Additional Nexus reference PDFs:

Nexus legacy documentation:

This information is for Vicon Nexus 2.10. For up-to-date help, see the latest Nexus documentation.

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The Pipeline Tools pane enables you to create and manage a customized sequence of operations to automate the processing of a trial.

Pipeline processing is optional, but is useful for automating the data processing operations that you use frequently or on a large number of trials.

The Pipeline Tools pane contains the following sections:

  • Available Operations section
    The Available Operations section enables you to select the type of pipeline you want to create and the operations to run. Operations are grouped under the following types:

  • Current Pipeline section
    At the top of the Current Pipeline section, the configuration management controls enable you to create or manage configurations for the settings specified in the Pipeline Tools pane.

    The middle of the Current Pipeline section enables you to manage the pipeline operations and view their status with the playback controls and progress bar.
     
    In the list at the bottom of the Current Pipeline section, you can view the operations included in the currently loaded pipeline.

    For information on using pipelines, see Work with pipelines in the Vicon Nexus User Guide.


    Tip
    Pipeline operations are run in the order they appear in this list. You can drag operations into the desired position in the list. Alternatively, you can run an individual operation by right-clicking on it and clicking Run selected Op.

  • Properties pane
    You can view or change settings for the selected pipeline operation in the Properties pane at the bottom of the Pipeline Tools pane.

Pipeline operations

Pipeline operations are found in the Pipeline Tools pane, in the Available Operations section.

File Import operations

Use File Import operations to automate the import of trial files to Vicon Nexus from third-party software packages.

OperationDescription
Import AVIImport a video .avi file to be saved and associated with the current trial.
Import MPImport subject parameters specified in a .mp file into the active subject.
Import VSKImport a labeling skeleton (.vsk) file.
Import XCPImport a calibration file (.xcp) into the current trial to replace the current calibration.

Core Processing operations

Use Core Processing operations to automate the processing of offline reconstruction, labeling, and kinematic fitting to produce 3D trajectories from raw marker data.

OperationDescription
Combined ProcessingPerforms one or more of: reconstruction, labeling, and subject motions. Running this operation is faster than running each process individually.
Reconstruct3D trajectories are reconstructed from the raw 2D marker data.
LabelControls how 3D trajectories are labeled with subject data
Kinematic FitControls how the labeling skeleton contained in the .vsk is kinematic-fitted to the marker data. In addition to specifying the frames on which to operate, you can adjust settings for:
  • Prior importance: Weighting given to the uncalibrated values from the VST. Range is 0-100, default is 25.
  • Mean pose ratio: Ratio of tracking pose as prior (where 0 = mean pose only; 1 (default) = external (or tracking) prior only.)
Tip
The equivalent settings for Live processing can be found in the Local Vicon System properties, found in the System Resources pane.

Subject Calibration operations

Use Subject Calibration operations to automate the processing of labeling skeleton calibration.

OperationDescription
Set Autolabel PoseSets the pose for Autolabel Static to be the pose at the selected frame.
Autolabel StaticRun on a reconstructed static trial to automatically label the labeling skeleton in a single frame, using information from the .vst file. It matches the shape of the reconstruction to the shape of the subject template for that pose.
The labels are applied to the whole trajectory, not just the chosen frame. It works best when all the markers have been reconstructed and there are no additional markers or clutter in the scene.
This operation does not require a .vsk file.
Scale Subject VSKScales the labeling skeleton to be the same size as a labeled set of reconstructions on a particular frame. The scale factor is calculated assuming that the subject is in the same pose as was used for Autolabel Static (see above).
(Note that this scaling respects any constraints that you may have specified in the template. For example if your template specifies (ie a StaticParameter) that a segment is 100mm long, the segment will not be scaled. Only parameters are considered for scaling.)
Functional Skeleton CalibrationCalibrate the subject's bone lengths, joint locations, and marker locations from a whole trial. Use to calibrate a whole ROM trial.
Functional Skeleton Calibration - Markers-onlyCalibrate the subject's marker locations from a whole trial. This is useful, for example if a marker becomes detached from the subject and you need to re-run the calibration with the replaced marker.
Static Skeleton CalibrationCalibrate the subject's bone lengths, joint locations, and marker locations from a single frame. Use to calibration a static calibration, as in versions of Vicon Nexus earlier than 2.0.
Static Skeleton Calibration - Markers-onlyUses a single frame to update the marker locations for the labeling skeleton. This operation both fits the subject pose (that is, the pose that was defined when the labeling skeleton was created) to the labeled reconstructions and calibrates the marker locations.
Fitting the subject pose allows for the likely situation of your subject standing close to the template pose. Again, this operation respects any constraints specified in the labeling skeleton template and changes only parameters.
This operation is useful, for example if a marker becomes detached from the subject and you need to re-run the calibration with the replaced marker.
Update Skeleton ParametersInitial label booting can be improved by providing more representative data from a movement or ROM trial. This operation enables you to do this by updating the default values of a selected skeleton with movement or ROM trial data contained in the current calibrated labeling skeleton (VSK). The options for this operation are:
  • Update Marker Covariances Marker covariance is used by the labeler to account for skin motion, so the default for this option is Selected.
  • Update Parameters If you have calibrated a skeleton from the Labeling Template Builder, select this check box.
  • Update Joint Mean & Covariance Joint covariance is used in booting the labeling. If you have a very flexible subject, a larger covariance will help, so select this check box.
  • Update Joint Ranges Joint ranges can be enforced to detect infeasible joint angles. If you have a very flexible subject, larger joint ranges are needed, so select this check box.
Calculate Skeleton Joint & Marker StatisticsMeasure the subject's labeling statistics from a whole trial.
Calibrate OCSTFinds the Optimum Common Shape
Calibrate SCoRE/SARACalibrate joint positions using the Symmetrical Center of Rotation Estimation and Symmetrical Axis of Rotation Analysis.

