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

[Claude LEPAGE]

Hi Matthijs,

I looked at the scan. This is a mouse. :-)

The mask you sent me covers the entire head. You would get better
results with a tighter mask that includes only the brain, since there
are lots of hyperintense voxels in the tissues surrounding the
brain. These can affect the splines in N3.

The old N3-1.10, which you used, had a major bug in it in terms of
damping. For a masked human brain in stereotaxic space at 1mm, the 
damping was equivalent to about 3e-05 at a shrink factor of 4. (Note
that the old N3 was still good at those settings, so don't panic
about your old results.) This effective damping was normalized by
the number of sampling points in the mask in one hard-coded
coefficient. For a mouse with different voxel sizes, total brain size, 
shrink factor, you need to be careful about the meaning of damping in 
the old vs new N3. In the newer version, the formulation is now invariant
to sampling resolution and damping means damping. For example, resampling
at 0.5mm or 1.0mm will now give the same answer.

This is why you observed quite different results with 1.10 and 1.12. 

The instabilities in 1.11 or 1.12 were due to a too small damping
coefficient and likely also a too generous mask. You can also try
to add a bit of padding around the current field of view (use
autocrop -isoexpand). 

You should talk to Jason Lerch, also at Phenogenomics, for suitable
parameters for N3 (spline distance, for example). 8mm might be too
large a value for a mouse brain.

Good luck,

Claude

> >> 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?
> >
> It happens in about 40% of the cases (about 20 files so far). The masks 
> cover around 45% of the volume. I checked one of the files where this 
> happens, the mask touches one of the borders of the volume. (Maybe 
> interesting to note, is that in that area around the mask at that 
> border, the output file is very bright) The files are t2 weighted. The 
> resolution for these files are:
>
> image: unsigned short 0 to 65535
> image dimensions: zspace yspace xspace
>      dimension name         length         step        start
>      --------------         ------         ----        -----
>      zspace                    152        0.056         -4.2
>      yspace                    294        0.056        -8.19
>      xspace                    225        0.056        -6.27
>
>
> > 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).
>
> The commands I used are:
>
> nu_estimate -distance 8 -iterations 100 -stop 0.0001 -fwhm 0.15 -shrink 
> 4 -mask mask.mnc input.mnc  output.imp
>
> and
>
> nu_evaluate  -mapping  output.imp  input.mnc input_nu_evaluated.mnc
>
> Using -lambda 1.0e-6 made it a lot better. It almost fixed it, but you 
> can still see a slight "halo" on the outside of the corrected brain. I 
> have uploaded the input and output files to McGill, and actually saw 
> that the other version of N3 I was using was 1.10, not 1.11.
>
> Thanks very much!
> Matthijs
>
> > 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
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>