MTP XML Reference

<NMSMPipelineDocument Version="1.5.0">
    <MuscleTendonPersonalizationTool>
        <!--Name of the directory where results are written. Be default this is the directory in which the setup file is be  executed.-->
        <results_directory>MTPResults</results_directory>
        <!--Name of file containing input model, if using the application this has no effect as current model is used.-->
        <input_model_file>model.osim</input_model_file>
        <!--The name of the osimx file that results from MuscleTendon personalization to be used by downstream steps.-->
        <input_osimx_file>model.osimx</input_osimx_file>
        <!--The name of the folder containing preprocessed data to run the MuscleTendonPersonalizationTool.-->
        <data_directory>MTPInputsDir</data_directory>
        <!--Coordinates Muscle-Tendon Personalization tracked their joint moments. Leave empty for none. Muscles spanning these coordinates will be extracted automatically.-->
        <coordinate_list>coordinate_1 coordinate_2 coordinate_3</coordinate_list>
        <!--*Optional* The vMaxFactor to use. Default is 10.-->
        <v_max_factor>10</v_max_factor>
        <!--A space-separated list of the activation muscle groups.-->
        <activation_muscle_groups>activation_group_1 activation_group_2 activation_group_3</activation_muscle_groups>
        <!--A space-separated list of the normalized fiber length muscle groups.-->
        <normalized_fiber_length_muscle_groups>fiber_length_group_1 fiber_length_group_2 fiber_length_group_3</normalized_fiber_length_muscle_groups>
        <!--A space-separated list of missing EMG channel names.-->
        <missing_emg_channel_muscle_groups>missing_emg_group_1 missing_emg_group_2 missing_emg_group_3</missing_emg_channel_muscle_groups>
        <!--A space-separated list of collected EMG channel names.-->
        <collected_emg_channel_muscle_groups>emg_channel_1 emg_channel_2 emg_channel_3</collected_emg_channel_muscle_groups>
        <!--Properties that describe MuscleTendonLengthInitialization settings.-->
        <MuscleTendonLengthInitialization>
            <!--Boolean (true, false) indicating if muscle tendon length initialization should be performed before muscle tendon personalization.-->
            <is_enabled>true</is_enabled>
            <!--Directory containing kinematics and moments for passive trials. Leave blank if passive data will not be used.-->
            <passive_data_input_directory>PassiveDataDir</passive_data_input_directory>
            <!--Maximum normalized fiber length. If a muscle has a normalized fiber length above this value, it will be penalized with a cost term.-->
            <max_normalized_muscle_fiber_length>1</max_normalized_muscle_fiber_length>
            <!--Minimum normalized fiber length. If a muscle has a normalized fiber length below this value, it will be penalized with a cost term.-->
            <min_normalized_muscle_fiber_length>0.6</min_normalized_muscle_fiber_length>
            <!--Flag indicating whether the maximum muscle stress value, provided below and shared by all muscles, should be adjusted.-->
            <optimize_maximum_muscle_stress>true</optimize_maximum_muscle_stress>
            <optimize_absolute_length_changes>false</optimize_absolute_length_changes>
            <!--Flag indicating whether muscle-specific maximum isometric force values will be adjusted in response to changes in muscle properties.-->
            <optimize_isometric_max_force>true</optimize_isometric_max_force>
            <!--Initial maximum muscle stress value used if optimizing muscle stress.-->
            <maximum_muscle_stress>610000</maximum_muscle_stress>
            <!--Cost term set for the MuscleTendonLengthInitialization.-->
            <RCNLCostTermSet>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>passive_joint_moment</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>2</max_allowable_error>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>optimal_muscle_fiber_length</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.3</max_allowable_error>
                    <!--Optional for specific terms.-->
                    <error_center>1</error_center>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>tendon_slack_length</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>1</max_allowable_error>
                    <!--Optional for specific terms.-->
                    <error_center>1</error_center>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>minimum_normalized_muscle_fiber_length</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.3</max_allowable_error>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>maximum_normalized_muscle_fiber_length</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.03</max_allowable_error>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>maximum_muscle_stress</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.1</max_allowable_error>
                    <!--Optional for specific terms.-->
                    <error_center>1.2</error_center>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>false</is_enabled>
                    <!--Type of cost term.-->
                    <type>passive_muscle_force</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>10</max_allowable_error>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>grouped_normalized_muscle_fiber_length</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.1</max_allowable_error>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>grouped_maximum_normalized_muscle_fiber_length</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.1</max_allowable_error>
                </RCNLCostTerm>
            </RCNLCostTermSet>
        </MuscleTendonLengthInitialization>
        <!--Properties that describe MTPSynergyExtrapolation settings.-->
        <MTPSynergyExtrapolation>
            <!--Flag indicating if synergery extrapolation should be performed as part of this task.-->
            <is_enabled>true</is_enabled>
            <!--Specify the matrix factorization approach for MSA; PCA or NMF, default to PCA.-->
            <matrix_factorization_method>PCA</matrix_factorization_method>
            <!--Number of synergies, default to 5.-->
            <number_of_synergies>5</number_of_synergies>
            <!--Indicate categorization of variability for synergy extrapolation: task, trial, or subject, default to trial.-->
            <synergy_extrapolation_categorization>trial</synergy_extrapolation_categorization>
            <!--Indicate categorization of variability for muscle activation residuals: task, trial, or subject, default to task.-->
            <residual_categorization>task</residual_categorization>
            <!--Cost term set for the MuscleTendonLengthInitialization.-->
