[MINC-users] mincresample and linear 'deformations'

Thu Aug 18 11:00:14 EDT 2016

Hi all,

Thanks for all your input. I'm still trying to figure out how to do what I
want, which is really to convert an arbitrary xfm into a deformation field
and have everything "just work", but I have some ideas that I'll pursue.

Bert, whatever the "right thing" is for mincresample, I'm pretty sure we
don't want to change its current behaviour; however, do you think it would
be feasible to add an option to it to control this? Would require
implementing what you suggest, and then adding a mincresample option to
insert the fill value as opposed to assuming '0 displacement'.

-- A

On Thu, Aug 18, 2016 at 10:37 AM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi all,
>
> The core of the issue from an implementation perspective is the function
> evaluate_grid_volume(), which is responsible for evaluating the grid
> transform for a point in world space. If the point lies outside the grid,
> this function silently returns zero for all of the displacements, so the
> point is not transformed and the original data is copied.
>
> It is trivial to modify this function to return an error indication if the
> point is outside the grid, so that the resampling process could "do the
> right thing", whatever that is...
>
>     -bert
>
> On Wed, Aug 17, 2016 at 8:38 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
> > Note that xfm2def does not have to calculate the sampling of the grid
> > from the input volume. You can define this output grid transform
> > sampling however you choose. This will solve your current problem, but
> > not all problems like this as the input xfm can be any xfm, which
> > itself may have a defined sampling (eg: def grid)
> >
> > I'd argue that what you are seeing is correct behaviour, I use this
> > feature of mincresample regularly when doing resampling of large (TB
> > scale) microscopy data. In this case you perform the registration on
> > chunks and then perform some magic to smoothly interpolate the
> > resulting deformation grids at the edges. Move edges, repeat, iterate.
> >
> >
> > a
> >
> > On 18 August 2016 at 08:05, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> > > Thanks, Louis, Vlad!
> > >
> > > I was getting to the same conclusion as Vlad's explanation; but that
> > still
> > > leaves me with the problem that two conceptually the same operations
> > > generate very different output:
> > >
> > > 1) voxel-wise transformation inversion fails (due to lack of support)
> =>
> > 0
> > > deformation => insert source image value
> > > 2) voxel-wise transformation ok/no inversion needed, points outside
> input
> > > image => insert 0 (or fill value).
> > >
> > > Not sure how to deal with this, unless by adding an option to
> > mincresample
> > > that would insert a 0 (fill value) when the transformation inversion
> > fails,
> > > as opposed to treating that as '0 transformation'. E.g.,
> > -fill_def_missing
> > > or some such.
> > >
> > > Alternatively, pad or transform the deformation grid lattice to allow
> for
> > > the inversion to work?
> > >
> > > -- A
> > >
> > >
> > >
> > > On Wed, Aug 17, 2016 at 5:24 PM, Vladimir S. FONOV <
> > vladimir.fonov at gmail.com
> > >> wrote:
> > >
> > >> xfm2def samples forward deformation in the space of input image.
> > >> Then when you apply the transformation, mincresample will try to
> > calculate
> > >> the inverse (numerically) in the space of output image.
> > >> So, if your transformation is a shift of 30mm the forward
> transformation
> > >> will have the same vector everywhere. However when inverse is
> > calculated,
> > >> mincresmple will reach the edge of the domain where vectors are
> defined
> > and
> > >> will take value of 0 for the translation outside of this domain -
> that's
> > >> why you have a sudden jump in the result.
> > >>
> > >> However, if you invert the original affine transformation,  and sample
> > it
> > >> for every voxel and then invert again (applying xfminvert to a
> > non-linear
> > >> transformation doesn't actually recompute the transform, only adds a
> > flag
> > >> that it have to be inverted), then when mincresample will run, it will
> > >> again apply the inverse of the transform, on top of inverted
> transform ,
> > >> negating the need to actually numerically recompute the
> transformation.
> > >>
> > >>
> > >>
> > >> On 2016-08-17 04:30 PM, Alex Zijdenbos wrote:
> > >>
> > >>> Right - I am aware of that, but I don't think that explains any of
> this
> > >>> though?
> > >>>
> > >>> On Wed, Aug 17, 2016 at 3:21 PM, Vladimir S. FONOV <
> > >>> vladimir.fonov at gmail.com
> > >>>
> > >>>> wrote:
> > >>>>
> > >>>
> > >>> When you apply "simple" forward transform, mincresample have to
> invert
> > it
> > >>>> internally.
> > >>>>
> > >>>> On Wed, Aug 17, 2016 at 1:50 PM, Alex Zijdenbos <
