[Paraview] Volume positioning

[Cory Quammen]

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
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>>>>
>>>>
>>>>
>>
>>
>



-- 
Cory Quammen
Staff R&D Engineer
Kitware, Inc.