Author: Alexandre Terrier, EPFL-LBO
Last update: 2019-01-28
In the 2018 version, adding a SCase is done in 3 steps:
- 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.
- Perform some tasks in amira, according to SOP. (Might be done by Matlab?, still manually)
- Use measureSCase to perform measurements and produce file data/Excel/xlsFromMatlab/anatomy.csv (and/or xls)
- 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: ??
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
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