[Paraview] Volume positioning

[Shawn Waldon]

Cory,

I think that reader is a plugin.  There is a plugin with NIFTI in the name
anyway.

HTH,
Shawn

On Mon, Nov 14, 2016 at 5:11 PM, Cory Quammen <cory.quammen at kitware.com>
wrote:

> Are you somehow opening these files in ParaView? I was not able to
> either gzipped or not, which is what I expect because ParaView does
> not have a Nifti reader to my knowledge.
>
> In Slicer, which can open these files, the volumes are reported to
> occupy the same space with an origin at (102.536, 106.413, 30.149).
>
> Please provide more details, step-by-step, about how you are viewing
> these files in ParaView.
>
> Thanks,
> Cory
>
> On Mon, Nov 14, 2016 at 10:29 AM, padraig <padraig.looney at gmail.com>
> wrote:
> > Attached are two volumes that have an overlap in paraview but the ITK
> volume
> > I find using the code below means there should be no overlap
> >
> >
> >
> >
> >
> > On 14/11/16 15:09, Cory Quammen wrote:
> >>
> >> MHA and NIFTII definitely contain position information that ParaView
> >> should read. Do you have any small-ish representative volumes you can
> >> share (privately with me if needed).
> >>
> >> On Mon, Nov 14, 2016 at 10:04 AM, padraig <padraig.looney at gmail.com>
> >> wrote:
> >>>
> >>> I have used MHA and NIFTII. I have converted the MHA into NIFTII using
> >>> both
> >>> c3d and ITK.
> >>>
> >>>
> >>>
> >>> On 14/11/16 14:59, Cory Quammen wrote:
> >>>>
> >>>> What file format are you using to load the volumes into ParaView? A
> >>>> number of formats support volume positioning, so this should be
> >>>> possible, unless you are loading a series of TIFF images, for example.
> >>>>
> >>>> Thanks,
> >>>> Cory
> >>>>
> >>>> On Mon, Nov 14, 2016 at 5:32 AM, padraig <padraig.looney at gmail.com>
> >>>> wrote:
> >>>>>
> >>>>> Dear list,
> >>>>>
> >>>>> I have been having problems with the positioning of volumes using
> >>>>> Paraview.
> >>>>> ITK tells me that, using,
> >>>>>
> >>>>>       IteratorType  it2( img_input,
> >>>>> img_input->GetLargestPossibleRegion()
> >>>>> );
> >>>>>
> >>>>>       it2.GoToBegin();
> >>>>>       ImageType::IndexType begin = it2.GetIndex();
> >>>>>       img_input->TransformIndexToPhysicalPoint(it2.GetIndex(),p0);
> >>>>>       it2.GoToEnd();
> >>>>>       --it2;
> >>>>>       img_input->TransformIndexToPhysicalPoint(it2.GetIndex(),p1);
> >>>>>       std::cout << p0 <<  p1 << std::endl;
> >>>>>
> >>>>>    two volumes I have have the positions
> >>>>>
> >>>>>
> >>>>> [-102.536, -106.413, 30.1491][102.512, 106.414, 177.564]
> >>>>>
> >>>>> and
> >>>>>
> >>>>> [-102.536, -106.413, 30.1491][102.512, 106.414, -117.265]
> >>>>>
> >>>>> When I load these into Paraview they occupy the same volume. In
> >>>>> Slicer3D
> >>>>> the
> >>>>> volumes are distinct as I expect above.
> >>>>>
> >>>>> Thanks
> >>>>> Pádraig
> >>>>> _______________________________________________
> >>>>> Powered by www.kitware.com
> >>>>>
> >>>>> Visit other Kitware open-source projects at
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> >>>>>
> >>>>> Please keep messages on-topic and check the ParaView Wiki at:
> >>>>> http://paraview.org/Wiki/ParaView
> >>>>>
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> >>>>>
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> >>>>
> >>>>
> >>>>
> >>
> >>
> >
>
>
>
> --
> Cory Quammen
> Staff R&D Engineer
> Kitware, Inc.
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
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>
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