer surface. | |||
:For more information on importing image and surface files from third-party applications, follow the tutorial [[Surface3D:_How_to_Import_Third_Party_Files|How To: Import Third-Party Image and Surface Files]] | :For more information on importing image and surface files from third-party applications, follow the tutorial [[Surface3D:_How_to_Import_Third_Party_Files|How To: Import Third-Party Image and Surface Files]] | ||
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Revision as of 21:46, 9 July 2021
Language: | English • français • italiano • português • español |
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The purpose of this tutorial is to guide you in the creation of a subject file in DSX Manager.
The instructions for this tutorial are purposely designed to be general so that you can use your own data.
Subject
Create New Subject |
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In order to create a new subject you can either use the Ctrl + N shortcut or can select File in the menu bar and clicking on New Subject. This will open a standard file browser window that will allow you to choose a new file name and save the New Subject file in the location of your choosing. |
Complete New Subject Info |
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Once a new subject has been created it will appear as 0000 in the left hand field. Select the 0000 and the right hand field will be populated with the following fields:
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Sessions
Add Sessions |
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Click the arrow button to the left of the Subject ID number in the left hand field to expand the list. Left click on the Sessions Label so that the Add Sessions option appears. Click on Add Sessions. This will cause an arrow to appear to the left of the Sessions Label. Click on the arrow in order to expand the list. It will expand to show the label newsessions, which can in turn be expanded to show the labels Objects and Configurations. |
Complete Session Info | ||||||
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Once a new session has been created it will appear as newsession in the left hand field. Select the newsession and the right hand field will be populated with the following fields:
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Calibration Devices
Add Calibration Device |
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Complete Calibration Device | ||||||
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Click on the new calibration device in the tree view to display its properties in the panel on the right.
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Grid Devices
Add Grid Device |
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Complete Grid Device | ||||
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Click on the new grid device in the tree view to display its properties in the panel on the right.
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Trackable Objects
Add Trackable Objects |
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Complete Trackable Objects | ||||||||||||
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Click on the new object in the tree view to display its properties in the panel on the right.
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Configurations
Add Configurations |
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Complete Configurations | ||||||||||||||
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Trials
Add Trials |
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Complete Trials | ||||||||
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Second Configuration
Add A Second Configuration |
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Using the instructions above, create a second configuration named "Left Level Walk" and complete it with the following information: General Name - Left Level Walk Setup Name view1 - inline Name view2 - offset Calibration - General Inline - 1796.0 Offset - 1795.0 Calibration - Uniformity Name - intensity Type - Uniformity Time - 3:54 PM View Name - inline Raw File, File Path - iwhite4.cine File Format - CINE Frequency (Hz) - 150.00 View Name - offset Raw File, File Path - owhite4.cine File Format - CINE Frequency (Hz) - 150.00 Calibration - Distortion Name - grid Type - Distortion Time - 3:54 View Name - inline Raw File, File Path - igrid4.cine File Format - CINE Frequency (Hz) - 150.00 View Name - offset Raw File, File Path - ogrid4.cine File Format - CINE Frequency (Hz) - 150.00 Calibration - 3D Name - cube Type - 3D Calibration Time - 3:54 PM Mocap Parameters, C3D File Name - cube4.c3d Tracked Bodies - Checkmark next to cube View Name - inline Raw File, File Path - cube4_Cam_Inline_Cine1.cine File Format - CINE Frequency (Hz) - 150.00 View Name - offset Raw File, File Path - cube4_Cam_Offset_Cine1.cine File Format - CINE Frequency (Hz) - 150.00 Trials - LLW 2 Name - LLW 2 Type - Motion Reference Trial - LeftStand Time - 3:54 PM Mocap Parameters C3D File Name - llw2.c3d Time Offset - 0.00 Generalized Coordinates Name - FlexExt Min - -90 Max - 90 Tracked Bodies - Checkmark next to left_femur and left_tibia View Name - inline Raw File, File Path - llw2_Cam_Inline_Cine1.cine File Format - CINE Frequency (Hz) - 150.00 View Name - offset Raw File, File Path - llw2_Cam_Offset_Cine1.cine File Format - CINE Frequency (Hz) - 150.00 |
Reference Trials |
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General Name - LeftStand Type - Reference Time - 3:55 PM Mocap Parameters If the Mocap Parameters section does not update the fields automatically, navigate to another screen and back to the reference trial.
The files listed above are explained in detail in the motion capture guide. Generalized Coordinates Name - FlexExt Min - -90 Max - 90 Tracked Bodies Place a checkmark next to left_femur and left_tibia. Views Name - inline Raw File, File Path - lstand1_Cam_Inline_Cine1.cine File Format - CINE Frequency (Hz) - 150.00 Name - offset Raw File, File Path - lstand1_Cam_Offset_Cine1.cine File Format - CINE Frequency (Hz) - 150.00 |