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R8218/README.md
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# Description of folder /shoulder/methods/matlab/database
Author: Alexandre Terrier, EPFL-LBO
Last update: 2019-01-28
## Comments
In the 2018 version, adding a SCase is done in 3 steps:
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.
2. Perform some tasks in amira, according to SOP. (Might be done by Matlab?, still manually)
3. Use measureSCase to perform measurements and produce file data/Excel/xlsFromMatlab/anatomy.csv (and/or xls)
## Updated
* 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: ??
## 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
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