I think that you can start using Miji to use Fiji with Matlab.
http://fiji.sc/Mijihttp://www.mathworks.com/matlabcentral/fileexchange/47545-mij--a-java-package-for-bi-directional-communication-and-data-exchange-from-matlab-to-imagej-fijiAbout the bone, can you please attach some images to better understand the problem?
Thank you,
Emanuele
Image Analyst @Ifom-IEO research campus -MI-