[MINC-users] mincresample and linear 'deformations'

[Alex Zijdenbos]

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.
> > >>
> > >> Thoughts?
> > >>
> > >> -- A
> > >>
> > >> ​
> > >>  lsq3_verify.png
> > >> <https://drive.google.com/file/d/0B5fOtqpIs4sKd0U0UVQ3al95WT
> > >> A/view?usp=drive_web>
> > >> ​
> > >> _______________________________________________
> > >> MINC-users at bic.mni.mcgill.ca
> > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >>
> > >>
> > >
> > > --
> > > 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
> > >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>