[MINC-users] rawtominc & nu_correct difficulties

[Audette, Michel]

Dear Vladimir, 

your suggestion seemed to do the trick, in terms of allowing nu_correct to process the image. However, it seems as though the correction underestimates what is actually a pretty severe nonuniformity. 

I can forward to anyone my minc volume, in case someone has an idea what to tweak. 

Thanks to Andrew, for your suggestion too. I was about to try that next. Do you think that the byte-vs-short issue is responsible for this underestimation?

Cheers, 

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Vladimir FONOV
Sent: Wed 8/1/2007 2:39 PM
To: MINC users mailing list
Subject: Re: [MINC-users] rawtominc & nu_correct difficulties
 
Hello ,

> On 8/1/07, Audette, Michel <Michel.Audette at medizin.uni-leipzig.de> wrote:
> > Dear folks,
> >
> > subsequent to yesterday's discussion, I'm trying to run nu_correct on a volume converted from tiff to raw to minc, as the volume has significant intensity inhomogeneity, but there is apparently something that I've neglected to do in the conversion. See below, where I've used some of Vladimir Fonov's parameters.
> >
> > maudette at icaw164201:~/data/ENTdata> cat HumanS16885_Stack.gray | rawtominc -clobber -byte -range 0 255 -orange 0 255 -real_range 0 255 -unsigned -zyx HumanS16885_Stack2.mnc 340 366 489
> > maudette at icaw164201:~/data/ENTdata> nu_correct  HumanS16885_Stack2.mnc HumanS16885_Stack2_nuc.mnc
> > nu_estimate_np_and_em: crashed while running volume_stats (termination status=11)
> > nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
> >

Maybe you have to specify real coordinates:

rawtominc ........ -xstart <X> -ystart <Y> -zstart <Z> -xstep <...>
-ystep <...> -zstep <...>

-- 
Best regards,
 Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
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