[Insight-users] Insight-users Digest, Vol 59, Issue 33
David Pastor
david.pastor at die.upm.es
Tue Mar 10 10:20:14 EDT 2009
Hi,
2. Use itk::ImageRegionIterators to copy from the original image into
the larger image at a particular offset.
This is what is was trying now and it'll give me the solution, but I was
hoping there was a shorter way. I meant just the opposite operation to a
"crop image filter". The result would be a larger image with the same
content in the same scaling than the original one. Problem was that tiling
images with different sizes dont align the images in their original
position.
For example tiling a 5x5x5 with a 3x3x3 image will return a 5x5x5x2 image,
but the second frame will be located in a corner of the volume and not in
its original position. That's why I need to create a larger image embedding
the original.
It's true that you need another image, it was just bad speaking.
thanks!
david
----- Original Message -----
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To: <insight-users at itk.org>
Sent: Tuesday, March 10, 2009 1:48 PM
Subject: Insight-users Digest, Vol 59, Issue 33
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> Today's Topics:
>
> 1. Segmentation filters (Eduardo - LNCC)
> 2. Enlarge the image (David Pastor)
> 3. Re: Enlarge the image (kent williams)
> 4. Re: Enlarge the image (Andreas Schuh)
> 5. Re: Segmentation filters (Luis Ibanez)
> 6. Re: Curves2DExtractor not working (Luis Ibanez)
> 7. Re: Curves2DExtractor not working (Rick Giuly)
> 8. Re: Validation of deformable registration (Marta)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 Mar 2009 14:53:22 -0300
> From: Eduardo - LNCC <camargo at lncc.br>
> Subject: [Insight-users] Segmentation filters
> To: insight-users at itk.org
> Message-ID:
> <846025900903091053k2943ddd4w6d836b5e7550d470 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
>
> Can I replace the itkFastMarchingImageFilter class by class
> itkDanielssonDistanceMapImageFilter without have problems in the
> segmentation filters below?
>
>
> - itkShapeDetectionLevelSetImageFilter
> - itkGeodesicActiveContourLeveSetImageFilter
> - itkThresholdSegmentationLevelSetImageFilter
> - itkCannySegmentationLevelSetImageFilter
> - itkLaplacianSegmentationLevelSetImageFilter
>
>
>
> Sorry for my english
>
> --
> Atenciosamente,
>
> Eduardo Camargo
> Analista de Sistemas
> HeMoLab - http://hemolab.lncc.br/equipe/desenv/eduardo.htm
> Laborat?rio Nacional de Computa??o Cient?fica - LNCC
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> Message: 2
> Date: Mon, 9 Mar 2009 19:13:11 +0100
> From: "David Pastor" <david.pastor at die.upm.es>
> Subject: [Insight-users] Enlarge the image
> To: <insight-users at itk.org>
> Message-ID: <006001c9a0e2$b4a22cb0$a337048a at POSEIDON>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I need to enlarge an image, change its size type to a bigger one without
> modifying the content of the original one, so there is no rescaling. Any
> direct filter for this?
>
> cheers
> david
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> ------------------------------
>
> Message: 3
> Date: Mon, 9 Mar 2009 14:55:07 -0500
> From: kent williams <nkwmailinglists at gmail.com>
> Subject: Re: [Insight-users] Enlarge the image
> To: itk users <Insight-users at itk.org>
> Message-ID:
> <44f773f50903091255q41e0edecid3b5ed6c96572bae at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> What you said, as it stands, makes no sense. First of all, the
> default behavior is to not to modify the input image at all. A new
> image is generated. There are some special cases of 'in place' filters
> that are supposed to change the input, because the input and output
> are the same image.
>
> Second of all, if you resize an image, you're going to be resampling.
>
> What I think you mean is you either want to go from 2D to 3D (for
> example), or embed an image unmodified inside a larger image.
>
> In the former case, you can use itk::CastImageFilter. In the latter
> case, it's more complicated.
>
> 1. Create and Allocate the larger output image.
> 2. Use itk::ImageRegionIterators to copy from the original image into
> the larger image at a particular offset.
>
> If you can clarify what you're trying to do we can provide a better
> answer.
>
> On Mon, Mar 9, 2009 at 1:13 PM, David Pastor <david.pastor at die.upm.es>
> wrote:
>> Hello,
>>
>> I need to enlarge an image, change its size type to a bigger one without
>> modifying the content of the original one, so there is no rescaling. Any
>> direct filter for this?
