[Insight-users] Load Vector Image with itk-Python
Dženan Zukić
dzenanz at gmail.com
Tue Jun 28 03:35:17 EDT 2011
I never used python. I cannot help you there :(
On Mon, Jun 27, 2011 at 18:32, Oscar Esteban <oesteban at die.upm.es> wrote:
> Hi Dženan,
>
> Thank you very much for your answer, I will try it as 4D image. Probably it
> will work :)
>
> The problem is that I selected the component vector because I didn't find a
> way to add a new timestep to a 4D image in ITK-Python :( . Any clue?
>
> Bests, and thank you all again :)
>
> 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
>
>
>
> On 27 June 2011 09:43, Dženan Zukić <dzenanz at gmail.com> wrote:
>
>> 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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>>>>>
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>>>>>
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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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>>> Visit other Kitware open-source projects at
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>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
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>
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