Fig. 2

Automation of muscle-fat ROI on which ITSA was applied. (A) The Otsu algorithm was used to estimate a threshold that can be used to generate a binary mask of the muscle border. The OpenCV contours function is used to determine the coordinates of the estimated muscle border, represented by the red dashed line. (B) Snake algorithm is used to adjust and improve accuracy of the muscle border coordinates, represented by the blue dashed line. Mistakenly included a piece of subcutaneous fat in contact with the tibia, and marked for removal is in orange. (C) Bone, represented by grey, is segmented by expanding a seed point identified by maximum summated marrow signal across slices, merged with a void signal mask containing cortices and removed from the ROI, represented by white. (D) Final muscle mask represented by translucent red is overlaid on top of the raw MRI slice. (E) final cropped muscle ROI