Antwort: Re: Antwort: Re: [Insight-users] Inserting 2D image in 3D volume

Tue Dec 5 08:00:23 EST 2006

Hi Gaetan,

thanks for extending the SliceBySliceImageFilter to multiple inputs (and
sorry for my late response to your mail). Right now I solved my problem
without your filter, simply by extracting single slices from the source
voulumes, registering them and finally pasting the transformed slices in
the target volume. This works fine but requires indeed a considerable
amount of programming. So the more elegant solution would be certainly to
use the SliceBySliceImageFilter, however I'm still not sure, whether it is
applicable for my problem. There are 2 little problems I see.

1. Registration, i.e. the transformation of the moving image, requires a
filter chain. First, one needs the registration method (which has to be
assigned an optimizer, a transformation etc. ) and then a resampling filter
which uses the transformation and the obtained parameters to transform the
moving image. How would one pass such a filter chain to the
SliceBySliceImageFilter?

2. itk::ImageRegistrationMethod has methods SetFixedImage and
SetMovingImage which set attributes m_FixedImage and m_MovingImage. However
the SliceBySliceImageFilter calls m_Filter->SetInput( i, internalInputs[i]
); which does not set these attributes to my understanding.

So can the SliceBySlice image filter exclusively be used in connection with
actual filters, or can a 'special' task such as image registration be
handeled as well?

Thanks a lot,

Matthias

             "Gaetan Lehmann"                                              
             <gaetan.lehmann at j                                             
             ouy.inra.fr>                                               An 
                                        "Luis Ibanez"                      
             27.11.2006 11:39           <luis.ibanez at kitware.com>,         
                                        matthias.honal at uniklinik-freiburg. 
                                        de                                 
                                                                     Kopie 
                                        insight-users at itk.org              
                                                                     Thema 
                                        Re: Antwort: Re: [Insight-users]   
                                        Inserting 2D image in 3D volume    

Hi Matthias,

SliceBySliceImageFilter now supports several inputs and outputs of same
size and type.
In the future, it should be possible to relax the condition on size if
needed, but not I don't think it should be possible to relax condition on
type.

http://voxel.jouy.inra.fr/darcs/contrib-itk/sliceBySlice/itkSliceBySliceImageFilter.h

http://voxel.jouy.inra.fr/darcs/contrib-itk/sliceBySlice/itkSliceBySliceImageFilter.txx

And there is also the solution proposed by Luis - I was to busy making ads

for my filters to reply to your question :-)

Gaetan

On Sun, 26 Nov 2006 21:25:15 +0100, Luis Ibanez <luis.ibanez at kitware.com>
wrote:

> Hi Mattias,
>
> You may want to look at the PasteImageFilter:
>
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1PasteImageFilter.html
>
>
>     Regards,
>
>
>         Luis
>
>
> ------------------------------------------------
> matthias.honal at uniklinik-freiburg.de wrote:
>>   Hi Gaetan,
>>  the SliceBySliceImageFilter really looks interesting to me, however
>> maybe that my problem is to complex to use the filter. Precisely I'm
>> planning to do a slice by slice 2D registration (to compare it later on

>> with a 3D registration). So the problem is that I have two input
>> volumes which I would like to process slice by slice, i.e. I would like

>> to compute a tranformed image from each slice pair. Then the
>> transformed image should be written in the output volume.
>> Up to now, I did not see how the filter could be used for that problem.

>> Or do you think there is a solution?
>>  Thanks a lot,
>>  Matthias
>>   -----Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr> schrieb: -----
>>      An: matthias.honal at uniklinik-freiburg.de, insight-users at itk.org
>>     Von: Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>>     Datum: 11/26/2006 05:42PM
>>     Thema: Re: [Insight-users] Inserting 2D image in 3D volume
>>      Hi Matthias,
>>      I have wrote a filter to process an image slice by slice, and
>>     submited it      to the insight journal:
>>        http://hdl.handle.net/1926/368
>>      Please let me know if it fits your need, or if there is some
>> things to      change to make it useful for you.
>>      Regards,
>>      Gaetan
>>       Le Sun, 26 Nov 2006 17:29:40 +0100,      a écrit:
>>       > Hi all,
>>      >
>>      > I'm trying to process a 3D data volume slice by slice. To do so,

>> I       > extract first
>>      > the desired slice from the complete volume using the
>>     ExtractImageFilter       > and
>>      > process it using several filters. Finally I would like to copy
>>     the slice       > to a
>>      > certain position in my output volume, which has previously been

>>      > allocated.
>>      > However I found no way to do that, except for copying pixel by
>> pixel.
>>      > So do I miss a fundamental concept of ITK here, or didn't I
>>     simply find       > the
>>      > appropriate filter or method to insert a 2D slice in a 3D volume.
>>      >
>>      > Thanks a lot in advance,
>>      >
>>      > Matthias
>>      >
>>        --     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://voxel.jouy.inra.fr <http://voxel.jouy.inra.fr/>
>>
>> ------------------------------------------------------------------------
>>  _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users

--
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://voxel.jouy.inra.fr