            <RCNLCostTermSet>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>measured_inverse_dynamics_joint_moment</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>2</max_allowable_error>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>extrapolated_muscle_activation</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.5</max_allowable_error>
                </RCNLCostTerm>
                <RCNLCostTerm>
                    <!--Indicate whether the term is enabled or not. Default is false.-->
                    <is_enabled>true</is_enabled>
                    <!--Type of cost term.-->
                    <type>residual_muscle_activation</type>
                    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                    <max_allowable_error>0.01</max_allowable_error>
                </RCNLCostTerm>
            </RCNLCostTermSet>
        </MTPSynergyExtrapolation>
        <!--List of tasks to be completed by the tool, each Task is a separate optimization.-->
        <MTPTaskList>
            <MTPTask>
                <!--Indicate whether the task is enabled or not.-->
                <is_enabled>true</is_enabled>
                <!--Index indicates the order of the tasks. The task with the smallest index is completed first.-->
                <index>1</index>
                <!--Use muscle specific electromechanical delays.-->
                <muscle_specific_electromechanical_delays>true</muscle_specific_electromechanical_delays>
                <!--Boolean (true, false) indicating if electromechanical delays should be optimized for this task.-->
                <optimize_electromechanical_delays>true</optimize_electromechanical_delays>
                <!--Boolean (true, false) indicating if activation time constants should be optimized for this task.-->
                <optimize_activation_time_constants>true</optimize_activation_time_constants>
                <!--Boolean (true, false) indicating if activation nonlinearity constants should be optimized for this task.-->
                <optimize_activation_nonlinearity_constants>true</optimize_activation_nonlinearity_constants>
                <!--Boolean (true, false) indicating if EMG scale factors should be optimized for this task.-->
                <optimize_emg_scale_factors>true</optimize_emg_scale_factors>
                <!--Boolean (true, false) indicating if optimal fiber lengths should be optimized for this task.-->
                <optimize_optimal_fiber_lengths>true</optimize_optimal_fiber_lengths>
                <!--Boolean (true, false) indicating if tendon slack lengths should be optimized for this task.-->
                <optimize_tendon_slack_lengths>true</optimize_tendon_slack_lengths>
                <!--Cost term set for the MTPTask.-->
                <RCNLCostTermSet>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>inverse_dynamics_joint_moment</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>2.5</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>activation_time_constant</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.02</max_allowable_error>
                        <!--Optional for specific terms.-->
                        <error_center>0.015</error_center>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>activation_nonlinearity_constant</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.1</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>optimal_muscle_fiber_length</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.1</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>tendon_slack_length</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.1</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>emg_scale_factor</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.2</max_allowable_error>
                        <!--Optional for specific terms.-->
                        <error_center>0.3</error_center>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>normalized_muscle_fiber_length</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.01</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>passive_muscle_force</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>50</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>grouped_normalized_muscle_fiber_length</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.05</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>grouped_emg_scale_factor</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.1</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>grouped_electromechanical_delay</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.2</max_allowable_error>
                    </RCNLCostTerm>
                    <RCNLCostTerm>
                        <!--Indicate whether the term is enabled or not. Default is false.-->
                        <is_enabled>true</is_enabled>
                        <!--Type of cost term.-->
                        <type>muscle_excitation_penalty</type>
                        <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
                        <max_allowable_error>0.25</max_allowable_error>
                        <!--Optional for specific terms.-->
                        <error_center>0.5</error_center>
                    </RCNLCostTerm>
                </RCNLCostTermSet>
            </MTPTask>
        </MTPTaskList>
        <!--*Optional* The minimum step of the least squares algorithm. Default is 1e-6 -->
        <diff_min_change>0.0001</diff_min_change>
        <!--*Optional* The step tolerance determines when the lsqnonlin algorithm stops. The larger it is, the earlier the algorithm stops, but with lower accuracy. Default is 1e-16-->
        <step_tolerance>1e-6</step_tolerance>
        <!--*Optional* The optimality tolerance determines when the lsqnonlin algorithm stops. The larger it is, the earlier the algorithm stops, but with lower accuracy. Default is 1e-3-->
        <optimality_tolerance>1e-6</optimality_tolerance>
        <!--*Optional* The function tolerance determines when the lsqnonlin algorithm stops. The larger it is, the earlier the algorithm stops, but with lower accuracy. Default is 1e-6-->
        <function_tolerance>1e-6</function_tolerance>
        <!--*Optional* The number of allowed iterations of the fmincon optimization,  setting this lower can help cancel an optimization that won't converge. Default is 1e3-->
        <max_iterations>1000</max_iterations>
        <!--*Optional* The number of allowed cost function calls for the fmincon optimization,  setting this lower can help cancel an optimization that won't converge.-->
        <max_function_evaluations>100000000</max_function_evaluations>
    </MuscleTendonPersonalizationTool>
</NMSMPipelineDocument>