[MINC-users] minctracc/masking bug?

Thu May 9 23:31:50 EDT 2013

Alex,

You got me curious here.

If you mirror your image in x (param2xfm -scales -1 1 1) and perform
the registration to the (symmetric) model, do you still observe the
same bias? Has the bias been mirrored? Mirror the mask as well.

I don't know if this can be related, but autocrop causes a shift in
world coordinates. If this shift can be in autocrop, it can be in 
other minc tools. To keep it simple, use autocrop -isostep 0.5 
on a file of labels. You will see that the xspace:start position is
the same before and after. However, the start position is centroid
based in voxel space. If the new voxel is 0.5mm instead of 1mm, its
centroid will be shifted 0.25mm to the left. The formula to preserve
world coordinates is:
  new_start = old_start - 0.5*old_voxel_size + 0.5*new_voxel_size

Now, let's say you are resampling a displacement field from a 4mm grid 
to a 2mm grid... 

For my work on the bigbrain (histology at 10 microns), I have the 
following notes in my alignment script for non-linear registration:

# 5 - Non-linear alignment of current histo_mid to average position
#     avg_id.mnc of id_prev and id_next. NEVER use a mask because
#     it will cause misregistration near borders where the target
#     mask differs from the source slice.

# 7 - Full non-linear transform from original histo_mid to avg in previous step.
#     NOTE: Do NOT use a mask here with -init_xfm. There is a BUG in minctracc.

Here, the slices are pre-masked, but I don't use a mask during
registration. minctracc evaluates the displacement field everywhere
in the field of view. In the rare cases I use a mask, I use only the
target mask (without source mask) and I activate the mask only on
the smallest grid. I don't remember the details for this approach,
but I do remember that I had to do this for minctracc to be reliable.

Claude

> 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
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
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> >
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