[MINC-users] proper use of nu_correct

[Jason Lerch]

First question: what version of N3 are you using? We did have some bugs 
recently, so you should make sure to grab the latest sources of the 
web-age - I believe the most up-to-date release is 1.09. Let us know if 
the problems you are encountering are indeed with that version.

Cheers,

Jason

On Sep 12, 2004, at 6:47 PM, Jon Frederick wrote:

> Hello,
> We're hoping someone can explain what we're doing wrong with 
> nu_correct.
>
> We introduced an artificial bias field into a 256x256x256 MRI image, 
> that increased by one (on a pixel intensity scale of zero to 256) with 
> each coronal slice (only in the masked area of the brain... the 
> unmasked area remained black or zero).
>
> We ran
> nu_correct -iterations 150 -stop .00001 temp.mnc -clobber temp-corr.mnc
>
> After converting the output image back to raw and putting our header 
> back on, the bias field could still easily be seen in the sagittal or 
> axial views.
>
> nu_estimate of the uncorrected file returns c.v of field change=7.6 
> e-5. For the corrected file, the value is 2.5 e-5. Are both of these 
> numbers rather small? John Sled's dissertation shows graphs with 
> c.v.'s on the scale of 0.01.
>
> Could the problem be related to our conversion to minc format? I.e.,
> dd conv=swab if=temp.raw | rawtominc -coronal -byte -unsigned -ystep 1 
> -zstep 1 -xstep 1 -mri -origin 0 0 0 -range 0 255 -real_range 0 255 
> -clobber temp.mnc 256 256 256
>
> Apologies in advance if this is a really dumb question.
>
> Thanks in advance,
>
> Jon Frederick, Ph.D.
> University of Texas Health Science Center
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