[Insight-users] Filter plans

Robert Tamburo robert.tamburo at gmail.com
Thu Oct 19 01:56:30 EDT 2006 

Hi,

I started to write up an email describing the filter, but decided  
that I should just go ahead and write up an article and submit it to  
the Insight Journal. I also submitted the filter code and example  
code for using the filter.

The URL to the filter article is : http://insight-journal.org/dspace/ 
handle/1926/323

Let me know if you have any questions or problems.

-Robert

On Oct 18, 2006, at 1:30 AM, Prename Surname wrote:

> Hey Robert
> That sounds really interresting. What approach are you using in  
> your filter? I would very much like to hear more.
>
> Best of regards
>
>
> 2006/10/18, Robert Tamburo <robert.tamburo at gmail.com>:
> Hi guys,
>
>
> I'm actually working on a similar filter and should have it  
> finished in a couple of days (depending on how my cold progresses).  
> Basically the image takes as input a vector of input images and  
> produces a single image with the "interesting" voxels from the  
> input images labeled. I can post the filter when finished.
>
>
> -Robert
>
> On Oct 17, 2006, at 6:15 PM, Prename Surname wrote:
>
>> Aha, that would of course also be an idea to do like that. I dont  
>> know any of these filters.
>> So your interresting suggestion is to subclass the
>> itk::NaryFunctorImageFilter< TInputImage, TOutputImage, TFunction >
>> so that it accepts 3 input images in the constructor, and then  
>> internally does what?
>>
>>
>> 2006/10/17, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
>> Le Tue, 17 Oct 2006 21:18:16 +0200, Prename Surname
>> < bsd.diverse at gmail.com > a écrit:
>>
>> > aha i see...
>> > Yes, of course i know this is simple, but starting simple is  
>> always the
>> > way
>> > to go :)
>>
>> sure
>>
>> >
>> > I think maybe you have misunderstood what i want to do. I dont  
>> want to
>> > make
>> > a RGB image, i just want to combine 3 different binary mask  
>> images into a
>> > single grayscale mask image with values 0,1,2,3 (0=background,  
>> 1=gm,
>> > 2=wm,3=wm)
>> > If i just manage this i can port it to vtk no problem.
>> > So i just wanted to create a composite filter to do this for me.
>> > Do you see what i mean?
>>
>> Yes, I think :-)
>> This mean you are sure that the object in an image is never  
>> overlapping
>> with the objects in the other images. Is it the case ?
>> If yes, you can use ChangeLabelImageFilter to change the value of  
>> your
>> background pixels to 0 (if it's not already the case), and the  
>> values of
>> the foreground pixel to 1 in the first image, 2 in the second one,  
>> and 3
>> in the last one. Finally, you can add your 3 images with
>> NaryAddImageFilter to produce the image you want.
>> It can be quite boring to instantiate 4 filters to do that - perhaps
>> that's the right time to implement a custom filter based on
>> NaryFunctorImageFilter :-)
>>
>> Gaetan
>>
>> >
>> > Many regards :)
>> >
>> >
>> > 2006/10/17, Gaëtan Lehmann < gaetan.lehmann at jouy.inra.fr>:
>> >>
>> >>
>> >> Hi,
>> >>
>> >> Most of the time, the simple manipulation like this one can  
>> already be
>> >> done in ITK or VTK, so you shouldn't have to create a new  
>> filter to do
>> >> that :-)
>> >> However, we are always pleased to see someone motivated to  
>> develop some
>> >> new features for the toolkit, especially if he/she want to  
>> contribute
>> >> that
>> >> code to the community. I'm pretty sure you'll find something  
>> useful to
>> >> code soon :-)
>> >>
>> >> To combine your 3 images, you can use ComposeRGBImageFilter  
>> (1), which
>> >> takes 3 input images and give you a RGB image.
>> >> However, I'm not sure you can pass the rgb image directly to vtk
>> >> (perhaps
>> >> something to code :-)). You'll have to pass the 3 binary images  
>> in vtk
>> >> with ImageToVTKImageFilter, and compose the color image in vtk.
>> >>
>> >> Gaetan
>> >>
>> >> (1)
>> >> http://www.itk.org/Doxygen/html/ 
>> classitk_1_1ComposeRGBImageFilter.html
>> >>
>> >>
>> >>
>> >> Le Tue, 17 Oct 2006 19:56:04 +0200, Prename Surname
>> >> < bsd.diverse at gmail.com> a écrit:
>> >>
>> >> > Hello.
>> >> > I am beginning to feel a bit more at home in itk/vtk now.  
>> There are
>> >> > still a
>> >> > zillion things to learn about it, but its getting a bit  
>> better. So
>> >> now i
>> >> > have decided that i want to try and make my own filter to get  
>> more
>> >> > acquainted with the whole pipeline approach.
>> >> >
>> >> > I have read chapter 13 in the itksoftwareguide, and i have  
>> thought
>> >> about
>> >> > a
>> >> > approach to make my filter. I was hoping some of you experts  
>> would
>> >> tell
>> >> > me
>> >> > if i am completely off, or if my idea is okay.
>> >> > My situation is this:
>> >> > I have a greyscale volume consisting of 182 slices that are  
>> 182x218
>> >> > pixels
>> >> > of a brain.
>> >> > I have a mask of corresponding size with values 0 and 255 for  
>> the
>> >> > positions
>> >> > of greymatter
>> >> > I have a mask of corresponding size with values 0 and 255 for  
>> the
>> >> > positions
>> >> > of whitematter
>> >> > I have a mask of corresponding size with values 0 and 255 for  
>> the
>> >> > positions
>> >> > of CSF(brainfluid)
>> >> >
>> >> > Basically i want my filter to combine the 3 masks to a single  
>> image,
>> >> so
>> >> > that
>> >> > i can visualize this image in vtk with different colors for
>> >> greymatter,
>> >> > whitematter and CSF.
>> >> >
>> >> >
>> >> > Making a filter (lets call it masking)that subclasses
>> >> ImageToImageFilter,
>> >> > and then takes 2 input images and somehow combining them to a  
>> single
>> >> > image
>> >> > by just adding them together.
>> >> >
>> >> > I then want to make a compositefilter that actually makes a  
>> pipeline
>> >> of
>> >> 2
>> >> > masking filters, taking first 2 masks, combining them in the  
>> masking
>> >> > filter,
>> >> > takes the output of this and combine it with the third mask  
>> using
>> >> again
>> >> > the
>> >> > masking filter, and then outputting the final masked image.
>> >> >
>> >> > Does this sound  feasible, and more important is this a good  
>> approach?
>> >> > I hope for some feedback.
>> >> >
>> >> > Many regards and thank you
>> >>
>> >>
>> >>
>> >> --
>> >> 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
>> >>
>>
>>
>>
>> --
>> 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
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
>

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