[MINC-users] minctracc/masking bug?

[Alex Zijdenbos]

Hi Andrew,

In this particular set of tests I had adapted the minctracc
parameters, but I also usually scale the brains up to roughly human
size (by the way, the mice down under must be really tiny, or the
humans very large - I always use a scale of ~12x for mouse-growing (in
each dimension)). However I tried the same registration after scaling
using a vanilla nlfit series, and got very similar results.

The mask size definitely has an impact here; if I grow the mask, at
some point the problem will by-and-large go away. There also appears
to be a strong dependency on the grid step size; various experiments
still running.

When you mention a bias, are you talking about a directional bias?
Because that is what I see coming back in all my experiments - and it
has me rather concerned as a consistent directional bias in image
deformation would likely cause bias in population analyses, especially
for anybody looking at L/R differences. I suppose one solution to this
would be to run all deformations twice, once 'normal' and once
'flipped'; but ideally this wouldn't be necessary (and I suspect not
many people are actually doing this).

-- A


On Wed, May 8, 2013 at 10:41 PM, Andrew Janke <a.janke at gmail.com> wrote:
> 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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