[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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