[MINC-users] Issue with itk_convert_xfm

[Robert D. Vincent]

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
>