Shoulder Database handling and measurements

Introduction

This repository contains Matlab codes to import anonymised clinical cases in a shoulder database (shoulderDB), and update this database with complementary clinical, radiological, morphological, or biomechanical data. This project is a collaboration between Laboratory of Biomechanical Orthopedics of the Ecole Polytechnique Federal de Lausanne (EPFL-LBO), the ARTORG center of the University of Bern, the Orthopedic Service of the University Hospital of Lausanne (CHUV-OTR), and the Radiological Department of the University Hospital of Lausanne (CHUV-RAD).

Setup

Download

Clone or download this repository. Open MATLAB, set the working directory to be the downloaded repository and run setup.m. This setup() function will create a config.json file that is detailed below.

Write the config file

The base folder must contain a "config.json" with the following keys:

• maxSCaseIDDigits: This is the maximum allowed number of digits in the SCase IDs.
  
  "maxSCaseIDDigits": 3 -> 'P123' is a valid ID, 'P1234' is not valid.

• SCaseIDValidTypes: These are the allowed letters used as a prefix in the SCase IDs.
  
  "SCaseIDValidTypes": ["N", "P"] -> 'P123' is a valid ID, 'Z123' is not valid.

• pythonDir: This is the path to the rotator cuff segmentation system.

• dataDir: This is the root path to the data used i.e. "/shoulder/dataDev" or "/shoulder/data" on lbovenus.epfl.ch

• casesToMeasure: Array of cases ID to be measured when executing measureSCase() (with no argument).
  
  "casesToMeasure": "*" -> measureSCase() will measure all the cases found in the database. "casesToMeasure": "P1" -> measureSCase() will measure P1 if it's in the database. "casesToMeasure": ["P1", "P2"] -> measureSCase() will measure P1 and P" if they are found in the database.

• shouldersToMeasure: Hash table used by measureSCase() where keys correspond to the four available shoulders of a case and values are booleans allowing the shoulders to be measured. For example:
  
  "shouldersToMeasure" { "rightAuto": true, "rightManual": false, "leftAuto": true, "leftManual": false }

• standardMeasurementsToRun: Hash table used by measureSCase() where keys correspond to the standard measurement steps of measureSCase() and values are booleans allowing the steps to be run. For example:
  
  "standardMeasurementsToRun":{ "loadData":true, "morphology":true, "measureFirst":true, "measureSecond":false }

These standard measurements are built in a way that the next measurement needs the results of the former measurement, e.g "morphology" needs to be run after "loadData". The successive standard measurements are "loadData", "morphology", "measureFirst", "measureSecond".

• specialMeasurementsToRun: Hash table used by measureSCase() where keys correspond to specific SCase functions and values are booleans allowing these functions to be called. For example:
  
  "specialMeasurementsToRun":{ "sliceAndSegment":true, "calcDensity":false }

All the special measurements are called after the execution of the standard measurements. The special measurements SCase functions are recursively called in a Shoulder object and all the objects within.

• specialMeasurementsArguments: Hash table used by measureSCase() where keys correspond to the specific SCase functions listed in "specialMeasurementsToRun" and values are arrays of arguments to give to the functions for their execution. For example:
  
  "specialMeasurementsArguments":{ "sliceAndSegment":[], "calcDensity":[] }

• numberOfMuscleSubdivisions: Hash table used by measureSCase() where keys correspond to the muscle divisions dimensions and values are the number of these divisions. For example:
  
  "numberOfMuscleSubdivisions":{ "radial": 10, "angular": 10 }

• overwriteMeasurements: Boolean that will tell measureSCase() to create an empty SCase (true) or to load an existing SCase (false) before measuring it.

• saveMeasurements: Boolean used by measureSCase() to save or not each individual SCase.mat after measurements.

• saveAllMeasurementsInOneFile: Boolean used by measureSCase() to save all the SCase.mat loaded from the whole database into one file in dataDir/matlab/SCaseDB.mat. This won't take into account the last measurements if "saveMeasurements" is false.

How to use

There are five main features within this system. Be sure to add this system's folders and subfolders to your MATLAB path.

Access data

Data are restricted to authorised users, in a dedicated EPFL server. The data related to a specific case can be accessed thanks to the ShoulderCaseLoader class. For example:

database = ShoulderCaseLoader();
SCase = database.loadCase('P527');

Will load the data related to the case 'P527' into the variable SCase. The function loadSCase() will do the same even more directly:

SCase = loadSCase('P527');

The ShoulderCaseLoader class features several other methods to access the data. To get the list of all the available cases run:

database = ShoulderCaseLoader();
SCaseList = database.getAllCasesIDs();

To load all the available cases in an cell array run:

database = ShoulderCaseLoader();
AllTheSCases = database.loadAllCases();

Visualize data

All the measured data are directly available in a loaded ShoulderCase's properties.

To observe and interact with a cases's data run:

database = ShoulderCaseLoader();
SCase = database.loadCase('P527');
SCase.plot();

or

plotSCase('P527');

Update data

To update the measured values of the shoulder cases use the function measureSCase(). Refer to the function's documentation for further informations.

Import new data

To import new cases (basically add a CT-files folder at the right place) use the importSCase GUI. The importSCase code is located in the sub-directory importSCase. Its description is detailed there. It currently only work for Windows.

Export data

For a loaded SCase, you can have all of the measurements by calling getTableOfData method of ShoulderCase.m as:

SCase.getTableOfData();

The result will be a table with all of the information and measurements for the SCase. Also you can have all of the information and measurements for all of the SCases by calling exportSCaseData function as:

exportSCaseData("SCaseList", "*", "saveInFile", filename);

The filename is your specified csv or excel file where all the measurements will be exported. Refer to the function docstring for more details.