See also Labeling skeleton calibration in detail.

Events & Timebar operations

Use Events & Timebar operations to automate processes relating to events and the timebar.

OperationDescription
Auto Crop TrialFor trials where the subject starts outside the volume, moves into the volume and then exits, Nexus can automatically determine the first and last frame where the subject is fully in the volume.
  • First Frame and Last Frame Set these options to the frames during which the subject enters and leaves the volume.
  • Start % and End % Set these options to the required minimum percentage of markers (ie, the percentage expected from the total number of markers in your subject's labeling skeleton) that must be labeled in each case.
  • Frames Required If necessary, adjust this option to set a minimum number of frames where the Start % criterion must be met. This is helpful if early single frames of data meet the percentage, but the point at which the trial is intended to start (ie, the point at which the percentage is maintained over a number of frames) is later in the trial.
Autocorrelate EventsBased on user-defined parameters, this operation detects the pattern of the tracked marker at the set events and defines these events for the rest of the trial. The available parameters are: marker being tracked; the X, Y, or Z component of the marker; and the position, velocity, or acceleration of the marker. An Advanced property (Correlation Method) enables you to choose the correlation method to automatically place events at the correct location in the time bar, from the choice of Legacy, Least Squares or Pearson Coefficient (see Correlation Method parameters). Autocorrelate Events is normally used after the Detect Events from Forceplate operation.
Detect Events from ForcePlateAutomatically detects gait cycle events and adds them to the time bar throughout the trial using vertical GRFs measured by a force plate connected to the Vicon system. Includes the option to set the force threshold and the label of the markers attached to the front and back of the foot for both sides.
Delete Timebar EventsDelete events from the specified range for the subject(s). Advanced options lets you choose:
  • Range to Delete Whether to delete events that are inside or outside the specified range of frames.
  • Context Whether to delete events from All, Left, Right or General contexts.

To delete custom events:
  1. Click the downward arrow next to the Context field and clear the Macro check box.
  2. In the Context field, enter the name of the custom event.
  3. Run the pipeline.

Correlation Method parameters

  • Legacy (reproduces the behavior from Nexus 2.5 and earlier)
    Maximizes the value of:
  • Least Squares (default)
    Minimizes the value of:
  • Pearson Coefficient
    Maximizes the value of:

    Whereindicates the mean of x over the sample range

Fill Gap & Filter Data operations

Use Fill Gap & Filter Data operations to automate gap-filling and other post-processing.

