[MINC-users] problem with nu_estimate_np_and_em

[Simon Fristed Eskildsen]

Now that we are on the subject of nu_correct. I just compiled the latest of everything from packages/tgz on ubuntu 64bit --with-minc2, and nu_correct rewarded me with the following.

> nu_correct native/t1_native.mnc test.mnc
Bad buffer size 0 in set_loop_buffer_size
Bad buffer size 0 in set_loop_buffer_size
Bad buffer size 0 in set_loop_buffer_size
Transforming slices:..............................................Done
Bad buffer size 0 in set_loop_buffer_size
Bad buffer size 0 in set_loop_buffer_size
Bad buffer size 0 in set_loop_buffer_size
Bad buffer size 0 in set_loop_buffer_size
Must have one or bins per histogram
sharpen_volume: crashed while running volume_hist (termination status=256)
nu_estimate_np_and_em: crashed while running sharpen_volume (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)

Am I missing something?

Regards,
Simon
----- "Andrew Janke" <a.janke at gmail.com> wrote:

> > On Wed, Oct 1, 2008 at 5:41 AM, Tejaswini Ganapathi
> > <tejasvinee at gmail.com> wrote:
> >> 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"
> >
> > I reckon you have hit on a bug.  And amusingly I cannot find these
> two
> > executables that you are talking about on my system (or yorick!)
> > either. I suspect that you are using a little used part of the N3
> > package that has escaped inspection/execution for a long time.
> 
> 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.
> 
> 
> -- 
> Andrew Janke - andrew.janke at anu.edu.au
> Department of Geriatric Medicine, ANU
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
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