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

Tue Jun 14 23:32:57 EDT 2011

Hi Claude,

On 2011-06-14, at 6:25 PM, Claude LEPAGE wrote:

> Hi Matthijs,
> 
> I looked at the scan. This is a mouse. :-)
> 

Yes :-) I don't work with anything else!

> 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.

I had no idea, thank you.

> 
> 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.
> 

Good to know that the old results are still okay. I'll sit down with Jason and John, so they can tell me a bit more about damping and to figure out what settings are appropriate for mouse brains.

Thanks very much!
Matthijs

> 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
>>> _______________________________________________
>>> MINC-development mailing list
>>> MINC-development at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> 
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