The summary of every exported variable definition is given below.

id: ShoulderCase.id is the id of the shoulder case as it appears in the database [NP][0-9]{1,3} diagnosis: ShoulderCase.diagnosis is the given diagnosis (found in REDCap export) treatment: ShoulderCase.treatment is the given treatment data_ct_path: ShoulderCase.dataCTPath is the path to the folder containing the dicom folder and other data related to the case (Amira/3DSlicer segmentations, rotator cuff segmentations, matlab measurements,...) patient_id: Patient.id is the id in the anonymised database (ShoulderCase.id DUPLICATE) patient_id_med: Patient.idMed is the id of the medical center DEADVAR patient_gender: Patient.gender is the patient's gender found in dicom metadata patient_age: Patient.age is the patient's age at time of preoperative CT scan found in dicom metadata patient_ethnicity: Patient.ethnicity is a medical metadata DEADVAR patient_weight: Patient.weight is the patient's height found in dicom metadata patient_height: Patient.height is the patient's weight found in dicom metadata patient_BMI: Patient.BMI is the patient's Body Mass Index computed with dicom metadata (BMI = weight / height^2) patient_comment: Patient.comment DEADVAR shoulder_side: Shoulder.side is the considered shoulder side ("R"/"L" tells Right/Left) shoulder_landmarks_acquisition: Shoulder.landmarksAcquisition is the method used to obtain scapula landmarks ("auto" or "manual") shoulder_has_measurements: Shoulder.hasMeasurements indicates the presence of scapula landmarks (1/0 tells presence/absence) shoulder_ct_scan: Shoulder.CTScan DEADVAR shoulder_comment: Shoulder.comment DEADVAR shoulder_scapula_angulus_inferior: Scapula.angulusInferior indicates the presence of angulus inferior landmark coordinates (1/0 tells presence/absence) shoulder_scapula_angulus_inferior_x: Scapula.angulusInferior gives the x coordinates of angulus inferior landmark shoulder_scapula_angulus_inferior_y: Scapula.angulusInferior gives the y coordinates of angulus inferior landmark shoulder_scapula_angulus_inferior_z: Scapula.angulusInferior gives the z coordinates of angulus inferior landmark shoulder_scapula_trigonum_spinae: Scapula.trigonumSpinae indicates the presence of trigonum spinae landmark coordinates (1/0 tells presence/absence) shoulder_scapula_trigonum_spinae_x: Scapula.trigonumSpinae gives the x coordinates of trigonum spinae landmark shoulder_scapula_trigonum_spinae_y: Scapula.trigonumSpinae gives the y coordinates of trigonum spinae landmark shoulder_scapula_trigonum_spinae_z: Scapula.trigonumSpinae gives the z coordinates of trigonum spinae landmark shoulder_scapula_processus_coracoideus: Scapula.processusCoracoideus indicates the presence of processus coracoideus landmark coordinates (1/0 tells presence/absence) shoulder_scapula_processus_coracoideus_x: Scapula.processusCoracoideus gives the x coordinates of processus coracoideus landmark shoulder_scapula_processus_coracoideus_y: Scapula.processusCoracoideus gives the y coordinates of processus coracoideus landmark shoulder_scapula_processus_coracoideus_z: Scapula.processusCoracoideus gives the z coordinates of processus coracoideus landmark shoulder_scapula_acromio_clavicular: Scapula.acromioClavicular indicates the presence of acromio clavicular landmark coordinates (1/0 tells presence/absence) shoulder_scapula_acromio_clavicular_x: Scapula.acromioClavicular gives the x coordinates of acromio clavicular landmark shoulder_scapula_acromio_clavicular_y: Scapula.acromioClavicular gives the y coordinates of acromio clavicular landmark shoulder_scapula_acromio_clavicular_z: Scapula.acromioClavicular gives the z coordinates of acromio clavicular landmark shoulder_scapula_angulus_acromialis: Scapula.angulusacromialis indicates the presence of angulus acromialis landmark coordinates (1/0 tells presence/absence) shoulder_scapula_angulus_acromialis_x: Scapula.angulusacromialis gives the x coordinates of angulus acromialis landmark shoulder_scapula_angulus_acromialis_y: Scapula.angulusacromialis gives the y coordinates of angulus acromialis landmark shoulder_scapula_angulus_acromialis_z: Scapula.angulusacromialis gives the z coordinates of angulus acromialis landmark shoulder_scapula_spino_glenoid_notch: Scapula.spinoGlenoidNotch indicates the presence of spino glenoid notch landmark coordinates (1/0 tells presence/absence) shoulder_scapula_spino_glenoid_notch_x: Scapula.spinoGlenoidNotch gives the x coordinates of spino glenoid notch landmark shoulder_scapula_spino_glenoid_notch_y: Scapula.spinoGlenoidNotch gives the y coordinates of spino glenoid notch landmark shoulder_scapula_spino_glenoid_notch_z: Scapula.spinoGlenoidNotch gives the z coordinates of spino glenoid notch landmark shoulder_scapula_friedmansLine_origin: Scapula.friedmansLine indicates the presence of friedmansLine vector origin coordinates (1/0 tells presence/absence) shoulder_scapula_friedmansLine_origin_x: Scapula.friedmansLine gives the x coordinates of friedmansLine vector origin shoulder_scapula_friedmansLine_origin_y: Scapula.friedmansLine gives the y coordinates of friedmansLine vector origin shoulder_scapula_friedmansLine_origin_z: Scapula.friedmansLine gives the z coordinates of friedmansLine vector origin shoulder_scapula_friedmansLine_target: Scapula.friedmansLine indicates the presence of friedmansLine vector target coordinates (1/0 tells presence/absence) shoulder_scapula_friedmansLine_target_x: Scapula.friedmansLine gives the x coordinates of friedmansLine vector target shoulder_scapula_friedmansLine_target_y: Scapula.friedmansLine gives the y coordinates of friedmansLine vector target shoulder_scapula_friedmansLine_target_z: Scapula.friedmansLine gives the z coordinates of friedmansLine vector target shoulder_scapula_coordSys_ml: CoordinateSystemAnatomical.ML indicates the presence of medio-lateral axis coordinates (1/0 tells presence/absence) shoulder_scapula_coordSys_ml_x: CoordinateSystemAnatomical.ML gives the x coordinates of medio-lateral axis shoulder_scapula_coordSys_ml_y: CoordinateSystemAnatomical.ML gives the y coordinates of medio-lateral axis shoulder_scapula_coordSys_ml_z: CoordinateSystemAnatomical.ML gives the z coordinates of medio-lateral axis shoulder_scapula_coordSys_pa: CoordinateSystemAnatomical.PA indicates the presence of postero_anterior axis coordinates (1/0 tells presence/absence) shoulder_scapula_coordSys_pa_x: CoordinateSystemAnatomical.PA gives the x coordinates of postero_anterior axis shoulder_scapula_coordSys_pa_y: CoordinateSystemAnatomical.PA gives the y coordinates of postero_anterior axis shoulder_scapula_coordSys_pa_z: CoordinateSystemAnatomical.PA gives the z coordinates of postero_anterior axis shoulder_scapula_coordSys_is: CoordinateSystemAnatomical.IS indicates the presence of infero-superior axis coordinates (1/0 tells