[MINC-users] mincresample and linear 'deformations'

[Alex Zijdenbos]

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
> _______________________________________________
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>