OperationDescription
Fill Gaps - CyclicFor trials that contain captured data that is cyclic in nature (for example, when a motion on a treadmill or other repetitive motion is captured), fills gaps using patterns from earlier or later gait cycles. You can specify the Gap Length, Units, First and Last Frame, and select the trajectories to fill.
Fill Gaps - KinematicFills all gaps in trajectories that pass through a selected segment, based on calculated kinematics. To run this operation, you must have already obtained the kinematic data on which to base gap-filling, for example, by running the Nexus Legacy Fit Motion pipeline.
Fill Gaps - PatternFills the selected gap using the shape of another trajectory without a gap. Use this tool only if there is a suitable marker with a trajectory similar to the one whose gap you wish to fill.
Fill Gaps - Rigid BodyFills gaps in a trajectory based on other trajectories in a rigid body. This option is the Nexus equivalent of the Replace 4 option, which is available in BodyBuilder. Use this option when a rigid or semi-rigid relationship exists between markers.
Fill Gaps - WoltringRun on labeled dynamic trials to fill in gaps using Woltring quintic spline interpolation. Includes the option to choose maximum gap frame length to fill.
You can configure the following settings in the Properties section:
  • Max Gap Length The maximum length of any gap in a marker trajectory that will be filled with this operation.
    Default: 5
  • First Frame The first of the range of frames in the region of interest of the trial that you wish to analyze. For example, if the capture includes the subject entering the capture volume, you are strongly advised to set the range of frames to exclude this portion of the capture. That will simplify the job of cleaning up your data. You can specify the following settings:
    • First Frame: The first frame of the trial.
    • Selected Start: The frame indicated by the Start Range Frame indicator on the time bar ruler.
    • Current Frame: The frame indicated by the Current Time indicator on the time bar ruler.
    • First Full Frame: First full frame of range to process
      Default: Selected Start
  • Last Frame The last of the range of frames in the region of interest of the trial that you wish to analyze. For example, if the capture includes the subject leaving the capture volume, you are strongly advised to set the range of frames to exclude this portion of the capture. That will simplify the job of cleaning up your data. You can specify the following settings:
    • End Frame: The last frame of the trial.
    • Selected End: The frame indicated by the End Range Frame indicator on the time bar ruler.
    • Current Frame: The frame indicated by the Current Time indicator on the time bar ruler.
    • Last Full Frame: Last full frame of range
      Default: Selected End
Filter Analog Data - ButterworthFilter analog device data using a low-pass digital Butterworth filter. The filter is by default setup as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 300 Hz using a fourth order filter with zero lag (see descriptions below for an explanation of these parameters).
Note: For force plates, only the calculated Force and Moment signals can be filtered. Raw and Center of Pressure signals cannot be filtered.
You can configure the following settings in the Properties section:
  • Cut-Off Frequency The filter cut-off frequency, separating the low-frequency signal from high frequency noise. Data at frequencies above the cut-off frequency are attenuated increasingly as the frequency increases. The attenuation exactly at the cut-off frequency is designed to be "half power," or -3 dB. Note Cut-off frequencies greater than half of the analog device sampling frequency (often called the Nyquist frequency) cannot be used and will result in an error message and no filtering of the data.
  • Filter Order The Second Order filter performs a single pass of the filter in the forwards (increasing time) direction, resulting in a "lag," or "phase shift" in the analog data. The Fourth Order filter performs two passes of the filter, in first the forward, then the reverse direction, resulting in any lag being cancelled out (hence "zero lag"). The parameters of the Fourth Order filter are adjusted, such that the attenuation exactly at the cut-off frequency is maintained at "half power," or -3 dB.
  • Filter Type Can be Low Pass (the default) or High Pass. Select High Pass to filter low-frequency noise from your data.
  • Devices A comma separated list of Devices, Outputs and Components can be typed, or the Macros All or Selected can be used. All will always filter the data from every device currently connected and Selected will filter the data from the devices, device outputs, and output components with names matching those currently selected in the System resource pane and in the 3D Perspective view.
Filter Model Outputs - ButterworthFilter subject model outputs using a low-pass digital Butterworth filter. The filter is by default setup as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 6 Hz using a Fourth Order filter with zero lag.
You can configure the following settings in the Properties section:
  • Cut-Off Frequency Same as Analog Data above.
  • Filter Order Same as Analog Data above.
  • Model Outputs A comma separated list of Model Outputs can be typed, or the Macros All or Selected can be used. All will always filter all Model Outputs calculated for a subject and Selected will filter Model Outputs with names matching those currently selected on the Subjects tab of the Resources pane and in the 3D Perspective view. You can use the * wildcard for all model outputs.
Filter Trajectories - ButterworthFilter trajectories using a low-pass digital Butterworth filter. The filter is by default set up as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 6 Hz using a Fourth Order filter with zero lag.
You can configure the following settings in the Properties section:
  • Cut-Off Frequency Same as Analog Data above.
  • Filter Order Same as Analog Data above.
  • Trajectories A comma separated list of trajectories can be typed, or the Macros All, All Labeled, or Selected can be used. All will always filter every trajectory, including unlabeled ones, All Selected will filter every currently labeled trajectory, and Selected will filter trajectories with names matching those labeled trajectories currently selected on the Subjects tab of the Resources pane and in the 3D Perspective view.
Filter Trajectories - VCM SplineVicon Gait Model event VCM Spline Filter
Filter Trajectories - WoltringFilters the data using the Woltring filter to ensure smooth trajectories for calculating kinetics.
Residual Analysis - ButterworthEnables you to run a residual analysis to determine the optimum cut-off frequencies to apply for a low-pass filter for your devices.
Results are displayed in the Log and saved in the trial History.

