[MINC-users] proper use of nu_correct

[Jon Frederick]

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