> zijdenbos at gmail.com>
> > >>>> wrote:
> > >>>>
> > >>>> These were simple forward resamplings. I experimented a bit with
> > various
> > >>>>> sequences of inversions, and found that this process:
> > >>>>>
> > >>>>> xfminvert( xfm2def( xfminvert( lin.xfm )))
> > >>>>>
> > >>>>> Yields a deformation grid that I can use in a forward resampling
> call
> > >>>>> and
> > >>>>> have it produce the same result as resampling using lin.xfm
> directly.
> > >>>>>
> > >>>>> Well I am puzzled.
> > >>>>>
> > >>>>> -- A
> > >>>>>
> > >>>>> For some more details, I tried these steps. Starting with
> > >>>>>
> > >>>>> param2xfm -translation 10 20 30 lsq3.xfm
> > >>>>> mincresample -use_input_sampling -transform lsq3_D.xfm in.mnc
> res.mnc
> > >>>>>
> > >>>>> I had done this:
> > >>>>>
> > >>>>> xfm2def -float [lattice from input volume] lsq3.xfm lsq3_D.xfm
> > >>>>> mincresample -use_input_sampling -transform lsq3_D.xfm in.mnc
> > res_D.mnc
> > >>>>>
> > >>>>> which "fails". Similarly, this:
> > >>>>>
> > >>>>> xfminvert lsq3_D.xfm lsq3_D_inv.xfm
> > >>>>> mincresample -use_input_sampling -transform lsq3_D_inv.xfm -invert
> > >>>>> in.mnc
> > >>>>> res_D_inv.mnc
> > >>>>>
> > >>>>> reproduces res_D.mnc (the "bad" result). Note that the xfminvert
> > call in
> > >>>>> this case only sets the "Invert" flag in the xfm, it doesn't
> actually
> > >>>>> invert the deformation field. But now, this:
> > >>>>>
> > >>>>> xfminvert lsq3.xfm lsq3_inv.xfm
> > >>>>> xfm2def -float [lattice from input volume] lsq3_inv.xfm
> > lsq3_inv_D.xfm
> > >>>>> mincresample -use_input_sampling -transform lsq3_inv_D.xfm -invert
> > >>>>> in.mnc
> > >>>>> res_inv_D.mnc
> > >>>>>
> > >>>>> Exactly reproduces res.mnc (the "good" result). So inverting the
> > linear
> > >>>>>
> > >>>> xfm
> > >>>>
> > >>>>> first, then converting it to a deformation and resampling with
> > >>>>> inversion,
> > >>>>> somehow does the right thing. Then this:
> > >>>>>
> > >>>>> xfminvert lsq3.xfm lsq3_inv.xfm
> > >>>>> xfm2def -float [lattice from input volume] lsq3_inv.xfm
> > lsq3_inv_D.xfm
> > >>>>> xfminvert lsq3_inv_D.xfm lsq3_inv_D_inv.xfm
> > >>>>> mincresample -use_input_sampling -transform lsq3_inv_D.xfm in.mnc
> > >>>>> res_inv_D_inv.mnc
> > >>>>>
> > >>>>> also does the right thing.
> > >>>>>
> > >>>>>
> > >>>>> On Wed, Aug 17, 2016 at 12:28 PM, Vladimir S. FONOV <
> > >>>>> vladimir.fonov at gmail.com> wrote:
> > >>>>>
> > >>>>> It looks like it's a problem of finding an inverse of the
> > >>>>>>
> > >>>>> transformation
> > >>>>
> > >>>>> outside of the domain where it's defined.
> > >>>>>>
> > >>>>>> When you apply the transform do you apply it directly or with
> > >>>>>> -invert_transformation ?
> > >>>>>>
> > >>>>>>
> > >>>>>> On 2016-08-17 11:54 AM, Alex Zijdenbos wrote:
> > >>>>>>
> > >>>>>> Hi all,
> > >>>>>>>
> > >>>>>>> I was always under the impression that one could turn a linear
> xfm
> > >>>>>>>
> > >>>>>> into
> > >>>>
> > >>>>> a
> > >>>>>
> > >>>>>> deformation field (using xfm2def), and that the application of the
> > >>>>>>> resulting deformation would be equivalent to using the linear
> xfm.
> > >>>>>>> However,
> > >>>>>>> mincresample disagrees.
> > >>>>>>>
> > >>>>>>> In the attached image, I've created a simpe lsq3 (param2xfm
> > >>>>>>>
> > >>>>>> -translation
> > >>>>
> > >>>>> 10
> > >>>>>>> 20 30) linear xfm, generated a 'deformation' field out of that
> > using
> > >>>>>>> xfm2def (same lattice as the input volume), and resampled the
> input
> > >>>>>>>
> > >>>>>> volume
> > >>>>>
> > >>>>>> with both xfms. Clearly, in the case of a 'deformation' xfm, the
> > >>>>>>>
> > >>>>>> volume
> > >>>>
> > >>>>> is
> > >>>>>
> > >>>>>> filled with unmodified voxels where I didn't expect them.
> > >>>>>>>
> > >>>>>>> This is tied to the sampling lattice of the deformation field,
> > which
> > >>>>>>>
> > >>>>>> in
> > >>>>
> > >>>>> this example is the same as the input volume. The resamplings are
> > done
> > >>>>>>> using -use_input_sampling btw. The two bottom rows show the
> > resampling
> > >>>>>>> using a padded input volume (no change), and using a
> 'deformation'
> > >>>>>>>
> > >>>>>> grid
> > >>>>
> > >>>>> with a larger extent (generated on a lattice that is 10 voxels
> larger
> > >>>>>>>
> > >>>>>> all
> > >>>>>
> > >>>>>> around).
> > >>>>>>>
> > >>>>>>> To pre-empt Vladimir, itk_resample behaves the same way ;-)
> > >>>>>>>
> > >>>>>>> Bug, or feature? I'd say the former.
> > >>>>>>>
> > >>>>>>>
> > >>
> > >> --
> > >> Best regards,
> > >>
> > >>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> > >> _______________________________________________
> > >> MINC-users at bic.mni.mcgill.ca
> > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >>
> > > _______________________________________________
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