[MINC-users] minctracc/masking bug?

[Andrew Janke]

Hi Alex,

To add to Claudes suggestions.

I see you are using mouse data, have you scaled the mouse data to
"human" size (~ x30) or have you modified all the parameters of
minctracc? If the second any problem you see will be exacerbated by
constants.

>From all the tests I have done over the years, minctracc does have a
very small undershoot and consistent bias. This is an artifact of the
way the minimisation works but is usually very very small and not a
problem. (thus my comments on scale).

I think your mask is too tight to use as a fit mask as you loose all
the nice edge information. Once the data starts heading off the edge
of the mask, minctracc has no idea where it is as it's no longer
factored into the minimsation function. Perhaps pre-mask your data
(with a blurred edge) and then fit using an expanded mask (5 or so
voxels? with mincmorph) such that minctracc can benefit from the edge
information.


a


On 8 May 2013 13:28, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Hello all,
>
> I have been chasing some strange behaviour of minctracc, and finally
> narrowed it down to something that I would say is a bug in the way
> minctracc deals with masks.
>
> I have generated symmetric (about x=0), blurred source- and target images,
> and a mask derived from the target image by a simple threshold (and thus
> also symmetric). If I run minctracc to register these two without masks, I
> end up with a deformation field that is by and large symmetric as well.
> However if I add the symmetric mask via the -model_mask option to an
> otherwise identical minctracc call, the resulting deformation becomes
> highly asymmetric, and drags the source image out. I am using mni_autoreg
> 0.99.6, libminc 2.1
>
> Summarized in this image:
>
> https://dl.dropboxusercontent.com/u/5709165/test_minctracc.jpg
>
> Row 1: source image
> Row 2: target image
> Row 3: target mask
> Row 4: deformation field magnitude without using mask
> Row 5: resampled source image with target mask outline
> Row 6/7: as rows 4/5, but after adding the target mask to minctracc
>
> Clearly the addition of the mask has a strong negative (and asymmetric)
> impact on the registration, while it seems it shouldn't have much of an
> effect at all.
>
> I have actually seen this behaviour before but was never able to pinpoint
> it so clearly. What appears to be happening is that masked registrations
> have a tendency to 'flow out' in a particular direction (towards the top
> right in coronal sections).
>
> Thoughts/suggestions, anyone?
>
> Thanks,
>
> -- Alex
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