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Transmural Analysis

Use cardio-analysis to extract transmural profiles from angle and FA maps generated by cardio-tensor.

Before You Start

  • In the config file, set WRITE_ANGLES = True and TEST = False.
  • Run cardio-tensor on your dataset.
  • Make sure outputs exist in OUTPUT_PATH:
    • HA, IA if ANGLE_MODE = ha_ia
    • EL, AZ if ANGLE_MODE = az_el
    • FA

Run the Tool

$ cardio-analysis ./parameters_example.conf

Useful options:

  • --N-slice: slice index to open first.
  • --N-line: number of sampled lines (default: 5).
  • --angle-range: angular spread in degrees (default: 20).
  • --image-mode: map shown first (HA, IA, EL, AZ, FA), depending on available outputs.

Quick Workflow

  1. Choose a slice with a clear myocardium wall.
  2. Click and drag from endocardium to epicardium.
  3. Set Angle range and Number of lines.
  4. Click Plot profile to see the transmural plot.
  5. Click Save Profile to export CSV.
Cardio-analysis GUI
Main GUI for profile definition and plotting.

The dataset used as an example here can be find at DOI

Warning

Choose the beginning and end of the line carefully. If the path includes trabeculae, cavity, or epicardium borders, the profile can be biased and difficult to interpret.

What the Plot Represents

  • X-axis: normalized transmural depth.
  • Y-axis: selected map value (HA/IA or EL/AZ, plus FA).
  • Multiple lines are averaged to get a smoother profile.
  • The 5 and 95 percentiles are plotted as a gray region around the average curve.

Example: Effect of Number of Lines

With 10 lines:

Transmural profile
Profile computed with low line count (more local variability).

With 500 lines:

Transmural profile
Profile computed with high line count (smoother average). The vertical red line shows where the compact myocardium starts.

Tips

  • Increase number of lines for smoother curves.
  • If the curve looks unstable, move the line to a cleaner wall region and re-plot.
  • Use the menu bar to change slice, switch map, and set plot limits.