[MINC-users] mincresample and linear 'deformations'

Wed Aug 17 16:36:57 EDT 2016

this is indeed the issue. the inverse of the source to target transform is required for mincresample or itk_resample to be able to identify the source voxels needed to interpret the intensity value for the voxel in the target volume.   unless the xfm transform is explicitly represented in its inverse form, mincresample uses an iterative scheme to invert the transform numerically.  Depending on the magnitude of the error to be minimized, it is possible that the greedy optimization procedure used by mincresample does not arrive at the proper value in the limited (n=50?) number of iterations allowed.  I’m not sure if the same procedure is used in itk_resample.
-Louis
> On 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