======================= Specimen demographics ======================= oks001 Right knee Age: 71 yrs Gender: Male Height: 1.83 m Weight: 77.1 kg BMI: 23.1 oks002 Right knee Age: 67 yrs Gender: Female Height: 1.55 m Weight: 45.3 kg BMI: 18.9 oks003 Left knee Age: 25 yrs Gender: Female Height: 1.73 m Weight: 68 kg BMI: 22.8 oks004 Right knee Age: 46 yrs Gender: Female Height:1.575 m Weight: 54.43 kg BMI: 21.9 oks006 Right knee Age: 71 yrs Gender: Female Height: 1.524 m Weight: 49.4 kg BMI: 21.3 oks007 Right knee Age: 71 yrs Gender: Male Height: 1.7 m Weight: 65.77 kg BMI: 22.7 oks008 Right knee Age:40 yrs Gender: Male Height: 1.778 m Weight: 63.5 kg BMI: 20.09 oks009 Left knee Age: 34 yrs Gender: Male Height: 1.8 m Weight:68.03 kg BMI: 20 ==================== Folder descriptions ==================== joint_mechanics Folder contains - 1. All mechanical testing data for both tibiofemoral and patellofemoral joints for each specimen. 2. each .zip folder contains a readme.txt with details of the subfolders and files. --------------------------------------- MRI Folder contains magnetic resonance imaging data for each specimen. MRI protocols: 1. General purpose imaging: 3D T1-weighted without fat suppression, isotropic, 0.5 mm resolution. 2. Cartilage imaging: 3D T1-weighted with fat suppression, 0.35 mm sagittal plane resolution, 0.7 mm out of plane resolution. 3. Connective tissue imaging: Proton density, turbo spin echo in sagittal, axial, and coronal planes, 0.35 mm in plane and 2.8 mm out of plane resolution. Specimen: oks001 Protocol Deviations: None Files: General purpose imaging: 1.3.12.2.1107.5.2.19.45406.2014100710220888421542662.0.0.0.nii Cartilage imaging: 1.3.12.2.1107.5.2.19.45406.2014100710433217692143626.0.0.0.nii Soft tissue imaging - axial plane: 1.3.12.2.1107.5.2.19.45406.2014100711193292568244326.0.0.0.nii Soft tissue imaging - sagittal plane: 1.3.12.2.1107.5.2.19.45406.2014100711262396541244530.0.0.0.nii Soft tissue imaging - coronal plane: 1.3.12.2.1107.5.2.19.45406.2014100711323578731244734.0.0.0.nii Specimen: oks002 Protocol Deviations: None Files: General purpose imaging: 0003.0320.2014.11.04.11.20.53.124440.359899718.nii Cartilage imaging: 0004.0224.2014.11.04.11.20.53.124440.359906184.nii Soft tissue imaging - axial plane: 0007.0001.2014.11.04.11.20.53.124440.359915938.nii Soft tissue imaging - sagittal plane: 0005.0050.2014.11.04.11.22.47.588987.359909764.nii Soft tissue imaging - coronal plane: 0006.0001.2014.11.04.11.20.53.124440.359913880.nii Specimen: oks003 Protocol Deviations: None Files: General purpose imaging: 1.3.12.2.1107.5.2.19.45406.2014120210113013368841431.0.0.0.nii Cartilage imaging: 1.3.12.2.1107.5.2.19.45406.2014120210325342222042395.0.0.0.nii Soft tissue imaging - axial plane: 1.3.12.2.1107.5.2.19.45406.2014120211145041394943484.0.0.0.nii Soft tissue imaging - sagittal plane: 1.3.12.2.1107.5.2.19.45406.2014120211045428131243076.0.0.0.nii Soft tissue imaging - coronal plane: 1.3.12.2.1107.5.2.19.45406.2014120211095362283243280.0.0.0.nii Specimen: oks004 Protocol Deviations: 1. Patella registration marker assembly was not placed on the patella for imaging. 2. Coronoal image set for ligament specific scans is missing for oks004 (a repeated sagittal image set was acquired instead). Files: General purpose imaging: 1.3.12.2.1107.5.2.19.45406.2014072210222363865584064.0.0.0.nii Cartilage imaging: 1.3.12.2.1107.5.2.19.45406.2014072211413113536586664.0.0.0.nii Soft tissue imaging - axial plane: 1.3.12.2.1107.5.2.19.45406.2014072211351581496185970.0.0.0.nii Soft tissue imaging - sagittal plane: 1.3.12.2.1107.5.2.19.45406.2014072211404233708286174.0.0.0.nii Soft tissue imaging - sagittal plane 2: 1.3.12.2.1107.5.2.19.45406.2014072212133281316387345.0.0.0.nii Specimen: oks006 Protocol Deviations: None. Files: General purpose imaging: 1.3.12.2.1107.5.2.19.45406.2015010611354553104280874.0.0.0.nii Cartilage imaging: 1.3.12.2.1107.5.2.19.45406.2015010611570880894681838.0.0.0.nii Soft tissue imaging - axial plane: 1.3.12.2.1107.5.2.19.45406.2015010612350885610582739.0.0.0.nii Soft tissue imaging - sagittal plane: 1.3.12.2.1107.5.2.19.45406.2015010612301630598082535.0.0.0.nii Soft tissue imaging - coronal plane: 1.3.12.2.1107.5.2.19.45406.2015010612400137121082943.0.0.0.nii Specimen: oks007 Protocol Deviations: None Files: General purpose imaging: 1.3.12.2.1107.5.2.19.45406.2015020310331641962506155.0.0.0.nii Cartilage imaging: 1.3.12.2.1107.5.2.19.45406.2015020310560389569607119.0.0.0.nii Soft tissue imaging - axial plane: 1.3.12.2.1107.5.2.19.45406.2015020311391094492308224.0.0.0.nii Soft tissue imaging - sagittal plane: 