Q: All of my installed files (exe files) are in /usr/bin. Infact nu_correct,nu_estimate and nu_evaluate work fine. I’m having this problem only with nu_estimate_np_and_em

Ive tried the following on the shell command line,$ nu_estimate_np_and_em -normalize_field -save_fields -mask mask.mnc breast.mnc fields_time.mnc

nu_estimate_np_and_em: couldn’t find program “class_statistics” nu_estimate_np_and_em: couldn’t find program “estimate”
http://www.bic.mni.mcgill.ca/pipermail/minc-users/2008-October/002228.html

A: An update on this one, I have been in contact with the original Author of N3 (John Sled) and he tells me that these errors are due to the script in question trying to use another version of intensity correction that is based upon the EM algorithm. nu_estimate_np_and_em was written to compare the two methods. He tells me that it is likely not worth resurrecting the EM method (although I did find the code hidden deep in an archive — Thanks Mike and Sylvain). So the “fix” for now is to not use the -mean or -tag options and be sure to use a -sharpen x y option.

The default option for sharpen is:

  -sharpen 100 0.01

Mind you this he tells me is why nu_correct and nu_estimate were written as they are simply wrappers for the bits of code in question that make sure that only the NP method (or N3) is used.

There is now a “fix” in CVS for this that should make the next release that will warn users of this.