Import and update shoulderDB

Author: Alexandre Terrier, EPFL-LBO

Last update: 2019-02-19

Project description

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 Orthopedic Service of the University Hospital of Lausanne (CHUV-OTR), and the Radiological Department of the University Hospital of Lausanne (CHUV-RAD).

Matlab codes are tested with version 2018a. A config.txt file can be add in the main directory to locate the shoulderDB, which should be mounted locally. The config file is described and used by function openConfigFile.

Import

The import code is located in the sub-directory import. Its description is detailed there. It currently only work for Windows.

Update

The update of the shoulderDB is performed by the function measureSCase. This function should be run from current directory. The update function is based on the matlab class ShoulderCase.

Analyse

Currently, the analysis is limited to the graphical display of an entry (SCase) of the shoulderDB, with the function plotSCase.

Updated in 2018

• measureSCase.m: function to measure (and save) SCase (all or part of database)
• dicominfoSCase.m: function to get dicom info if SCase, to replace CT/infoCT
• listSCase.m: funcion to list SCase in /shoulder/data/
• plotSCase.m: function to plot SCase
• csv2xlsSCase.m: fonction to write a xls file from a csv file (for SCase)
• statSCase.m: script to perform statistical analyses on SCaseDB
• ShoulderCase: directory with classes related to the shoulder cases
• log: Directory with log files
• segmentation: Directory with functions related to the automatic segementaton of the CT

• 1. Oldies to be rewritten and/or removed
• anatomy: Directory with functions related to the anatomical analysis of the shoulder CT
• CT: Directory with functions for the reading of dicom field
• Generated_Amira_TCL_Scripts: Ditrectory with tcl scripts for Amira, created by matlab functions
• muscles: Directory with functions related to the analysis of muscle degeneration
• XLS_MySQL_DB: Directory with function related to the access to the MySQL database
• CylinderReferences_P403_AmiraCode.dat: To be checked

• 1. To be cleaned
• imageToolsExperimentation.m: ??
• Button 1 pushed.ps: ??
• LBODicomViewer.fig: ??
• LBODicomViewer.m: ??
• tempInfo.mat: ??

• 1. To do
• Link to the automated segmentation
• R/L identification at import
• Glenoid type automated identification
• Batch update
• Automated muscle degeneration
• Humerus bone quality
• Deltoid Tuberosity Index
• Restore link with MySQL
• Link with musculoskeletal model
• Web interface for import, update, and analyse

Main repository should not be divided (it seems to increase complexity without gain)

It might still be organized as folder, well documented in a README

• One folder for class ShoulderCase
• One folder for importSCase
• One folder for measureSCase
• One folder for anatomy (to be removed)
• One folder for CT (to be removed)
• One folder for muscles (integrated to class and measure, and removed)
• One folder for XLS_MySQL_DB (to be integrated to import and measure, and removed)
• One folder for other common files

• 1. Contributors
• Julien Ston
• Antoine Dewarrat
• Raphael Obrist
• Killian Cosendey
• Valérie Malfroy Camine
• Jorge Solana-Muñoz
• Bharath Narayanan
• Paul Cimadomo