project_CML_MRI_analysis

Overview

This is prototype code that provides a reasonable first estimate of septal wall thickness. It does not require user-intervention once the parameters have been set up.

Workflow

• Pull the latest repo of https://github.com/Campbell-Muscle-Lab/MATLAB_utilities
• Add it to your MATLAB path

Estimate LV area for each frame in each dicom file

• Run <repo>/MATLAB_code/extract_lv_properties.m

This function:

• cycles through all of the dicom files in the designated folder
  • cycles through all the frames in each dicom
  • tries to find the LV automatically
  • saves the LV area plus a few other metrics
• writes the data to file

Deduce the end-diastolic frame

• Run <repo>/MATLAB_code/deduce_ed_frame.m

This function:

• fits a polynomial to the area / frame data
• notes the frame with the largest area as the end diastolic frame
• calculates the r_squared value for the polynomial as a metric of the reliability of the approach
• write the data to file

Collate the wall thickness data

• Run <repo>/MATLAB_code/collate_data.m

This function:

• Cycles through all the dicom files
• Picks those with a reliable end diastolic frame (from the polynomial r_squared)
• Finds the LV again
• Uses profile analysis to estimate wall thickness data for a range of angles around the lv centroid
• Finds the longest sequence of angles where the profile analysis worked
• Assigns that sequence as the septum
• Writes the data to file