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Interpolation

This may be x4 in each direction in-plane, or to 0.25 mm pixels (using the original resolution read in from the NII header). The convention at the Steiner Suite has been to use the former option for Genscan images x4, and the latter for UKBB data.

Defining perimeter from a segmentation

This proceeds in stages, as depicted in the Processing Workflow PDF.

• First, slices with too few pixels in the segmented blood pool are discarded.
• Next, an attempt is made to draw a perimeter outside the blood pool and wholly within the myocardium, in the remaining slices.
• Failing that, the border pixels of the blood pool are counted, and if enough of these are in contact with the myocardium, then a "contingent" ROI is formed from the intersection of the blood pool and the convex hull of the myocardium.
• If even this operation fails to return a usable ROI, an error condition is reported; however, this could only occur in principle, in the event of a gross failure at the segmentation step (an inside-out mis-labelling of the blood pool and the myocardium), and we have never seen it in practice.

Slice selection for analysis

All slices actually present in the image grayscale stack are analysed, and the results reported; however, there is an option to keep or discard the first and slices in the calculation of the global, basal and apical summary statistics.

Error codes

For slices actually present in the grayscale image stack:

• Meagre blood pool (quite common, depending on the initial processing threshold).
• Sparse myocardium (uncommon).
• No ROI created (conceivable in principle, but never seen in practice).
• FD measure failed (seen occasionally).

In addition:

• The statistics summary file has room for 20 slices, but the FD for those not actually present is reported as NaN.
• If an attempt is made to process a sub-folder which is missing either the grayscale image or segmentation, then the sub-folder name is written to the summary file, but the rest of the data row is set to white space. This signals an error without disrupting the workflow for multiple datasets.

Fractal dimension analysis

Once a perimeter has been established, the interior is used to select a region for a two-stage fractal-dimension analysis. First, a Bias-Field Elimination/Level-Set Estimation step creates an edge-detected contour within the working perimeter, and second, the FD is estimated using a multi-resolution box-counting algorithm. A failure at this stage results in an error condition; otherwise, the FD for the slice is written to the summary master file. At all events, processing advances smoothly to the next slice or the next folder. Two progress bars display the number of folders processed so far, and the number of slices in the current folder.

A comprehensive audit trail, consisting of images, plots and small CSV files, is created for each slice in its own output directory. Filenames are self-explanatory and document the processing for each slice, including any error conditions.