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

Oscar Esteban oesteban at die.upm.es
Mon Jun 27 03:18:26 EDT 2011


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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