diff --git a/README.md b/README.md index 753baef..95a1b87 100755 --- a/README.md +++ b/README.md @@ -1,55 +1,77 @@ -# Description of folder /shoulder/methods/matlab/database +# Import and update shoulderDB Author: Alexandre Terrier, EPFL-LBO -Last update: 2019-01-28 +Last update: 2019-02-19 -## Comments -In the 2018 version, adding a SCase is done in 3 steps: +## 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). -1. Import CT - - Use CT/dicomCopier (to be updated) to move CT from pending to N/P. Update ShoulderDatabase.xlsx - - Use dicominfoSCase to get CT info and produce file data/Excel/xlsFromMatlab/CTdicomInfo.csv (and/or xls). (2 could be merged with 1) - - Not yet mendatory, run the automatic segmentation. Could be done after or before 3, or even merged with 1. +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. -2. Perform some tasks in amira, according to SOP. (Might be done by Matlab?, still manually) +## Import +The import code is located in the sub-directory **import**. Its description is detailed there. It currently only work for Windows. -3. Use measureSCase to perform measurements and produce file data/Excel/xlsFromMatlab/anatomy.csv (and/or xls) +## 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 +## 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 ## 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 ## To be cleaned * imageToolsExperimentation.m: ?? * Button 1 pushed.ps: ?? * LBODicomViewer.fig: ?? * LBODicomViewer.m: ?? * tempInfo.mat: ?? +## To be done +* 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 +* 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 * 1 folder for class ShoulderCase * 1 folder for importSCase * 1 folder for measureSCase * 1 folder for anatomy (to be removed) * 1 folder for CT (to be removed) * 1 folder for muscles (integrated to class and measure, and removed) * 1 folder for XLS_MySQL_DB (to be integrated to import and measure, and removed) * 1 folder for other common files + +## Contributors +* Julien Ston +* Antoine Dewarrat +* Raphael Obrist +* Killian Cosendey +* Valérie Malfroy Camine +* Jorge Solana-Muñoz +* Bharath Narayanan +* Paul Cimadomo