Important: This feature is for low pass filtering analysis only, eg, for force plates and plantar pressure plates, and not for high-pass filter devices like EMG.

In the (Advanced) Properties section, in addition to the usual First Frame, Last Frame options (see above), you can configure these settings:
  • Filter Order See Filter Analog Data - Butterworth, above.
  • Devices Select whether to apply the value to All or Selected devices.
  • Steps Specify the number of frequencies to evaluate. Default =50, minimum = 5 and maximum = 200.
  • Rho Squared Specify the minimum rho-squared value to accept. This is used to determine the linear region of the residual-frequency curve via a simple linear regression. Default = 0.95, minimum = 0 and maximum = 1.

After running the pipeline, the results of the analysis for each channel are displayed in the Log, enabling you to decide which channel output to use to apply as the cut-off frequency for the Filter Analog Data - Butterworth pipeline operation.
The filter cut-off is dependent on the type of device to which it is applied, eg, how noisy a force plate is: this may differ for analog vs. digital devices.
You can use the Residual Analysis as part of a batch process.
Results of the Residual Analysis are saved in the trial History.
Delete Optional Subject MarkerRun on a any trial to delete a specified group of subject markers from the marker list that will not be used during the dynamic captures.
Delete Unlabeled TrajectoriesRun on a fully labeled trial to delete any remaining unlabeled trajectories. Includes the option to choose maximum length of unlabeled trajectory to delete.

Data Processing operations

Use Processing operations to automate real-time and offline motion capture data processing.

OperationDescription
Process Static Plug-in Gait ModelRuns the static Plug-In Gait model on the active subject of the current trial.
For more information, see Modeling with Plug-in Gait in the Vicon Nexus User Guide and the Plug-in Gait Reference Guide .
Run Static Oxford Foot ModelRuns the static Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.
Run Static BodyLanguage ModelRuns the static BodyLanguage model
Process Dynamic Plug-in Gait ModelRuns the dynamic Plug-In Gait model on the active subject of the current trial.
For more information, see Modeling with Plug-in Gait in the Vicon Nexus User Guide and the Plug-in Gait Reference Guide .
Run Dynamic Oxford Foot ModelRuns the dynamic Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.
Run Dynamic BodyLanguage ModelRuns the dynamic BodyLanguage model
Process OCSTFinds the coordinate system trace using the Optimum Common Shape Technique.
For more information, see Biomechanics workflow.
Process SCoRE / SARAGenerates joint position model outputs using Symmetrical Center of Rotation Estimation and Symmetrical Axis of Rotation Analysis.
For more information, see Biomechanics workflow.
Calculate Gait Cycle ParametersCalculate Vicon Gait Model temporal parameters and enables calculation of step width and limp index. Includes the option to set the output units.
For more information, see Calculate step width and limp index in the Vicon Nexus User Guide.
Calculate Gait Deviation IndexGenerates a GDI (Gait Deviation Index) score for the subject of the current trial. 1
When you run this operation on a trial, two GDI values (left and right), are output to the log and saved as subject parameters.

To output these values when you run the Export ASCII pipeline operation, select the Export Gait Cycle Parameters option.
Run MatLab OperationExecute MATLAB script.
For information on using MATLAB with Nexus, see Modeling with MATLAB.
Run ProCalc OperationRun ProCalc scripts/models directly from Nexus.
For information on Procalc, see the Vicon Procalc documentation.
Run Python OperationExecute Python script.
For information on using Python with Nexus, see Modeling with Python.
Delete Model OutputsEnables you to delete from the current trial the selected model output(s), all model outputs, or to specify a comma-separated list of model output names.
Tip: You can also access the same options by right-clicking the relevant node in the Subjects Resources tree.
Add Trial to Quick ReportAdds the current C3D to the Quick Reports window.
For more information, see Quick Reports.
CGM2 - CalibrationRun on static trials.
For more information, see Run the static CGM2 model.
CGM2 - Functional CalibrationProvides knee calibration with two options: 2DoF Calibration or SARA. Run between the static/calibration trials (see CGM2 - Calibration, above) and the dynamic/fitting trials (see CGM2 - Fitting, below).
For more information, see Run the knee calibration (CGM 2.6).
CGM2 - FittingRun on dynamic trials.
For more information, see Run the dynamic CGM2 model.
  1. The following research publication provides supporting information on the scientific basis and validation of Vicon's implementation of the calculation of the GDI score:
    SCHWARTZ, M. H., and ROZUMALSKI, A., The gait deviation index: A new comprehensive index of gait pathology, Gait & Posture 28 (2008), p351–357.

