Pipeline tools

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:
- File Import operations For automating the import of trial files into Vicon Nexus from third-party software packages.
- Core Processing operations For automating reconstruction, labeling, and kinematic fitting to produce 3D trajectories from raw marker data.
- Subject Calibration operations For automating the processing of system and subject calibration.
- Events & Timebar operations For automating operations involving events and/or normally performed using the time bar.
- Fill Gap & Filter Data operations For automating the post-processing of data, such as gap-filling.
- Data Processing operations For automating the production of model outputs (forces and moments, joint angles, etc).
- File Export operations For automating the export of trial files from Nexus to third-party software packages.
- System operations For automating offline camera calibration and applying a codec to video.
- Legacy operations For automating the processing of legacy trial data.

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.

Operation	Description
Import Video	Import a video .mp4 or .avi file to be saved and associated with the current trial.
Import MP	Import subject parameters specified in a .mp file into the active subject.
Import VSK	Import a labeling skeleton (.vsk) file.
Import XCP	Import a calibration file (.xcp) into the current trial to replace the current calibration.
Add Theia Data	Normally run after running Theia processing on Nexus video trials, either by using the Theia pipeline operation or the Theia Batch Interface. Combines rotation data from Theia with a Nexus trial. See also Run Theia processing on video files in the Vicon Nexus User Guide.

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.

Operation	Description
Combined Processing	Performs one or more of: reconstruction, labeling, and subject motions. Running this operation is faster than running each process individually.
Reconstruct	3D trajectories are reconstructed from the raw 2D marker data.
Label	Controls how 3D trajectories are labeled with subject data
Kinematic Fit	Controls 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.

Operation	Description
Set Autolabel Pose	Sets the pose for Autolabel Static to be the pose at the selected frame.
Autolabel Static	Run 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 VSK	Scales 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 Calibration	Calibrate 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-only	Calibrate 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 Calibration	Calibrate 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-only	Uses 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 Parameters	Initial 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 Statistics	Measure the subject's labeling statistics from a whole trial.
Calibrate OCST	Finds the Optimum Common Shape
Calibrate SCoRE/SARA	Calibrate joint positions using the Symmetrical Center of Rotation Estimation and Symmetrical Axis of Rotation Analysis.

Events & Timebar operations

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

Operation	Description
Auto Crop Trial	For 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 Events	Based 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 ForcePlate	Automatically 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 Events	Delete 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: Click the downward arrow next to the Context field and clear the Macro check box. In the Context field, enter the name of the custom event. 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:
Where indicates 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.

Operation	Description
Fill Gaps - Cyclic	For 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 - Kinematic	Fills 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 - Pattern	Fills 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 Body	Fills 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 - Woltring	Run on labeled dynamic trials to fill in gaps using Woltring quintic spline interpolation. Includes the option to choose maximum gap frame length to fill. For more information on Woltring filtration, see the FAQ What are the details of the Woltring filter? 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 - Butterworth	Filter 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 You can enter a comma-separated list of Devices, Outputs and Components, or use the macros All, Selected, Force Plates or Other Devices. All filters the data from every device currently connected. Selected filters the data from the devices, device outputs, and output components with names matching those currently selected in the System Resources pane and in the 3D Perspective view. Force Plates applies the filter to force plates that are connected to your system. Other Devices applies the filter to all other devices (except force plates) that are connected to your system.
Filter Model Outputs - Butterworth	Filter 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 - Butterworth	Filter 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 Spline	Vicon Gait Model event VCM Spline Filter
Filter Trajectories - Woltring	Filters the data using the Woltring filter to ensure smooth trajectories for calculating kinetics.
Residual Analysis - Butterworth	Enables 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 Marker	Run 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 Trajectories	Run 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.

