pQCT Density Distribution

This plugin is designed to perform the following pQCT analyses:

1Rantalainen T, Nikander R, Heinonen A, Daly RM, Sievanen H. An open source approach for regional cortical bone mineral density analysis. J. Musculoskelet. Neuronal Interact. 2011 Sep;11(3):243-8.
2 Rantalainen T, Nikander R, Heinonen A, Cervinka T, Sievanen H, Daly RM. Differential Effects of Exercise on Tibial shaft Marrow Density in Young Female Athletes. J. Clin. Endocrinol. Metab., in press.

If you use this program, or the Stratec pQCT file format reader in your work, please cite the pertinent papers. Contact Timo Rantalainen for further details on the functionality of this plugin, to request features or report bugs.

How to use the Density Distribution analysis:

screenshot

How are the density distribution results aligned?

What do the result headings mean?

How to interpret the distribution results

Polar distribution
polar distribution
The mean of the three radial divisions within a given sector is reported as the density of that sector.
applies to:
Radial distribution
radial distribution
The mean of the thirty six 10 degree sector within a given anatomical ring is reported as the density of that ring.
applies to:


Polar and radial distribution
Are a combination of the above.
Radii distribution
radial distribution
Endo- and pericortical radii are given as the distance from the centroid of the marrow cavity to the endo- and pericortical border, respectively. The radii are calculated prior to peeling off the layers of pixels from endosteal and periosteal border.

Batch processing sample

N.B. the plug-in works with setBatchMode(true), but does not work with command line execution using the -batch option (or at least it didn't work when I tried to save the results window from command line executed macro with saveAs("Results", savePath+saveFileName), whereas the same macro run from command line with -macro worked as expected).

Acknowledgements

Footnote

*Cleaving is made by looking at the ratios of distances between two points along the edge and the shortest distance between the points. If the maximum of the ratio is high enough (3 was arbitrarily selected), the highest ratio points will be connected with a straigth line and one of the resulting edges will be discarded. E.g. for a circle, the maximum ratio is (pi/2)/d ~= 1.57 and for square the maximum ratio is 2/sqrt(2) = sqrt(2) ~= 1.41.

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