[MINC-users] problem with nu_estimate_np_and_em

[Andrew Janke]

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
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>



-- 
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