File Export operations

Use File Export operations to export of data from Vicon Nexus for use with third-party software packages.

OperationDescription
Export 3D Overlay Video
Export a copy of the reference video .avi file(s) with the 3D Perspective data overlaid onto the video image. You can choose which 3D view option to display and select the codec used to compress the new .avi file.
You can configure the following settings in the Properties section:
  • View Options Set The .options configuration files that have been saved in the Options dialog box (F7). You can select settings for the 3D data to be exported with the .avi file. Select a configuration file from the drop-down list. If you do not specify a file, the current view options are used.
    Default: blank
  • Video Codec The video compression method to use when exporting the .avi file. Select a codec appropriate for the digital camera used to capture the .avi file.
    Default: (None)
  • First Frame and Last Frame Enables you to specify the range of frames to export.
Tip: If you want to export labeled subjects in the Nexus 3D workspace, use instead the Export Workspace to AVI button (available on the View pane toolbar) . For more information, see Export 3D Workspace as AVI in the Vicon Nexus User Guide.
Export ASCII
Export delimited ASCII format to a .csv or .txt file, or another format that you specify by clearing the Macro check box (click the downward arrow at the right of the extension list) and entering the required extension. You can select commas, tabs, or line feeds as the delimiter.
Export C3D
Export the current state of the processed data to a .c3d file. You can then import the data into other software for further processing or report generation. For example, in Vicon Polygon you can visualize the trajectories, kinematic model elements, and kinetics data.
If you manually import the corresponding .vst file into Polygon, it also visualizes the bones.
Export MKRExport an .mkr file. You can choose whether the exported file name is based on the active subject name(s) or active labeling skeleton template name(s). If you choose Active Labeling Skeleton Names, the name of any labeling skeleton template attached to the subject (for example, PlugInGait FullBody Ai) is used as the name of the MKR file. If more than one subject is present with the same model attached, a log message indicates that only one MKR file will be exported.
Export MOTExport files in .mot format for use in OpenSim.
Export MOX
Export Nexus data files in .mox format for MoXie
(http://moxie.smalll.eu/).
Export MPExport the current subject parameters to an .mp file (subject parameter file compatible with legacy software).
Export TRCExport a .trc file.
Export VSKExport a labeling skeleton (.vsk) file
Export XCPExport the current calibration file to an .xcp file in a specified location.
Save Trial - C3D + VSKSave the files associated with the currently open trial.

For more information on how to use the export operations, see Export trial data in the Vicon Nexus User Guide.

System operations

Use System operations to automate oflline camera calibration and applying codecs to video files.

OperationDescription
Process Offline Camera CalibrationRun on a captured trial of a calibration wand wave to calibrate a system (instead of calibrating the system live).
Transcode Video for TrialAutomates transcoding the raw video files associated with the current trial. Enables you to choose the required codec.
Apply Codec to Video
Applies a codec to all AVIs associated with the current trial. You can select which codec to use, whether to keep the original movie file, and whether to remove interlacing.
Important: Reverting to the backup file to re-do the de-interlacing is not supported in Nexus. For more information, see De-interlace AVI files in the Vicon Nexus User Guide.
Reset force plate offsetsResets the force plate offsets. Enables you to specify the range of frames on which to operate, the affected device(s), and the range of frames to use for zeroing the force plate.
Set Delay CompensationSets the delay compensation for selected devices. After the pipeline has been run, the Delay Compensation value is saved and is displayed on the History tab.
Set Camera Calibration OriginSets the camera calibration origin using a calibration object.
Run MonitorEnables you to run a monitor as part of a pipeline. To do this:
  1. Create the monitor you want to use (see Create a monitor in the Vicon Nexus Reference Guide).
  2. Ensure Nexus is in Offline mode.
  3. Add Run Monitor to your pipeline and in its Properties, select the required monitor from the Monitor Configuration list.

Legacy operations

Use Legacy operations to automate the processing of legacy trial data:

OperationDescription
Nexus Legacy LabelerRun on fully reconstructed trials to label the subject as a whole instead of frame-by-frame as in the Core Processor. This operation requires a .vsk file.
Nexus Legacy Fit MotionRun on fully labeled trials to Kinematic Fit the trial as a whole instead of frame-by-frame as in the Core Processor.