[MINC-users] Issue with itk_convert_xfm

[Simon Eskildsen]

For what it's worth: I have had similar problems with converting back and
forth between nifti and minc. I often find myself tailoring the conversion
(flipping, changing dim order / step sign) whenever I need to go back and
forth. itk_convert and nii2mnc usually give different results. Quite a
nuisance.

On Fri, Jan 15, 2016 at 2:00 PM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> I'll check for issues with the minc to nifti converters...
>
>
> On Thu, Jan 14, 2016 at 5:46 PM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com
> > wrote:
>
> >
> > This code works properly:
> >
> >
> >
> > make_phantom phantom.mnc
> > param2xfm -translation 10 10 10 trans.xfm
> >
> > # Apply the xfm
> > mincresample -use_input_sampling -invert_transform -transform trans.xfm
> > phantom.mnc out.mnc -clob
> >
> > # Do the same transform in nifti space
> > itk_convert_xfm trans.xfm trans.mat --clob
> >
> > itk_convert phantom.mnc phantom.nii --clob
> > antsApplyTransforms --input phantom.nii \
> > --transform trans.mat \
> > --output out.nii \
> > --reference-image phantom.nii
> >
> > itk_convert out.nii thru_nifti.mnc --clob
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On 16-01-14 05:04 PM, Andrew Wood wrote:
> >
> >> Hi Vlad,
> >>
> >> I think I didn't explain my issue correctly. Let me
> >> add -invert_transformation to my mincresample invocation and try again.
> >>
> >>
> >> Here are the commands that I think illustrates a problem:
> >> $ make_phantom phantom.mnc
> >> $ param2xfm -translation 10 10 10 trans.xfm
> >>
> >> # Apply the xfm
> >> $ mincresample -use_input_sampling -*invert_transformation* -transform
> >> trans.xfm phantom.mnc out.mnc
> >>
> >> # Do the same transform in nifti space
> >> $ itk_convert_xfm trans.xfm trans.mat
> >> $ mnc2nii phantom.mnc phantom.nii
> >> $ antsApplyTransforms --input phantom.nii \
> >> --transform trans.mat \
> >> --output out.nii \
> >> --reference-image phantom.nii
> >>
> >> # Open result in a minc+nifti-friendly viewer, or convert back to minc
> >> $ nii2mnc out.nii thru_nifti.mnc
> >> $ register out.mnc thru_nifti.mnc
> >>
> >>
> >>
> >> As far as I can tell, out.mnc and thru_nifti.mnc should be identical,
> but
> >> they clearly are not.
> >>
> >> Best,
> >> Andrew
> >>
> >> On Thu, Jan 14, 2016 at 4:39 PM, Vladimir S. FONOV <
> >> vladimir.fonov at gmail.com
> >>
> >>> wrote:
> >>>
> >>
> >> antsApplyTransforms is basically equivalent to mincresample
> >>> -invert_transformation
> >>>
> >>> On Thu, Jan 14, 2016 at 3:18 PM, Andrew Wood <andrew at biospective.com>
> >>> wrote:
> >>>
> >>> Hi all,
> >>>>
> >>>> I came across a set of transforms generated by ANTs which I've been
> >>>>
> >>> trying
> >>>
> >>>> to convert and use on minc volumes. There seems to be a bug in one or
> >>>>
> >>> more
> >>>
> >>>> of the tools I'm using, where applying the transforms to nifti volumes
> >>>>
> >>> does
> >>>
> >>>> not give the same result as applying them to minc volumes.
> >>>>
> >>>> Likely culprits:
> >>>> - itk_convet_xfm
> >>>> - mnc2nii or nii2mnc
> >>>> - antsApplyTransforms
> >>>> - mincresample
> >>>>
> >>>> Somewhere along the way, several components of the transforms get
> >>>>
> >>> inverted.
> >>>
> >>>> Here is an example:
> >>>>
> >>>> $ make_phantom phantom.mnc
> >>>> $ param2xfm -translation 10 10 10 trans.xfm
> >>>>
> >>>> # Apply the xfm
> >>>> $ mincresample -use_input_sampling -transform trans.xfm phantom.mnc
> >>>>
> >>> out.mnc
> >>>
> >>>>
> >>>> # Do the same transform in nifti space
> >>>> $ itk_convert_xfm trans.xfm trans.mat
> >>>> $ mnc2nii phantom.mnc phantom.nii
> >>>> $ antsApplyTransforms --input phantom.nii \
> >>>> --transform trans.mat \
> >>>> --output out.nii \
> >>>> --reference-image phantom.nii
> >>>>
> >>>> # Open result in a minc+nifti-friendly viewer, or convert back to minc
> >>>> $ nii2mnc out.nii thru_nifti.mnc
> >>>> $ register out.mnc thru_nifti.mnc
> >>>>
> >>>> The result of this for me is that the z component of the transform was
> >>>> inverted, but the x and y components are OK.
> >>>>
> >>>>  From experimenting with various simple transforms, it seems that the
> >>>> following components are inverted:
> >>>>     - z translation
> >>>>     - z rotation
> >>>>     - x,y,z scale
> >>>>     - x shear
> >>>>
> >>>> Has anybody else noticed or dealt with this before?
> >>>>
> >>>> Thanks,
> >>>> Andrew
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>> _______________________________________________
> >> 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
>