presence/absence) shoulder_scapula_coordSys_is_x: CoordinateSystemAnatomical.IS gives the x coordinates of infero-superior axis shoulder_scapula_coordSys_is_y: CoordinateSystemAnatomical.IS gives the y coordinates of infero-superior axis shoulder_scapula_coordSys_is_z: CoordinateSystemAnatomical.IS gives the z coordinates of infero-superior axis shoulder_scapula_coordSys_origin: CoordinateSystemAnatomical.origin indicates the presence of the coordinate system's origin coordinates (1/0 tells presence/absence) shoulder_scapula_coordSys_origin_x: CoordinateSystemAnatomical.origin gives the x coordinates of the coordinate system's origin shoulder_scapula_coordSys_origin_y: CoordinateSystemAnatomical.origin gives the y coordinates of the coordinate system's origin shoulder_scapula_coordSys_origin_z: CoordinateSystemAnatomical.origin gives the z coordinates of the coordinate system's origin shoulder_scapula_plane_normal: Plane.normal indicates the presence of plane's normal vector coordinates (1/0 tells presence/absence) shoulder_scapula_plane_normal_x: Plane.normal gives the x coordinates of plane's normal vector shoulder_scapula_plane_normal_y: Plane.normal gives the y coordinates of plane's normal vector shoulder_scapula_plane_normal_z: Plane.normal gives the z coordinates of plane's normal vector shoulder_scapula_plane_point: Plane.point indicates the presence of plane's point coordinates (1/0 tells presence/absence) shoulder_scapula_plane_point_x: Plane.point gives the x coordinates of plane's point shoulder_scapula_plane_point_y: Plane.point gives the y coordinates of plane's point shoulder_scapula_plane_point_z: Plane.point gives the z coordinates of plane's point shoulder_scapula_plane_fitPerformance_rmse: Plane.fitPerformance.RMSE is the root mean square error of the points fitted by the plane and the plane itself shoulder_scapula_plane_fitPerformance_r2: Plane.fitPerformance.R2 is the coefficient of determination of the points to plane distances shoulder_scapula_segmentation: Scapula.segmentation indicates the type of scapula surface segmentation ("N"/"M"/"A" tells None/Manual/Automatic) shoulder_scapula_glenoid_center: Glenoid.center indicates the presence of glenoid's center coordinates (1/0 tells presence/absence). Glenoid's center is the point of the segmented glenoid's surface which is the closest to the mean of all the points of the segmeted glenoid's surface shoulder_scapula_glenoid_center_x: Glenoid.center gives the x coordinates of glenoid's center shoulder_scapula_glenoid_center_y: Glenoid.center gives the y coordinates of glenoid's center shoulder_scapula_glenoid_center_z: Glenoid.center gives the z coordinates of glenoid's center shoulder_scapula_glenoid_centerLocal: Glenoid.centerLocal indicates the presence of glenoid's center coordinates expressed in scapula's coordinate system (1/0 tells presence/absence) shoulder_scapula_glenoid_centerLocal_x: Glenoid.centerLocal gives the x coordinates of glenoid's center expressed in scapula's coordinate system shoulder_scapula_glenoid_centerLocal_y: Glenoid.centerLocal gives the y coordinates of glenoid's center expressed in scapula's coordinate system shoulder_scapula_glenoid_centerLocal_z: Glenoid.centerLocal gives the z coordinates of glenoid's center expressed in scapula's coordinate system shoulder_scapula_glenoid_radius: Glenoid.radius is the radius is the radius of the sphere fitted to the glenoid's surface points shoulder_scapula_glenoid_center_line: Glenoid.centerLine indicates the presence of glenoid's center line coordinates (1/0 tells presence/absence). Glenoid's center line is the vector from glenoid's center to glenoid's fitted sphere center shoulder_scapula_glenoid_center_line_x: Glenoid.centerLine gives the x coordinates of glenoid's center line shoulder_scapula_glenoid_center_line_y: Glenoid.centerLine gives the y coordinates of glenoid's center line shoulder_scapula_glenoid_center_line_z: Glenoid.centerLine gives the z coordinates of glenoid's center line shoulder_scapula_glenoid_posteroAnteriorLine_origin: Glenoid.posteroAnteriorLine.origin indicates the presence of glenoid's postero-anterior line origin coordinates (1/0 tells presence/absence). Glenoid's postero-anterior origin is the most posterior point of the glenoid's rim points shoulder_scapula_glenoid_posteroAnteriorLine_origin_x: Glenoid.posteroAnteriorLine.origin gives the x coordinates of glenoid's postero-anterior line origin shoulder_scapula_glenoid_posteroAnteriorLine_origin_y: Glenoid.posteroAnteriorLine.origin gives the y coordinates of glenoid's postero-anterior line origin shoulder_scapula_glenoid_posteroAnteriorLine_origin_z: Glenoid.posteroAnteriorLine.origin gives the z coordinates of glenoid's postero-anterior line origin shoulder_scapula_glenoid_posteroAnteriorLine_target: Glenoid.posteroAnteriorLine.target indicates the presence of glenoid's postero-anterior line target coordinates (1/0 tells presence/absence). Glenoid's postero-anterior target is the most anterior point of the glenoid's rim points shoulder_scapula_glenoid_posteroAnteriorLine_target_x: Glenoid.posteroAnteriorLine.target gives the x coordinates of glenoid's postero-anterior line target shoulder_scapula_glenoid_posteroAnteriorLine_target_y: Glenoid.posteroAnteriorLine.target gives the y coordinates of glenoid's postero-anterior line target shoulder_scapula_glenoid_posteroAnteriorLine_target_z: Glenoid.posteroAnteriorLine.target gives the z coordinates of glenoid's postero-anterior line target shoulder_scapula_glenoid_inferoSuperiorLine_origin: Glenoid.inferoSuperiorLine.origin indicates the presence of glenoid's infero-superior line origin coordinates (1/0 tells presence/absence). Glenoid's infero-superior origin is the most inferior point of the glenoid's rim points shoulder_scapula_glenoid_inferoSuperiorLine_origin_x: Glenoid.inferoSuperiorLine.origin gives the x coordinates of glenoid's infero-superior line origin shoulder_scapula_glenoid_inferoSuperiorLine_origin_y: Glenoid.inferoSuperiorLine.origin gives the y coordinates of glenoid's infero-superior line origin shoulder_scapula_glenoid_inferoSuperiorLine_origin_z: Glenoid.inferoSuperiorLine.origin gives the z coordinates of glenoid's infero-superior line origin shoulder_scapula_glenoid_inferoSuperiorLine_target: Glenoid.inferoSuperiorLine.target indicates the presence of glenoid's infero-superior line target coordinates (1/0 tells presence/absence). Glenoid's infero-superior target is the most superior point of the glenoid's rim points shoulder_scapula_glenoid_inferoSuperiorLine_target_x: Glenoid.inferoSuperiorLine.target gives the x coordinates of glenoid's infero-superior line target shoulder_scapula_glenoid_inferoSuperiorLine_target_y: Glenoid.inferoSuperiorLine.target gives the y coordinates of glenoid's infero-superior line target shoulder_scapula_glenoid_inferoSuperiorLine_target_z: