Details of gCNR computation

[nk7-98]

I’m trying to reproduce the gCNR metric exactly as used in the paper, and I want to confirm a few implementation details (especially around the ROIs and histogram/integration choices). I may have missed this in the repo/docs.

1) ROI construction details

From the paper: LV cavity vs myocardium, where myocardium is created by expanding the LV mask and subtracting the original mask.

• How much do you expand/dilate the LV mask to form the myocardium “ring” (kernel size / radius / iterations / structuring element)?
• Is dilation done in pixel space (fixed number of pixels), or relative to LV size (e.g., % of bbox / equivalent radius)?
• Do you apply any additional cleanup (closing/opening, hole filling, removing small components)?

2) LV “compression” + bottom truncation

The paper mentions compressing the LV ROI and truncating the bottom ~30% to reduce bias.

• What does “compress” mean operationally (erode? scale about centroid? shrink bbox? something else)?
• Is the 30% truncation based on:
  • LV mask height,
  • LV bounding box height,
  • image height,
  • or something else?
• Is “bottom” defined in image coordinates (increasing y), and do you apply truncation before/after dilation?

3) gCNR calculation specifics

I’m implementing gCNR as 1 - ∫ min(pA(x), pB(x)) dx using intensity distributions from the two ROIs.

• Are intensities computed on raw grayscale, or after any pre-processing (e.g., log compression, normalization, clipping)?
• Are distributions pA, pB computed via:
  • histogram (if so: #bins, bin range, density normalization),
  • KDE,
  • or something else?
• In the discrete implementation, do you compute:
  • sum(min(pA, pB)) * bin_width (integral approximation),
  • or just sum(min(pA, pB)) with already-normalized densities?
• Do you sample equal numbers of pixels from each ROI, or use all available pixels?
• Any special handling for frames where one ROI has too few pixels?

4) Where in the repo?

If this is already implemented:

• Could you point me to the exact file/function that constructs the ROIs and computes gCNR?

Thanks a lot — even a short pointer (or parameter values like dilation iterations/bins) would help me match your results.