[MINC-development] N3-1.12 changed behaviour using a mask

[Claude LEPAGE]

Hi Matthijs,

> I have recently installed N3-1.12 together with ebtks 1.6.4, and I am 
> getting different results when I run a non uniformity correction with a 
> mask as compared to N3-1.11. In 1.12 the image intensities outside of 
> the mask are "blown up"; they are about an order of magnitude brighter 
> than the voxels within the mask. Are there changes between the two 
> versions that can cause this?
>
> Thanks in advance,
> Matthijs

At first sight, this is unexpected. Does this happen on all subjects
or only on one of them? How large is your field of view outside the 
mask? Does the mask touch the borders of the field of view? Is this 
a regular t1 image? If not, what type of scan is it?

In 1.12, I improved the convergence of the field outside the mask when
voxels are not 1mm. The number of iterations was tuned for 1mm voxels,
so 1.12 did not converge fully on much smaller voxel sizes and was
much slower (I'm working with histology data at 10 microns). 

What command did you use? You can try with slightly more damping
(default -lambda 1.0e-7 so try 1.0e-6). 

If you can send me a typical scan, you can dump it in:
    http://www.bic.mni.mcgill.ca/cgi-bin/BICupload
Provide the original scan, its mask, and the outputs you obtained with
1.11 and 1.12, together with instructions on how to reproduce the 
problem.

Yours,

Claude