Glenoid.inferoSuperiorLine.target gives the z coordinates of glenoid's infero-superior line target shoulder_scapula_glenoid_depth: Glenoid.depth is the span of glenoid's surface points projections on glenoid's center line shoulder_scapula_glenoid_width: Glenoid.width is the span of glenoid's surface points projected on the most antero-posterior Principal Component Analysis axis of glenoid's surface points shoulder_scapula_glenoid_height: Glenoid.height is the span of glenoid's surface points projected on the most infero-superior Principal Component Analysis axis of glenoid's surface points shoulder_scapula_glenoid_antero_superior_angle: Glenoid.anteroSuperiorAngle is the angle between the scapula infero-superior axis and the most infero-superior Principal Component Analysis axis of glenoid's surface points shoulder_scapula_glenoid_version_amplitude: Glenoid.versionAmplitude is the angle between the glenoid's center line and the scapular medio-lateral axis shoulder_scapula_glenoid_version_orientation: Glenoid.versionOrientation is the angle between the scapular antero-posterior axis and the glenoid's center line projected on the scapular sagittal plane (superior is positive) shoulder_scapula_glenoid_version: Glenoid.version is the angle between the scapular medio-lateral axis and the glenoid's center line projected on the scapular axial plane (anterior is positive) shoulder_scapula_glenoid_inclination: Glenoid.inclination is the angle between the scapular medio-lateral axis and the glenoid's center line projected on the scapular fontal plane (superior is positive) shoulder_scapula_glenoid_retroversion: Glenoid.retroversion is the angle between the glenoid postero-anterior line and the line perpendicular to the Friedman's line that goes through the most anterior glenoid rim point shoulder_scapula_glenoid_rim_inclination: Glenoid.rimInclination is the angle between the glenoid infero-superior line and the line that goes through Trigonum Spinae and Spino-Glenoid Notch shoulder_scapula_glenoid_beta: Glenoid.beta is the angle between the line fitted to the scapular groove points (supraspinatus fossa landmarks) and the glenoid's supero-inferior line shoulder_scapula_glenoid_density_1: Glenoid.density(1) is the glenoid bone density in the first volume of interest shoulder_scapula_glenoid_density_2: Glenoid.density(2) is the glenoid bone density in the second volume of interest shoulder_scapula_glenoid_density_3: Glenoid.density(3) is the glenoid bone density in the third volume of interest shoulder_scapula_glenoid_density_4: Glenoid.density(4) is the glenoid bone density in the fourth volume of interest shoulder_scapula_glenoid_density_5: Glenoid.density(5) is the glenoid bone density in the fifth volume of interest shoulder_scapula_glenoid_density_6: Glenoid.density(6) is the glenoid bone density in the sixth volume of interest shoulder_scapula_glenoid_walch: Glenoid.walch is the Walch index read in lbovenus/shoulder/data(Dev)/Excel/ShoulderDataBase.xlsx shoulder_scapula_glenoid_fittedSphere_center: Glenoid.fittedSphere.center indicates the presence of glenoid's fitted sphere center coordinates (1/0 tells presence/absence). Glenoid's fitted sphere center is the center of the sphere fitted on the glenoid's surface points shoulder_scapula_glenoid_fittedSphere_center_x: Glenoid.fittedSphere.center gives the x coordinates of glenoid's fitted sphere center shoulder_scapula_glenoid_fittedSphere_center_y: Glenoid.fittedSphere.center gives the y coordinates of glenoid's fitted sphere center shoulder_scapula_glenoid_fittedSphere_center_z: Glenoid.fittedSphere.center gives the z coordinates of glenoid's fitted sphere center shoulder_scapula_glenoid_fittedSphere_radius: Glenoid.fittedSphere.radius is the radius of the sphere fitted on the glenoid's surface points (Glenoid.radius DUPLICATE) shoulder_scapula_glenoid_fittedSphere_r2: Glenoid.fittedSphere.R2 is the coefficient of determination of the fitted points to the computed sphere shoulder_scapula_glenoid_fittedSphere_rmse: Glenoid.fittedSphere.RMSE is the Root Mean Square Error of the fitted points to the computed sphere shoulder_scapula_acromion_ai: Acromion.AI is the Acromion Index (doi:10.2106/JBJS.D.03042) shoulder_scapula_acromion_csa: Acromion.CSA is the Critical Shoulder Angle (doi:10.1302/0301-620X.95B7.31028) shoulder_scapula_acromion_psa: Acromion.PSA is the Posterior Slope Angle (10.1016/S1058-2746(05)80036-9) shoulder_scapula_acromion_psl: Acromion.PSL is the length of segment between AA and AC shoulder_scapula_acromion_aaa: Acromion.AAA is the angle between the scapular antero-posterior axis and the vector that starts at the scapular origin and ends at the Angulus Acromialis landmark shoulder_scapula_acromion_aal: Acromion.AAL is the norm of the vector that starts at the scapular origin and ends at the Angulus Acromialis landmark shoulder_scapula_acromion_a_ax: Acromion.AAx is the x coordinates of the Angulus Acromialis landmark expressed in the scapular coordinate system (along postero-anterior axis) shoulder_scapula_acromion_a_ay: Acromion.AAx is the y coordinates of the Angulus Acromialis landmark expressed in the scapular coordinate system (along infero-superior axis) shoulder_scapula_acromion_a_az: Acromion.AAx is the z coordinates of the Angulus Acromialis landmark expressed in the scapular coordinate system (along medio-lateral axis) shoulder_scapula_acromion_a_cx: Acromion.ACx is the x coordinates of the Acromio-Clavicular landmark expressed in the scapular coordinate system (along postero-anterior axis) shoulder_scapula_acromion_a_cy: Acromion.ACx is the y coordinates of the Acromio-Clavicular landmark expressed in the scapular coordinate system (along infero-superior axis) shoulder_scapula_acromion_a_cz: Acromion.ACx is the z coordinates of the Acromio-Clavicular landmark expressed in the scapular coordinate system (along medio-lateral axis) shoulder_scapula_acromion_comment: Acromion.comment DEADVAR shoulder_scapula_comment: Scapula.comment DEADVAR shoulder_rotatorCuff_SC_name: RotatorCuff.SC.name is the Muscle.name property of the RotatorCuff.SC object and is thus "SC" (DUPLICATE with variable name) shoulder_rotatorCuff_SC_segmentation_name: Muscle.segmentationName is the base name used to find segmentation related files shoulder_rotatorCuff_SC_slice_name: Muscle.sliceName is the base name used to find slice related files shoulder_rotatorCuff_SC_pcsa: Muscle.PCSA is the Physiological Cross Section Area of the muscle's segmentation (in cm^2). It's the area of the healthy muscle shoulder_rotatorCuff_SC_atrophy: Muscle.atrophy is the ratio of atrophied muscle area over healthy muscle area shoulder_rotatorCuff_SC_fat: Muscle.fat is the ratio of muscle area with fat infiltration over healthy muscle area shoulder_rotatorCuff_SC_osteochondroma: Muscle.osteochondroma is the ratio muscle area with osteochondroma over healthy muscle area shoulder_rotatorCuff_SC_degeneration: Muscle.degeneration is the sum of atrophy, fat, and osteochondroma ratios shoulder_rotatorCuff_SC_centroid: Muscle.centroid indicates the presence of muscle's segmentation centroid coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_SC_centroid_x: Muscle.centroid gives the x coordinates of muscle's segmentation centroid shoulder_rotatorCuff_SC_centroid_y: Muscle.centroid gives the y coordinates of muscle's segmentation centroid shoulder_rotatorCuff_SC_centroid_z: Muscle.centroid gives the z coordinates of muscle's segmentation centroid shoulder_rotatorCuff_SC_insertion: Muscle.insertion indicates the presence of muscle's insertion coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_SC_insertion_x: Muscle.insertion gives the x coordinates of muscle's insertion shoulder_rotatorCuff_SC_insertion_y: Muscle.insertion gives the y coordinates of muscle's insertion shoulder_rotatorCuff_SC_insertion_z: Muscle.insertion gives the z coordinates of muscle's insertion shoulder_rotatorCuff_SC_force_application_point: Muscle.forceApplicationPoint indicates the presence of muscle's force application point coordinates (1/0 tells presence/absence). Muscle's force application point is the contact point of the muscle's fibre on the humeral head sphere shoulder_rotatorCuff_SC_force_application_point_x: Muscle.forceApplicationPoint gives the x coordinates of muscle's force application point shoulder_rotatorCuff_SC_force_application_point_y: Muscle.forceApplicationPoint gives the y coordinates of muscle's force application point shoulder_rotatorCuff_SC_force_application_point_z: Muscle.forceApplicationPoint gives the z coordinates of muscle's force application point shoulder_rotatorCuff_SC_forceVector_origin: Muscle.forceVector indicates the presence of muscle's force vector origin coordinates (1/0 tells presence/absence). Muscle's force vector origin is muscle's force application point DUPLICATE shoulder_rotatorCuff_SC_forceVector_origin_x: Muscle.forceVector gives the x coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_SC_forceVector_origin_y: Muscle.forceVector gives the y coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_SC_forceVector_origin_z: Muscle.forceVector gives the z coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_SC_forceVector_target: Muscle.forceVector indicates the presence of muscle's force vector target coordinates (1/0 tells presence/absence). Muscle's force vector target is towards muscle's centroid. The force vector norm is esqual to the muscle's PCSA multiplied by (1- muscle's degeneration) shoulder_rotatorCuff_SC_forceVector_target_x: Muscle.forceVector gives the x coordinates of muscle's force vector target shoulder_rotatorCuff_SC_forceVector_target_y: Muscle.forceVector gives the y coordinates of muscle's force vector target shoulder_rotatorCuff_SC_forceVector_target_z: Muscle.forceVector gives the z coordinates of muscle's force vector target shoulder_rotatorCuff_SS_name: RotatorCuff.SS.name is the Muscle.name property of the RotatorCuff.SS object and is thus "SS" (DUPLICATE with variable name) shoulder_rotatorCuff_SS_segmentation_name: Muscle.segmentationName is the base name used to find segmentation related files shoulder_rotatorCuff_SS_slice_name: Muscle.sliceName is the base name used to find slice related files shoulder_rotatorCuff_SS_pcsa: Muscle.PCSA is the Physiological Cross Section Area of the muscle's segmentation (in cm^2). It's the area of the healthy muscle shoulder_rotatorCuff_SS_atrophy: Muscle.atrophy is the ratio of atrophied muscle area over healthy muscle area shoulder_rotatorCuff_SS_fat: Muscle.fat is the ratio of muscle area with fat infiltration over healthy muscle area shoulder_rotatorCuff_SS_osteochondroma: Muscle.osteochondroma is the ratio muscle area with osteochondroma over healthy muscle area shoulder_rotatorCuff_SS_degeneration: Muscle.degeneration is the sum of atrophy, fat, and osteochondroma ratios shoulder_rotatorCuff_SS_centroid: Muscle.centroid indicates the presence of muscle's segmentation centroid coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_SS_centroid_x: Muscle.centroid gives the x coordinates of muscle's segmentation centroid shoulder_rotatorCuff_SS_centroid_y: Muscle.centroid gives the y coordinates of muscle's segmentation centroid shoulder_rotatorCuff_SS_centroid_z: Muscle.centroid gives the z coordinates of muscle's segmentation centroid shoulder_rotatorCuff_SS_insertion: Muscle.insertion indicates the presence of muscle's insertion coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_SS_insertion_x: Muscle.insertion gives the x coordinates of muscle's insertion shoulder_rotatorCuff_SS_insertion_y: Muscle.insertion gives the y coordinates of muscle's insertion shoulder_rotatorCuff_SS_insertion_z: Muscle.insertion gives the z coordinates of muscle's insertion shoulder_rotatorCuff_SS_force_application_point: Muscle.forceApplicationPoint indicates the presence of muscle's force application point coordinates (1/0 tells presence/absence). Muscle's force application point is the contact point of the muscle's fibre on the humeral head sphere shoulder_rotatorCuff_SS_force_application_point_x: Muscle.forceApplicationPoint gives the x coordinates of muscle's force application point shoulder_rotatorCuff_SS_force_application_point_y: Muscle.forceApplicationPoint gives the y coordinates of muscle's force application point shoulder_rotatorCuff_SS_force_application_point_z: Muscle.forceApplicationPoint gives the z coordinates of muscle's force application point shoulder_rotatorCuff_SS_forceVector_origin: Muscle.forceVector indicates the presence of muscle's force vector origin coordinates (1/0 tells presence/absence). Muscle's force vector origin is muscle's force application point DUPLICATE shoulder_rotatorCuff_SS_forceVector_origin_x: Muscle.forceVector gives the x coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_SS_forceVector_origin_y: Muscle.forceVector gives the y coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_SS_forceVector_origin_z: Muscle.forceVector gives the z coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_SS_forceVector_target: Muscle.forceVector indicates the presence of muscle's force vector target coordinates (1/0 tells presence/absence). Muscle's force vector target is towards muscle's centroid. The force vector norm is esqual to the muscle's PCSA multiplied by (1- muscle's degeneration) shoulder_rotatorCuff_SS_forceVector_target_x: Muscle.forceVector gives the x coordinates of muscle's force vector target shoulder_rotatorCuff_SS_forceVector_target_y: Muscle.forceVector gives the y coordinates of muscle's force vector target shoulder_rotatorCuff_SS_forceVector_target_z: Muscle.forceVector