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other:inspect3d:tutorials:visualizing_healthy_human_walking [2024/07/17 15:22] – sgrangerother:inspect3d:tutorials:visualizing_healthy_human_walking [2025/01/17 16:41] (current) – wikisysop
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 This tutorial uses publicly available data from the paper [[https://www.nature.com/articles/s41597-022-01817-1|A biomechanics dataset of healthy human walking at various speeds, step lengths and step widths]], which provides an overview of how the data was collected, processed, and stored. Briefly, force plate data and marker-based motion capture data were collected for 10 different participants over 33 walking trials each, with various step lengths, step widths, step frequencies, and speeds. Ground reaction force data were sampled at 1200 Hz and motion capture data were sampled at 120 Hz. This tutorial uses publicly available data from the paper [[https://www.nature.com/articles/s41597-022-01817-1|A biomechanics dataset of healthy human walking at various speeds, step lengths and step widths]], which provides an overview of how the data was collected, processed, and stored. Briefly, force plate data and marker-based motion capture data were collected for 10 different participants over 33 walking trials each, with various step lengths, step widths, step frequencies, and speeds. Ground reaction force data were sampled at 1200 Hz and motion capture data were sampled at 120 Hz.
  
-{{:healthyhumanwalking.jpg}}+{{ :healthyhumanwalking.jpg?600 }} 
 We are interested in the .c3d files that can be downloaded [[https://doi.org/10.6084/m9.figshare.c.5897423.v1|here]]. We are interested in the .c3d files that can be downloaded [[https://doi.org/10.6084/m9.figshare.c.5897423.v1|here]].
  
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 ==== Creating CMZ files in Visual3D ==== ==== Creating CMZ files in Visual3D ====
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-[[File:Tutorial-HHW-V3DPipeline.PNG|{{/images/thumb/6/6c/Tutorial-HHW-V3DPipeline.PNG/600px-Tutorial-HHW-V3DPipeline.PNG?600x294}}]] 
  
 Our first step is to process each participant's .c3d files into a [[Visual3D:Documentation:Definitions:File_Formats:CMZ_Format_|CMZ]] file with the necessary signals and events. Our first step is to process each participant's .c3d files into a [[Visual3D:Documentation:Definitions:File_Formats:CMZ_Format_|CMZ]] file with the necessary signals and events.
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 1. Open Visual3D and click on the **Pipeline** toolbar option. 1. Open Visual3D and click on the **Pipeline** toolbar option.
  
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 The Create_CMOs script loads a static trial and a model template for a set of dynamic trials, modifies force platform parameters in line with Visual3D's recommendations, cleans force assignments, computes gait events, and produces a report for the signals of interest. For this data set we want one CMZ per participant, so the following steps would need to be performed for each Participant separately. The Create_CMOs script loads a static trial and a model template for a set of dynamic trials, modifies force platform parameters in line with Visual3D's recommendations, cleans force assignments, computes gait events, and produces a report for the signals of interest. For this data set we want one CMZ per participant, so the following steps would need to be performed for each Participant separately.
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 +{{:Tutorial-HHW-V3DPipeline.PNG}}
  
 1. To create Participant 1's CMZ file, choose p1_c3dfiles/p1_standing_1.c3d file as the static calibration file. 1. To create Participant 1's CMZ file, choose p1_c3dfiles/p1_standing_1.c3d file as the static calibration file.
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 5. Choose Sample_Report_Template.rgt as the report template. 5. Choose Sample_Report_Template.rgt as the report template.
  
-[[File:Tutorial-HHW-V3DReports.PNG|{{/images/thumb/a/ac/Tutorial-HHW-V3DReports.PNG/1000px-Tutorial-HHW-V3DReports.PNG?1000x651}}]]+{{:Tutorial-HHW-V3DReports.PNG}}
  
 6. Save the results as Participant_1.cmz. 6. Save the results as Participant_1.cmz.
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 ==== Cleaning the data set in Inspect3D ==== ==== Cleaning the data set in Inspect3D ====
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-[[File:Tutorial-HHW-I3DCleanGRFZ.PNG|{{/images/thumb/c/c2/Tutorial-HHW-I3DCleanGRFZ.PNG/400px-Tutorial-HHW-I3DCleanGRFZ.PNG?400x335}}]] 
  
 The processing done in Visual3D allows us to extract signal traces from all of our desired gait sequences from the .c3d files, but not all of these are suitable for further analysis. The number of traces involved makes it impractical to clean this data set in Visual3D, there are more than 3000 traces for Participant 1 alone, but Inspect3D gives us the ability to visualize the ground reaction forces and make inclusion/exclusion decisions for each trace. A detailed explanation of this process can be found in the [[Other:Inspect3D:Tutorials:Clean_your_Data|Clean your data]] tutorial. The processing done in Visual3D allows us to extract signal traces from all of our desired gait sequences from the .c3d files, but not all of these are suitable for further analysis. The number of traces involved makes it impractical to clean this data set in Visual3D, there are more than 3000 traces for Participant 1 alone, but Inspect3D gives us the ability to visualize the ground reaction forces and make inclusion/exclusion decisions for each trace. A detailed explanation of this process can be found in the [[Other:Inspect3D:Tutorials:Clean_your_Data|Clean your data]] tutorial.
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 +{{:Tutorial-HHW-I3DCleanGRFZ.PNG}}
  
 1. Load **Participant_1.cmz** into the library. 1. Load **Participant_1.cmz** into the library.
  
-2. Open the {{:I3DGroups.png}} **Group Definitions** dialog and apply the GRF.q3d query definitions to compute three groups, one for each component of the ground reaction force.+2. Open the {{:I3DGroups.png?20}} **Group Definitions** dialog and apply the GRF.q3d query definitions to compute three groups, one for each component of the ground reaction force.
  
