[MINC-users] problem with nu_estimate_np_and_em

Wed Oct 22 11:11:41 EDT 2008

Hi Andrew,
Sorry for the delay on this subject. A lot of work was pushed onto my stack. Now I have popped down to this issue again.
Nothing seems to be wrong with the input image. In fact, nu_correct is running fine on the same image on my 32bit ubuntu work station (minc deb installation).

se at rom:~$ nu_correct -version
Program nu_correct, built from:
Package MNI N3, version 1.10.1, compiled by rotor at mavis (i686-pc-linux-gnu) on 2008-05-17 at 08:01:11

The version that breaks is:

se at cerebrum01:~> nu_correct -version
Program nu_correct, built from:
Package MNI N3, version 1.10.1, compiled by se at cerebrum01 (x86_64-unknown-linux-gnu) on 2008-10-07 at 11:35:07

Are there 64bit issues with the nu_correct script?

Simon

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

> Hi Simon,
> 
> No idea if you are missing anything but I just tried this same game
> (although in truth I built packages and installed them) and it works
> for me.
> 
> Is there something amiss with the histogram of t1_native.mnc ?  The
> error output would seem to indicate a dud histogram.
> 
> a
> 
> On Tue, Oct 7, 2008 at 9:06 PM, Simon Fristed Eskildsen
> <se at hst.aau.dk> wrote:
> > 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
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> 
> 
> 
> -- 
> 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users