gives the z coordinates of muscle's force vector target shoulder_rotatorCuff_IS_name: RotatorCuff.IS.name is the Muscle.name property of the RotatorCuff.IS object and is thus "IS" (DUPLICATE with variable name) shoulder_rotatorCuff_IS_segmentation_name: Muscle.segmentationName is the base name used to find segmentation related files shoulder_rotatorCuff_IS_slice_name: Muscle.sliceName is the base name used to find slice related files shoulder_rotatorCuff_IS_pcsa: Muscle.PCSA is the Physiological Cross Section Area of the muscle's segmentation (in cm^2). It's the area of the healthy muscle shoulder_rotatorCuff_IS_atrophy: Muscle.atrophy is the ratio of atrophied muscle area over healthy muscle area shoulder_rotatorCuff_IS_fat: Muscle.fat is the ratio of muscle area with fat infiltration over healthy muscle area shoulder_rotatorCuff_IS_osteochondroma: Muscle.osteochondroma is the ratio muscle area with osteochondroma over healthy muscle area shoulder_rotatorCuff_IS_degeneration: Muscle.degeneration is the sum of atrophy, fat, and osteochondroma ratios shoulder_rotatorCuff_IS_centroid: Muscle.centroid indicates the presence of muscle's segmentation centroid coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_IS_centroid_x: Muscle.centroid gives the x coordinates of muscle's segmentation centroid shoulder_rotatorCuff_IS_centroid_y: Muscle.centroid gives the y coordinates of muscle's segmentation centroid shoulder_rotatorCuff_IS_centroid_z: Muscle.centroid gives the z coordinates of muscle's segmentation centroid shoulder_rotatorCuff_IS_insertion: Muscle.insertion indicates the presence of muscle's insertion coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_IS_insertion_x: Muscle.insertion gives the x coordinates of muscle's insertion shoulder_rotatorCuff_IS_insertion_y: Muscle.insertion gives the y coordinates of muscle's insertion shoulder_rotatorCuff_IS_insertion_z: Muscle.insertion gives the z coordinates of muscle's insertion shoulder_rotatorCuff_IS_force_application_point: Muscle.forceApplicationPoint indicates the presence of muscle's force application point coordinates (1/0 tells presence/absence). Muscle's force application point is the contact point of the muscle's fibre on the humeral head sphere shoulder_rotatorCuff_IS_force_application_point_x: Muscle.forceApplicationPoint gives the x coordinates of muscle's force application point shoulder_rotatorCuff_IS_force_application_point_y: Muscle.forceApplicationPoint gives the y coordinates of muscle's force application point shoulder_rotatorCuff_IS_force_application_point_z: Muscle.forceApplicationPoint gives the z coordinates of muscle's force application point shoulder_rotatorCuff_IS_forceVector_origin: Muscle.forceVector indicates the presence of muscle's force vector origin coordinates (1/0 tells presence/absence). Muscle's force vector origin is muscle's force application point DUPLICATE shoulder_rotatorCuff_IS_forceVector_origin_x: Muscle.forceVector gives the x coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_IS_forceVector_origin_y: Muscle.forceVector gives the y coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_IS_forceVector_origin_z: Muscle.forceVector gives the z coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_IS_forceVector_target: Muscle.forceVector indicates the presence of muscle's force vector target coordinates (1/0 tells presence/absence). Muscle's force vector target is towards muscle's centroid. The force vector norm is esqual to the muscle's PCSA multiplied by (1- muscle's degeneration) shoulder_rotatorCuff_IS_forceVector_target_x: Muscle.forceVector gives the x coordinates of muscle's force vector target shoulder_rotatorCuff_IS_forceVector_target_y: Muscle.forceVector gives the y coordinates of muscle's force vector target shoulder_rotatorCuff_IS_forceVector_target_z: Muscle.forceVector gives the z coordinates of muscle's force vector target shoulder_rotatorCuff_TM_name: RotatorCuff.TM.name is the Muscle.name property of the RotatorCuff.TM object and is thus "TM" (DUPLICATE with variable name) shoulder_rotatorCuff_TM_segmentation_name: Muscle.segmentationName is the base name used to find segmentation related files shoulder_rotatorCuff_TM_slice_name: Muscle.sliceName is the base name used to find slice related files shoulder_rotatorCuff_TM_pcsa: Muscle.PCSA is the Physiological Cross Section Area of the muscle's segmentation (in cm^2). It's the area of the healthy muscle shoulder_rotatorCuff_TM_atrophy: Muscle.atrophy is the ratio of atrophied muscle area over healthy muscle area shoulder_rotatorCuff_TM_fat: Muscle.fat is the ratio of muscle area with fat infiltration over healthy muscle area shoulder_rotatorCuff_TM_osteochondroma: Muscle.osteochondroma is the ratio muscle area with osteochondroma over healthy muscle area shoulder_rotatorCuff_TM_degeneration: Muscle.degeneration is the sum of atrophy, fat, and osteochondroma ratios shoulder_rotatorCuff_TM_centroid: Muscle.centroid indicates the presence of muscle's segmentation centroid coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_TM_centroid_x: Muscle.centroid gives the x coordinates of muscle's segmentation centroid shoulder_rotatorCuff_TM_centroid_y: Muscle.centroid gives the y coordinates of muscle's segmentation centroid shoulder_rotatorCuff_TM_centroid_z: Muscle.centroid gives the z coordinates of muscle's segmentation centroid shoulder_rotatorCuff_TM_insertion: Muscle.insertion indicates the presence of muscle's insertion coordinates (1/0 tells presence/absence) shoulder_rotatorCuff_TM_insertion_x: Muscle.insertion gives the x coordinates of muscle's insertion shoulder_rotatorCuff_TM_insertion_y: Muscle.insertion gives the y coordinates of muscle's insertion shoulder_rotatorCuff_TM_insertion_z: Muscle.insertion gives the z coordinates of muscle's insertion shoulder_rotatorCuff_TM_force_application_point: Muscle.forceApplicationPoint indicates the presence of muscle's force application point coordinates (1/0 tells presence/absence). Muscle's force application point is the contact point of the muscle's fibre on the humeral head sphere shoulder_rotatorCuff_TM_force_application_point_x: Muscle.forceApplicationPoint gives the x coordinates of muscle's force application point shoulder_rotatorCuff_TM_force_application_point_y: Muscle.forceApplicationPoint gives the y coordinates of muscle's force application point shoulder_rotatorCuff_TM_force_application_point_z: Muscle.forceApplicationPoint gives the z coordinates of muscle's force application point shoulder_rotatorCuff_TM_forceVector_origin: Muscle.forceVector indicates the presence of muscle's force vector origin coordinates (1/0 tells presence/absence). Muscle's force vector origin is muscle's force application point DUPLICATE shoulder_rotatorCuff_TM_forceVector_origin_x: Muscle.forceVector gives the x coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_TM_forceVector_origin_y: Muscle.forceVector gives the y coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_TM_forceVector_origin_z: Muscle.forceVector gives the z coordinates of muscle's force vector origin DUPLICATE shoulder_rotatorCuff_TM_forceVector_target: Muscle.forceVector indicates the presence of muscle's force vector target coordinates (1/0 tells presence/absence). Muscle's force vector target is towards muscle's centroid. The force vector norm is esqual to the muscle's PCSA multiplied by (1- muscle's degeneration) shoulder_rotatorCuff_TM_forceVector_target_x: Muscle.forceVector gives the x coordinates of muscle's force vector target shoulder_rotatorCuff_TM_forceVector_target_y: Muscle.forceVector gives the y coordinates of muscle's force vector target shoulder_rotatorCuff_TM_forceVector_target_z: Muscle.forceVector gives the z coordinates of muscle's force vector target shoulder_rotatorCuff_imbalance_angle3_d: RotatorCuff.imbalanceAngle3D is the angle between the scapular medio-lateral axis and the force resultant of all the rotator cuff muscles' forces shoulder_rotatorCuff_imbalance_angle_orientation: RotatorCuff.imbalanceAngleOrientation is the angle between the scapular antero-posterior axis and the force resultant of the rotator cuff muscles projected on the scapular sagittal plane (superior is positive) shoulder_rotatorCuff_imbalance_angle_antero_posterior: RotatorCuff.imbalanceAngleAnteroPosterior is the angle between the scapular lateral-medial axis and the force resultant of the rotator cuff muscles projected on the scapular axial plane (posterior is positive) shoulder_rotatorCuff_imbalance_angle_infero_superior: RotatorCuff.imbalanceAngleAnteroPosterior is the angle between the scapular lateral-medial axis and the force resultant of the rotator cuff muscles projected on the scapular frontal plane (superior is positive) shoulder_humerus_insertionsRing_center: Humerus.insertionsRing.center indicates the presence of the coordinates of the center of the rotator cuff insertions ring on humerus (1/0 tells presence/absence). Rotator cuff insertions ring on humerus is measured with to insertions landmarks shoulder_humerus_insertionsRing_center_x: Humerus.insertionsRing.center gives the x coordinates of the center of the rotator cuff insertions ring on humerus shoulder_humerus_insertionsRing_center_y: Humerus.insertionsRing.center gives the y coordinates of the center of the rotator cuff insertions ring on humerus shoulder_humerus_insertionsRing_center_z: Humerus.insertionsRing.center gives the z coordinates of the center of the rotator cuff insertions ring on humerus shoulder_humerus_insertionsRing_radius: Humerus.insertionsRing.radius is the radius of the rotator cuff insertions ring on humerus shoulder_humerus_insertionsRing_normal_origin: Humerus.insertionsRing.normal indicates the presence of the origin of the normal vector of the rotator cuff insertions plane (1/0 tells presence/absence). Rotator cuff insertions plane contains rotator cuff insertions ring shoulder_humerus_insertionsRing_normal_origin_x: Humerus.insertionsRing.normal gives the x coordinates of the origin of the normal vector of the rotator cuff insertions plane shoulder_humerus_insertionsRing_normal_origin_y: Humerus.insertionsRing.normal gives the y coordinates of the origin of the normal vector of the rotator cuff insertions plane shoulder_humerus_insertionsRing_normal_origin_z: Humerus.insertionsRing.normal gives the z coordinates of the origin of the normal vector of the rotator cuff insertions plane shoulder_humerus_insertionsRing_normal_target: Humerus.insertionsRing.normal indicates the presence of the target of the normal vector of the rotator cuff insertions plane (1/0 tells presence/absence). Rotator cuff insertions plane contains rotator cuff insertions ring shoulder_humerus_insertionsRing_normal_target_x: Humerus.insertionsRing.normal gives the x coordinates of the target of the normal vector of the rotator cuff insertions plane shoulder_humerus_insertionsRing_normal_target_y: Humerus.insertionsRing.normal gives the y coordinates of the target of the normal vector of the rotator cuff insertions plane shoulder_humerus_insertionsRing_normal_target_z: Humerus.insertionsRing.normal gives the z coordinates of the target of the normal vector of the rotator cuff insertions plane shoulder_humerus_center: Humerus.center indicates the presence of the coordinates of the center of the humeral head (1/0 tells presence(absence). The humeral head is a sphere fitted to humeral head landmarks shoulder_humerus_center_x: Humerus.center gives the x coordinates of the center of the humeral head shoulder_humerus_center_y: Humerus.center gives the y coordinates of the center of the humeral head shoulder_humerus_center_z: Humerus.center gives the z coordinates of the center of the humeral head shoulder_humerus_radius: Humerus.radius is the radius of the humeral head. The humeral head is a sphere fitted to humeral head landmarks shoulder_humerus_shs_angle: Humerus.SHSAngle is the scapulo-humeral angle. It's the angle between the scapular medio-lateral axis and the vector that starts at glenoid center and ends at humerus center shoulder_humerus_shspa: Humerus.SHSPA is the angle between the scapular medio-lateral axis and projection on the scapular axial plane of the vector that starts at glenoid center and ends at humerus center (anterior is positive) shoulder_humerus_shsis: Humerus.SHSIS is the angle between the scapular medio-lateral axis and projection on the scapular frontal plane of the vector that starts at glenoid center and ends at humerus center (superior is positive) shoulder_humerus_shs_ampl: Humerus.SHSAmpl is the ratio of the norm of the projection on the scapular sagittal plane of the vector that starts at glenoid center and ends at humerus center over the humerus radius shoulder_humerus_shs_orient: Humerus.SHSOrient is the angle between the scapular antero-posterior axis and the projection on the scapular sagittal plane of the vector that starts at glenoid center and ends at humerus center shoulder_humerus_ghs_ampl: Humerus.GHSAmpl is the ratio of the norm of the vector from glenoid sphere center to glenoid center line (and perpendicular to it) over the humerus radius shoulder_humerus_ghs_orient: Humerus.GHSOrient is the angle between the scapular antero-posterior axis and the projection on the scapular sagittal plane of the vector from glenoid sphere center to glenoid center line (and perpendicular to it) shoulder_humerus_subluxation_index3_d: Humerus.subluxationIndex3D is the ratio of the sum of the norm of the projection on the glenoid postero-anterior line of the vector that starts at glenoid center and ends at humerus center plus the humerus radius over two times the humerus radius