 3. Select the GRF_Z group and **Plot all sequences**. 3. Select the GRF_Z group and **Plot all sequences**.
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 4. In the queried data, iteratively select traces that look anomalous and exclude them. The end result should look like the figure on the right. 4. In the queried data, iteratively select traces that look anomalous and exclude them. The end result should look like the figure on the right.
  
-5. Open the {{:I3DUpdateCMOsWithBadEvents.png}} **Update CMZs** dialog from the toolbar, select **Update Force Assignments...**, and then **Update CMOs**.+5. Open the {{:I3DUpdateCMOsWithBadEvents.png?20}} **Update CMZs** dialog from the toolbar, select **Update Force Assignments...**, and then **Update CMOs**.
  
 6. Plot all sequences for each GRF component in turn, verifying that there are no included traces that should be excluded. If there are any bad traces left, repeat steps 4 and 5 as necessary until you are satisfied with the remaining traces. 6. Plot all sequences for each GRF component in turn, verifying that there are no included traces that should be excluded. If there are any bad traces left, repeat steps 4 and 5 as necessary until you are satisfied with the remaining traces.
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 Now that Participant 1's CMZ file has been cleaned of any unwanted traces, we are ready to perform some preliminary analysis and visualize the data set. Our goal in this section is to reproduce [[https://www.nature.com/articles/s41597-022-01817-1/figures/3|Figure 3]] in the paper. Now that Participant 1's CMZ file has been cleaned of any unwanted traces, we are ready to perform some preliminary analysis and visualize the data set. Our goal in this section is to reproduce [[https://www.nature.com/articles/s41597-022-01817-1/figures/3|Figure 3]] in the paper.
  
-1. Open the {{:I3DShowOptions.png}} **Show Options** dialog, deselect **Auto-scale graphs**, and set both **Graph Rows** and **Graph Columns** to 3. This will create a 3x3 layout of grids in the Queried Data area. Move over to the **Colour Palette** tab and load the Healthy Human Walking L-R colour palette.+1. Open the {{:I3DShowOptions.png?20}} **Show Options** dialog, deselect **Auto-scale graphs**, and set both **Graph Rows** and **Graph Columns** to 3. This will create a 3x3 layout of grids in the Queried Data area. Move over to the **Colour Palette** tab and load the Healthy Human Walking L-R colour palette.
  
-[[File:Tutorial-HHW-I3DOptionsDialog.PNG|{{/images/thumb/5/5a/Tutorial-HHW-I3DOptionsDialog.PNG/600px-Tutorial-HHW-I3DOptionsDialog.PNG?600x405}}]]+{{:Tutorial-HHW-I3DOptionsDialog.PNG}}
  
-2. Open the {{:I3DGroups.png}} **Group Definitions** dialog and apply the HealthyHumanWalking-X.q3d query definitions. This extracts the X-component for all signals in the library without combining signals across the left and right sides of the body.+2. Open the {{:I3DGroups.png?20}} **Group Definitions** dialog and apply the HealthyHumanWalking-X.q3d query definitions. This extracts the X-component for all signals in the library without combining signals across the left and right sides of the body.
  
 3. Make sure that the top left graph (1,1) is active, indicated by the grey border. Select the RAnkleAngle_X and LAnkleAngle_X groups and plot the Group Means. 3. Make sure that the top left graph (1,1) is active, indicated by the grey border. Select the RAnkleAngle_X and LAnkleAngle_X groups and plot the Group Means.
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   * Bottom right (3,3) - RHipPower_X and LHipPower_X   * Bottom right (3,3) - RHipPower_X and LHipPower_X
  
-5. With the group means plotted for each of our signals, all that remains is to assign the appropriate graph and axis titles. To do this, reopen the {{:I3DShowOptions.png}} **Show Options** dialog and move over to the **Plot Styles** tab. For example, for the top left graph (1,1), provide the following input:+5. With the group means plotted for each of our signals, all that remains is to assign the appropriate graph and axis titles. To do this, reopen the {{:I3DShowOptions.png?20}} **Show Options** dialog and move over to the **Plot Styles** tab. For example, for the top left graph (1,1), provide the following input:
  
   * Deselect **Display Group Name as Title**   * Deselect **Display Group Name as Title**
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 6. Repeat Step 5 for the remaining graphs using the titles from Figure 3. 6. Repeat Step 5 for the remaining graphs using the titles from Figure 3.
  
-[[File:Tutorial-HHW-I3DAllPlots.PNG|{{/images/thumb/0/06/Tutorial-HHW-I3DAllPlots.PNG/1000px-Tutorial-HHW-I3DAllPlots.PNG?1000x709}}]]+{{:Tutorial-HHW-I3DAllPlots.PNG}}
  
  
other/inspect3d/tutorials/visualizing_healthy_human_walking.1721229720.txt.gz · Last modified: 2024/07/17 15:22 by sgranger