[MINC-users] minctracc/masking bug?

[Alex Zijdenbos]

Thanks, Claude - looking at your suggestions (and at the minctracc
source code). In the mean time, I performed some phenomenological
experiments that I thought would be interesting to share. Here's what
I did:

- take 100 subjects, already in linear template (stx) space
- register these with an nlfit*-like process, up to 4mm grid step
size, to a symmetric template+mask
- flip the subject image and its mask about x=0, repeat the registration
- flip the resampled image and the grid from the registration again about x=0
- calculate the magnitude of the difference between the 'normal' and
'2xflipped' grid (per subject)

- average the 'normal' and '2xflipped' grid files across subjects
- calculate the magnitude of the difference between the average
'normal' and average '2xflipped' grid files

In the end, what I am left with is the asymmetry in the deformation
field(s) due solely to the registration process; if minctracc were
unbiased, these difference images would be 0. This image:

https://dl.dropboxusercontent.com/u/5709165/def_diff_mag.jpeg

shows the average of the non-linearly registered images over these 100
subjects; and the magnitude of the difference of the average
deformation estimated 'normally' and '2xflipped'. Note that the in
these population averages, the maximum deformation magnitude is 2.86;
in individual subjects, the max magnitude of the deformation
difference is typically in the 10-20 range. In other words, the
asymmetry in the estimated deformation field purely caused by the
methodology, can be as high as 20mm.

I'd be very happy if somebody could run a similar experiment, if
anything on a single subject; just to confirm that I didn't do
anything fundamentally wrong somewhere (which would be great).

-- A





On Fri, May 10, 2013 at 2:00 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
> Alex,
>
>> So far the only explanation I can think of, is that the optimizer
>> follows a particular/fixed trajectory through the parameter space,
>> implicitly generating an "expansion force" in a particular direction
>> that can go unchecked given the right set of circumstances (a
>> particular mask being one of them). Anyways, still testing different
>> parameters, will report on what I find.
>
> Can you do only 1 iteration of minctracc? Is symmetry preserved?
> Try this 1 iteration with and without smoothing (set smoothing weight
> to zero). Still symmetric?
>
> Your suggestion above sounds like the result could be influenced by
> the order of the loops. This is a common mistake in numerical analysis.
> For example:
>    vec[i] = some_function( vec[i-1], vec[i], vec[i+1] );
> When you process vec[i+1], the value of its previous neighbour has
> changed, so running the loop forward/backward gives a different answer.
> You can check the code for something like this (good luck).
>
> Have you tried minctracc 0.99.3? Have you tried mincreshape to change
> the x,y,z ordering? I doubt this will have an impact on the results.
>
> Claude
>
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