[Paraview] Saving vti file to NifTI format - resulting geometry not correct

[Timothy Brown]

Hi Utkarsh,

Like you I suspect the NifTI/Analyze writers are not capturing the vtkImageData.

I will do the tests you suggest, and let you know results.

-Timothy

On Thu, 19 Sep 2013, Utkarsh Ayachit wrote:

> Timothy,
>
> If you try saving out a vti file, is everything working correctly?
> Seems to me the Nifti/Analyze writers are not respecting the spacing
> that vtkImageData is providing. I wonder if the writer was hard coded
> to use the meta-data provided by Nifti/Analyze readers to determine
> the spacing and hence could work if you opened and good Nifti file and
> then saved it out.
>
> Utkarsh
>
> On Wed, Sep 18, 2013 at 3:57 PM, Timothy Brown <timothy at cis.jhu.edu> wrote:
>> Hi ParaView users,
>>
>> I am converting vti data (MRI) to NifTI and am experiencing an error.  I
>> have attached an image that
>> illustrates the geometry, as well as what I think may be the issue.
>>
>> The voxels in the MRI were not isotropic.  The top row of the image shows
>> the head, the proportions
>> of which appear correct, as well as some of the Data Arrays information.
>> Note vtkVolumeSpacing
>> 0.9375, 2   - this matches the MRI acquisition.
>>
>> Using ParaView 4.0.1 (version included in graphic) I save data as NifTI. I
>> then loaded the NifTI, and
>> as you can see, colored pink on second row, it is compressed along one axis.
>> Note vtkVolumeSpacing
>> 1, 1 - I think this could be source of error.
>>
>> I also attempted to save to Analyze format with similar result.
>>
>> I'd appreciate any help/feedback,
>>
>> Many thanks,
>> -Timothy
>>
>>
>> Timothy Brown                 email: timothy at cis.jhu.edu
>> Computational Anatomist       phone: 410.516.7551
>> Center for Imaging Science    fax:   410.516.4557
>> Johns Hopkins University
>> 301 Clark Hall
>> 3400 N. Charles Street
>> Baltimore, MD 21218
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Timothy Brown                 email: timothy at cis.jhu.edu
Computational Anatomist       phone: 410.516.7551
Center for Imaging Science    fax:   410.516.4557
Johns Hopkins University
301 Clark Hall
3400 N. Charles Street
Baltimore, MD 21218