Documentation

Should be added here:

• datastructure design
• class diagram

Files/Folders

Folders

• ./anatomy contains scripts used by Amira manual measurements and what looks like deprecated scripts that are now part of the Scapula class.
• ./ShoulderCase contains the class and scripts used to update and access to the data. See here how are organized class files and folders.
• ./ImportSCase contains the GUI used to import new data into the database.
• ./Generated_Amira_TCL_Scripts used to store TCL scripts. Not tracked by git.
• ./log contains log files.
• ./XLS_MySQL_DB contains scripts used to read data in .xls files and write in SQL database.
• ./upsert contains a script to update and insert data in a database. Looks like it's an external not LBO-made feature.

Files

• *config.json* is mandatory.
• *csv2xlxSCase.m* Matlab script to transform CSV files into XLS files
• *dicominfoSCase.m* Matlab script used after new SCase importations. Check utility in ImportSCase SOP
• *listSCase.m* Matlab script that create a list of SCases. Deprecated, should be replaced by ShoulderCaseLoader methods everywhere.
• *loadDicomCTscan* Looks like a worksheet. Probably removable.
• *measureSCase.m* Matlab Script used to update data. (check SOP for more details)
• *openConfigFile.m* Deprecated, should be replaced by the ConfigFileExtractor methods everywhere.
• *openLogFile.m* Deprecated, should be replaced by the Logger methods everywhere.
• *plotSCase.m* Deprecated, should be replaced by ShoulderCase.plot() method everywhere.
• *statSCase.m* Statistical analysis on all the cases. Probably deprecated.

Version

Current version is 1.0.5

Contributors

• Alexandre Terrier, 2012-now
• Julien Ston, 2012-2014
• Antoine Dewarrat, 2014-2015
• Raphael Obrist, 2015-2017
• Killian Cosendey, 2017
• Valérie Malfroy Camine, 2017
• Jorge Solana-Muñoz, 2018-2019
• Bharath Narayanan, 2018
• Paul Cimadomo, 2018
• Lore Hoffmann, 2019
• Nathan Donini, 2019
• Benoit Delecourt, 2019
• Amirsiavosh Bashardoust, 2020
• Matthieu Boubat, 2019-now
• Pezhman Eghbalishamsabadi, 2021-now

License

EPFL CC BY-NC-SA 4.0 Int.