[MINC-users] minctracc/masking bug?

[Andrew Janke]

> In this particular set of tests I had adapted the minctracc
> parameters, but I also usually scale the brains up to roughly human
> size

ok. I know the phenogenomics crowd don't scale data and modify
minctracc parameters.

> (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)).

Guess I should mention that these are ex-vivo mouse brains imaged at
16.4T 30um isotropic.

> 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.

My gut feeling is that your step size is too small.

> 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).

The bias is directional but is very small. Within the noise floor and
also very likely well within the voxel discretisation and as such will
probably never be seen when using tools like minctracc. The
differences you are seeing are much larger than anything I have seen
before.



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