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

[Matthijs van Eede]

Hi Claude,

On 11-06-14 12:30 PM, Claude LEPAGE wrote:
> 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?
>
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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