Operation	Description
Process Static Plug-in Gait Model	Runs 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 Model	Runs the static Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.
Run Static BodyLanguage Model	Runs the static BodyLanguage model
Process Dynamic Plug-in Gait Model	Runs 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 Model	Runs the dynamic Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.
Run Dynamic BodyLanguage Model	Runs the dynamic BodyLanguage model
Process OCST	Finds the coordinate system trace using the Optimum Common Shape Technique. For more information, see Biomechanics workflow.
Process SCoRE / SARA	Generates 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 Parameters	Calculate 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 Index	Generates 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 Operation	Execute MATLAB script. For information on using MATLAB with Nexus, see Modeling with MATLAB.
Run ProCalc Operation	Run ProCalc scripts/models directly from Nexus. For information on Procalc, see the Vicon Procalc documentation.
Run Python Operation	Execute Python script. This operation uses the path to the Python script from the Python tab (Communications pane) as its default location, but you can change it on a per-operation basis if required. For information on using Python with Nexus, see Modeling with Python.
Run External Application	Run an external executable program. For more information, see Run an executable from a Nexus pipeline operation.
Run Theia ProCalc Scheme	Generate ProCalc joint angles from Nexus trial data that contains Theia rotations. Run this operation on the data after you have run the Add Theia Data pipeline operation. See also Run Theia processing on video files in the Vicon Nexus User Guide.
Delete Model Outputs	Enables 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 Report	Adds the current C3D to the Quick Reports window. For more information, see Quick Reports.
Theia	Runs Theia processing on one or more Nexus video trials. Normally run before the Add Theia Data operation. See also Run Theia processing on video files in the Vicon Nexus User Guide.
CGM2 - Calibration	Run on static trials. For more information, see Run the static CGM2 model.
CGM2 - Functional Calibration	Provides 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 - Fitting	Run on dynamic trials. For more information, see Run the dynamic CGM2 model.

For supporting information on the scientific basis and validation of Vicon's implementation of the calculation of the GDI score, see:
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.

Operation	Description
Export 3D Overlay Video	Export a copy of the reference video .mp4 or .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 video 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 .mp4 or .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 Cameras Choose which video cameras from which to export overlay video: either Selected Video Cameras or All Video Cameras. File Output The file type (.mp4 or .avi) and video compression method (h.264 or Uncompressed) to use when exporting the video file. Default: h.264 MP4 h.264 Compression If you selected any File Output option except Uncompressed, this sets the compression option. Choose between options ranging from Best Quality / Largest file (if the quality of the output is the priority) to Lowest Quality / Smallest File (if it is important to keep the file size as small as possible). Default: Best Quality / Largest file 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 Video button (available on the View pane toolbar) . For more information, see Export Workspace to video 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 MKR	Export 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 MOT	Export files in .mot format for use in OpenSim.
Export MOX	Export Nexus data files in .mox format for MoXie (http://moxie.smalll.eu/).
Export MP	Export the current subject parameters to an .mp file (subject parameter file compatible with legacy software).
Export TRC	Export a .trc file.
Export VSK	Export a labeling skeleton (.vsk) file
Export XCP	Export the current calibration file to an .xcp file in a specified location.
Save Trial - C3D + VSK	Save 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.

Operation	Description
Process Offline Camera Calibration	Run on a captured trial of a calibration wand wave to calibrate a system (instead of calibrating the system live).
Transcode Video for Trial	Automates 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 video files (.mp4 or .avi) associated with the current trial. You can select which codec to use, whether to keep the original movie file, and whether to force recompression (not recommended).
Reset force plate offsets	Resets 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 Compensation	Sets 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 Origin	Sets the camera calibration origin using a calibration object.
Run Monitor	Enables you to run a monitor as part of a pipeline. To do this: Create the monitor you want to use (see Create a monitor in the Vicon Nexus Reference Guide). Ensure Nexus is in Offline mode. 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:

Operation	Description
Nexus Legacy Labeler	Run 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 Motion	Run on fully labeled trials to Kinematic Fit the trial as a whole instead of frame-by-frame as in the Core Processor.

Nexus 2.16 Documentation