1.3.12.2.1107.5.2.19.45406.2015020311292575600307816.0.0.0.nii Soft tissue imaging - coronal plane: 1.3.12.2.1107.5.2.19.45406.2015020311341828039508020.0.0.0.nii Specimen: oks008 Protocol Deviations: None Files: General purpose imaging: 1.3.12.2.1107.5.2.19.45406.2015060311163837990581829.0.0.0.nii Cartilage imaging: 1.3.12.2.1107.5.2.19.45406.2015060311391849809482793.0.0.0.nii Soft tissue imaging - axial plane: 1.3.12.2.1107.5.2.19.45406.2015060312162325167483774.0.0.0.nii Soft tissue imaging - sagittal plane: 1.3.12.2.1107.5.2.19.45406.2015060312064169652083468.0.0.0.nii Soft tissue imaging - coronal plane: 1.3.12.2.1107.5.2.19.45406.2015060312113066906083621.0.0.0.nii Specimen: oks009 Protocol Deviations: None Files: General purpose imaging: 1.3.12.2.1107.5.2.19.45406.2015111710293432651200476.0.0.0.nii Cartilage imaging: 1.3.12.2.1107.5.2.19.45406.2015111710505772215301440.0.0.0.nii Soft tissue imaging - axial plane: 1.3.12.2.1107.5.2.19.45406.2015111711282322237402453.0.0.0.nii Soft tissue imaging - sagittal plane: 1.3.12.2.1107.5.2.19.45406.2015111711182762540902131.0.0.0.nii Soft tissue imaging - coronal plane: 1.3.12.2.1107.5.2.19.45406.2015111711232022410402284.0.0.0.nii --------------------------------------- doc Folder contains, 1. Documents to aid understanding of how the various tools required during mechanical testing are calibrated, used, programmed and controlled. 2. Document detailing notes taken on testing day and, any deviations from predefined specifications. 3. Static copies of following project web pages as of date of upload, https://simtk.org/plugins/moinmoin/openknee/Specifications/ExperimentationJointMechanics https://simtk.org/plugins/moinmoin/openknee/Specifications/SpecimenPreparation https://simtk.org/plugins/moinmoin/openknee/Specifications/Registration https://simtk.org/plugins/moinmoin/openknee/Specifications/PressureCalibration --------------------------------------- src Folder contains Python scripts to- 1. Generate transformation matrices necessasary to perform patella, tibia and femur registration and calculate registration errors. 2. Resample and plot the mechanical testing data and visualize the trial. 3. Process the pressure data for visualization and extraction of necessary metrics. Python scripts: JOINT MECHANICAL TESTING DATA PROCESSING Convert_2_image.py: • Performs patella, tibia and femur registration using digitized points on spheres collected during experimentation and, segmented spheres captured in MRI. • Within the registration directory, all processed tibiofemoral and patellofemoral trials are evaluated and transformation matrices needed for data analysis are saved using the trial name (.npz extension). • Registration error files are also saved for each bone (oksXXX_registration_errors_BONE.txt). Bone is defined as FEM for femur, TIB for tibia, and PAT for patella. Within this file, the radius and center of each sphere fit to digitized (transformed to image coordinate system) and stl surface points are reported. In addition, distances and vector coordinates between all registration markers are reported for both data sets. The error is reported as the difference in line segment length (expressed in mm and percent difference) and angle between line segments from each coordinate system (defined from digitized and stl surface points). • All transformation matrices are generated for each trial. • Requires xml file as input with knee directory, stl file names for bones and spheres. • For details see, https://simtk.org/plugins/moinmoin/openknee/Specifications/Registration and registration_methods.pdf in 'doc' folder. resampling_plotting.py • The script samples the data in a more usable format for comparison to model results and/or boundary conditions. • CSV file of all channels within the TDMS file at the re-sampled locations • Video animation of the test • Graphs of the JCS kinematics and loads (both raw and re-sampled) • For details see, registration_methods.pdf in 'doc' folder. PRESSURE DATA PROCESSING Tekscan_contact_metrics.py • Output - figure with pressure plot and all the metrics - xml file with all the metrics • xml file contains-- text file(s) (name(s) based on input file(s)) containing: input csv filename, sensor dimensions (sensel rows x columns), contact force (N), contact area (mm^2), peak pressure (MPa), peak pressure location (sensel indices (row,col), indexed from 1) Tekscan_subplot.py • Creates a plot with multiple pressure data subplots. • Input requires number of rows and columns on the plot and, pressure data file name(s)(.csv). • output - xml files with all the metrics for each csv file. - figure with pressure plots of all input files.