├── .gitignore ├── BUILD_OPENSIM.md ├── CHANGELOG.md ├── Geometry ├── capitate_lvs.vtp ├── capitate_rvs.vtp ├── hamate_lvs.vtp ├── hamate_rvs.vtp ├── hat_jaw.vtp ├── hat_ribs_scap.vtp ├── hat_skull.vtp ├── hat_spine.vtp ├── humerus_lv.vtp ├── humerus_rv.vtp ├── index_distal_lvs.vtp ├── index_distal_rvs.vtp ├── index_medial_lvs.vtp ├── index_medial_rvs.vtp ├── index_proximal_lvs.vtp ├── index_proximal_rvs.vtp ├── l_bofoot.vtp ├── l_femur.vtp ├── l_fibula.vtp ├── l_foot.vtp ├── l_patella.vtp ├── l_pelvis.vtp ├── l_talus.vtp ├── l_tibia.vtp ├── l_tibia_SOMEINVERTEDFACES.vtp ├── little_distal_lvs.vtp ├── little_distal_rvs.vtp ├── little_medial_lvs.vtp ├── little_medial_rvs.vtp ├── little_proximal_lvs.vtp ├── little_proximal_rvs.vtp ├── lunate_lvs.vtp ├── lunate_rvs.vtp ├── metacarpal1_lvs.vtp ├── metacarpal1_rvs.vtp ├── metacarpal2_lvs.vtp ├── metacarpal2_rvs.vtp ├── metacarpal3_lvs.vtp ├── metacarpal3_rvs.vtp ├── metacarpal4_lvs.vtp ├── metacarpal4_rvs.vtp ├── metacarpal5_lvs.vtp ├── metacarpal5_rvs.vtp ├── middle_distal_lvs.vtp ├── middle_distal_rvs.vtp ├── middle_medial_lvs.vtp ├── middle_medial_rvs.vtp ├── middle_proximal_lvs.vtp ├── middle_proximal_rvs.vtp ├── pisiform_lvs.vtp ├── pisiform_rvs.vtp ├── r_bofoot.vtp ├── r_femur.vtp ├── r_fibula.vtp ├── r_foot.vtp ├── r_patella.vtp ├── r_pelvis.vtp ├── r_talus.vtp ├── r_tibia.vtp ├── r_tibia_SOMEINVERTEDFACES.vtp ├── radius_lv.vtp ├── radius_rv.vtp ├── ring_distal_lvs.vtp ├── ring_distal_rvs.vtp ├── ring_medial_lvs.vtp ├── ring_medial_rvs.vtp ├── ring_proximal_lvs.vtp ├── ring_proximal_rvs.vtp ├── sacrum.vtp ├── scaphoid_lvs.vtp ├── scaphoid_rvs.vtp ├── thumb_distal_lvs.vtp ├── thumb_distal_rvs.vtp ├── thumb_proximal_lvs.vtp ├── thumb_proximal_rvs.vtp ├── trapezium_lvs.vtp ├── trapezium_rvs.vtp ├── trapezoid_lvs.vtp ├── trapezoid_rvs.vtp ├── triquetrum_lvs.vtp ├── triquetrum_rvs.vtp ├── ulna_lv.vtp └── ulna_rv.vtp ├── LICENSE ├── README.md ├── complex ├── README.md ├── computed_muscle_controls │ └── setup_cmc.xml ├── experimental_data │ ├── setup_grf.xml │ ├── setup_grf_after_rra.xml │ ├── static.c3d │ ├── static.trc │ ├── task.c3d │ ├── task.trc │ └── task_grf.mot ├── inverse_dynamics │ └── setup_id.xml ├── inverse_kinematics │ ├── ik_task_set.xml │ └── setup_ik.xml ├── joint_reaction_analysis │ └── setup_jra.xml ├── model │ ├── README.md │ ├── Rajagopal2015.osim │ ├── model_generic.osim │ ├── model_generic_1954.osim │ ├── model_generic_rajagopal.osim │ ├── reserve_actuators.xml │ └── tracking_tasks.xml ├── muscle_analysis │ └── setup_ma.xml ├── residual_reduction_algorithm │ └── setup_rra.xml ├── scale │ ├── marker_set │ │ ├── markers_gait_and_play_celine.xml │ │ ├── markers_gait_and_play_head.xml │ │ └── markers_stanford.xml │ ├── markers.xml │ └── setup_scale.xml ├── scripts │ ├── c3d_to_opensim.py │ ├── clean_results.sh │ ├── extract_emg_from_c3d.py │ ├── perform_analyses.py │ ├── utils.py │ └── wip_knematic_analysis.py └── static_optimization │ └── setup_so.xml ├── opensim_example ├── README.md ├── computed_muscle_controls │ └── setup_cmc.xml ├── experimental_data │ ├── setup_grf.xml │ ├── setup_grf_after_rra.xml │ ├── static.trc │ ├── task.trc │ └── task_grf.mot ├── inverse_dynamics │ └── setup_id.xml ├── inverse_kinematics │ ├── ik_task_set.xml │ └── setup_ik.xml ├── joint_reaction_analysis │ └── setup_jra.xml ├── model │ ├── Lerner2015.osim │ ├── README.md │ ├── Rajagopal2015.osim │ ├── model_generic.osim │ ├── model_generic_1954.osim │ ├── model_generic_rajagopal.osim │ ├── reserve_actuators.xml │ └── tracking_tasks.xml ├── muscle_analysis │ ├── #setup_ma.xml# │ ├── .#setup_ma.xml │ └── setup_ma.xml ├── residual_reduction_algorithm │ └── setup_rra.xml ├── scale │ ├── marker_set │ │ ├── markers_gait_and_play_celine.xml │ │ ├── markers_gait_and_play_head.xml │ │ └── markers_stanford.xml │ ├── markers.xml │ └── setup_scale.xml ├── scripts │ ├── clean_results.sh │ ├── perform_analyses.py │ ├── utils.py │ └── wip_knematic_analysis.py └── static_optimization │ └── setup_so.xml ├── simple ├── README.md ├── experimental_data │ ├── setup_grf.xml │ ├── static.c3d │ ├── static.trc │ ├── task.c3d │ ├── task.trc │ └── task_grf.mot ├── inverse_dynamics │ └── setup_id.xml ├── inverse_kinematics │ ├── ik_task_set.xml │ └── setup_ik.xml ├── joint_reaction_analysis │ └── setup_jra.xml ├── model │ ├── README.md │ ├── model_generic.osim │ ├── reserve_actuators.xml │ └── tracking_tasks.xml ├── muscle_analysis │ ├── muscle_set.xml │ └── setup_ma.xml ├── scale │ ├── marker_set │ │ ├── markers_gait_and_play_celine.xml │ │ ├── markers_gait_and_play_head.xml │ │ └── markers_stanford.xml │ ├── markers.xml │ └── setup_scale.xml ├── scripts │ ├── c3d_to_opensim.py │ ├── clean_results.sh │ ├── extract_emg_from_c3d.py │ ├── perform_analyses.py │ ├── utils.py │ └── wip_knematic_analysis.py └── static_optimization │ └── setup_so.xml └── tutorial ├── README.md ├── experimental_data ├── setup_grf.xml ├── static.c3d ├── static.trc ├── task.c3d ├── task.trc └── task_grf.mot 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