[Insight-users] Load Vector Image with itk-Python

Mon Jun 27 03:43:23 EDT 2011

Well your file was written as a 4D image, the vector components being the
4th dimension.

It should not be hard to convert the 4th dimension to 62-component vectors
in 3D image. I do not have any code excerpts which would help you though.

HTH,
Dženan

On Mon, Jun 27, 2011 at 09:18, Oscar Esteban <oesteban at die.upm.es> wrote:

> Hi Gaëtan,
>
> "print r" gives me the next output:
>
> <C itk::SmartPointer<(itk::ImageFileReader<(itk::VectorImage<(unsigned
>> short,3u)>,itk::DefaultConvertPixelTraits<(unsigned short)>)>)> instance at
>> _8058f60600000000_p_itk__SmartPointerTitk__ImageFileReaderTitk__VectorImageTunsigned_short_3u_t_itk__DefaultConvertPixelTraitsTunsigned_short_t_t_t>
>
>
>  These are the headers:
>
>> $ mri_info DTI.nii.gz
>> Volume information for DTI.nii.gz
>>           type: nii
>>     dimensions: 128 x 128 x 44 x 62
>>    voxel sizes: 2.0000, 2.0000, 3.0000
>>           type: FLOAT (3)
>>            fov: 256.000
>>            dof: 0
>>         xstart: -128.0, xend: -128.0
>>         ystart: -128.0, yend: -128.0
>>         zstart: -66.0, zend: -66.0
>>             TR: 5043.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
>> 0.00 degrees
>>        nframes: 62
>>        PhEncDir: UNKNOWN
>> ras xform present
>>     xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =
>> 6.7797
>>               : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a =
>>  50.8135
>>               : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =
>>  21.9552
>> Orientation   : LAS
>> Primary Slice Direction: axial
>>
>> voxel to ras transform:
>>                -2.0000   0.0000   0.0000   134.7797
>>                 0.0000   2.0000   0.0000   -77.1865
>>                 0.0000   0.0000   3.0000   -44.0448
>>                 0.0000   0.0000   0.0000     1.0000
>>
>> voxel-to-ras determinant -12
>>
>> ras to voxel transform:
>>                -0.5000   0.0000   0.0000    67.3898
>>                -0.0000   0.5000  -0.0000    38.5932
>>                -0.0000  -0.0000   0.3333    14.6816
>>                 0.0000   0.0000   0.0000     1.0000
>
>
> $ mri_info test.nii.gz
>> Volume information for test.nii.gz
>>           type: nii
>>     dimensions: 128 x 128 x 44
>>    voxel sizes: 2.0000, 2.0000, 3.0000
>>           type: FLOAT (3)
>>            fov: 256.000
>>            dof: 0
>>         xstart: -128.0, xend: -128.0
>>         ystart: -128.0, yend: -128.0
>>         zstart: -66.0, zend: -66.0
>>             TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
>> degrees
>>        nframes: 1
>>        PhEncDir: UNKNOWN
>> ras xform present
>>     xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =
>> 6.7797
>>               : x_a =   0.0000, y_a =  -1.0000, z_a =   0.0000, c_a =
>>  -205.1865
>>               : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =
>>  21.9552
>> Orientation   : LPS
>> Primary Slice Direction: axial
>> voxel to ras transform:
>>                -2.0000   0.0000   0.0000   134.7797
>>                 0.0000  -2.0000   0.0000   -77.1865
>>                 0.0000   0.0000   3.0000   -44.0448
>>                 0.0000   0.0000   0.0000     1.0000
>> voxel-to-ras determinant 12
>> ras to voxel transform:
>>                -0.5000   0.0000   0.0000    67.3898
>>                 0.0000  -0.5000   0.0000   -38.5932
>>                -0.0000  -0.0000   0.3333    14.6816
>>                 0.0000   0.0000   0.0000     1.0000
>
>
> I'm sorry about the delay, but the list rejected previous emails containing
> image captures.
>
> Thanks. Best Regards,
>
>
>
> *______________________________________*
> *Oscar Esteban*
> PhD Student / Researcher
> Biomedical Image Technologies (Universidad Politécnica de Madrid)
>
> ETSI Telecomunicación (Lab. C203)
> Av. Complutense s/n - E-28040 Madrid (Spain)
> +34 915 495 700 ext.4234
>
>
>
> 2011/6/21 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
>>
>> Hi,
>>
>> Le 21 juin 11 à 17:52, Oscar Esteban a écrit :
>>
>>
>>  Hi all,
>>>
>>> I'm trying to load a 62 component vector image with itk using the Python
>>> wrapping. I executed this:
>>>
>>> 1: import itk
>>> 2: r = itk.ImageFileReader.VIUS3.New( FileName='DTI.nii.gz' )
>>>
>>
>> can you run
>>
>>  r.Update()
>>  print r
>>
>> at this point, and give us the result?
>>
>>
>>  3: im = r.GetOutput()
>>> 4: im.SetVectorLength(62)
>>> 5: w = itk.ImageFileWriter.VIUS3.New( im, FileName='test.nii.gz' )
>>> 6: w.Update()
>>>
>>> I also tried with im.SetNumberOfPixelCompoents( 62 )
>>>
>>>  But test.nii.gz only contains 1 component (and, I think it is written as
>>> if it were a 62-component file).
>>>
>>>
>> can you show us the header of that file, or even better, the actual file?
>>
>>
>>  How should I configure the FileReader to get the 62 components?
>>>
>>
>> It should read the image with the right number of components...
>>
>> Regards,
>>
>> Gaëtan
>>
>>
>>  How should I add new components?
>>>
>>> thanks. Best Regards,
>>>
>>> Oscar Esteban
>>>
>>>
>>> ______________________________**________
>>> Oscar Esteban
>>> PhD Student / Researcher
>>> Biomedical Image Technologies (Universidad Politécnica de Madrid)
>>>
>>> ETSI Telecomunicación (Lab. C203)
>>> Av. Complutense s/n - E-28040 Madrid (Spain)
>>> +34 915 495 700 ext.4234
>>> +34 659 639 123
>>>
>>> ______________________________**_______
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>>
>> --
>> Gaëtan Lehmann
>> Biologie du Développement et de la Reproduction
>> INRA de Jouy-en-Josas (France)
>> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
>> http://mima2.jouy.inra.fr  http://www.itk.org
>> http://www.bepo.fr
>>
>>
>
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