>>
>> cheers
>> david
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
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>> Please keep messages on-topic and check the ITK FAQ at:
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>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 09 Mar 2009 22:39:28 +0100
> From: Andreas Schuh <andreas.schuh.84 at googlemail.com>
> Subject: Re: [Insight-users] Enlarge the image
> To: kent williams <nkwmailinglists at gmail.com>
> Cc: itk users <Insight-users at itk.org>
> Message-ID: <49B58C90.2070902 at googlemail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> my first thought was that you, David, might want to change just the
> spacing of the image such that it is physically bigger than before.
> Let's consider this as zooming. If this is what you want, you wouldn't
> need any filter as you can just reset the spacing of the image manually.
> On the other side, if you meant to keep the continuous image in physical
> space constant but change the size of the grid this continuous image is
> sampled on, you may have a look at the ResampleImageFilter. As the name
> implies, this filter resamples an image sampled on one grid on another
> one. Thus, if "I need to enlarge an image, change its size (type) to a
> bigger one" meant to increase the number of pixels of the discrete
> image, this may be what you're looking for.
>
> --
> regards
> Andreas
>
> kent williams schrieb:
>> What you said, as it stands, makes no sense. First of all, the
>> default behavior is to not to modify the input image at all. A new
>> image is generated. There are some special cases of 'in place' filters
>> that are supposed to change the input, because the input and output
>> are the same image.
>>
>> Second of all, if you resize an image, you're going to be resampling.
>>
>> What I think you mean is you either want to go from 2D to 3D (for
>> example), or embed an image unmodified inside a larger image.
>>
>> In the former case, you can use itk::CastImageFilter. In the latter
>> case, it's more complicated.
>>
>> 1. Create and Allocate the larger output image.
>> 2. Use itk::ImageRegionIterators to copy from the original image into
>> the larger image at a particular offset.
>>
>> If you can clarify what you're trying to do we can provide a better
>> answer.
>>
>> On Mon, Mar 9, 2009 at 1:13 PM, David Pastor <david.pastor at die.upm.es>
>> wrote:
>>
>>> Hello,
>>>
>>> I need to enlarge an image, change its size type to a bigger one without
>>> modifying the content of the original one, so there is no rescaling. Any
>>> direct filter for this?
>>>
>>> cheers
>>> david
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
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>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
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>>>
>>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
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>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 09 Mar 2009 19:26:04 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] Segmentation filters
> To: camargo at lncc.br
> Cc: insight-users at itk.org
> Message-ID: <49B5A58C.6050201 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Eduardo,
>
> Yes,
>
> You could replace the FastMarching filter with a
> DanielssonDistanceMap filter.
>
> Just create a binary image that is set to zeros everywhere,
> and only set to ones the pixels corresponding to the seed
> points that are now being passed to the FastMarching filter.
> Then use that image as input to the Danielsson distance map
> filter.
>
>
> Notice however that:
>
>
> A) In some of the examples, the seed points are set
> to initial negative values, in order to be able to
> define the initial level set as the iso-value == 0.
>
>
> B) The FastMarching filter is a lot faster than the
> Danielson Filter for the purpose of computing that
> distance map
>
>
> C) If you really want to stick to a distance filter,
> then you may want to try the SignedMaurer distance
> filter that is equivalent to the Danielson filter,
> but it executes a lot faster.
>
>
>
> Regards,
>
>
> Luis
>
>
>
> --------------------
> Eduardo - LNCC wrote:
>> Hi,
>>
>>
>> Can I replace the itkFastMarchingImageFilter class by class
>> itkDanielssonDistanceMapImageFilter without have problems in the
>> segmentation filters below?
>>
>> * itkShapeDetectionLevelSetImageFilter
>> * itkGeodesicActiveContourLeveSetImageFilter
>> * itkThresholdSegmentationLevelSetImageFilter
>> * itkCannySegmentationLevelSetImageFilter
>> * itkLaplacianSegmentationLevelSetImageFilter
>>
>>
>>
>> Sorry for my english
>>
>> --
>> Atenciosamente,
>>
>> Eduardo Camargo
>> Analista de Sistemas
>> HeMoLab - http://hemolab.lncc.br/equipe/desenv/eduardo.htm
>> Laborat?rio Nacional de Computa??o Cient?fica - LNCC
>>
>>
>> ------------------------------------------------------------------------
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 09 Mar 2009 19:28:02 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] Curves2DExtractor not working
> To: Rick Giuly <rgiuly at gmail.com>
> Cc: insight users <insight-users at itk.org>
> Message-ID: <49B5A602.7000507 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Rick,
>
> Could you post to a public web site the image that you are using
> as input to the Curve2DExtractor ?
>
>
> (Please do not send executables to the mailing list).
>
>
> Thanks
>
>
> Luis
>
>
> ------------------
> Rick Giuly wrote:
>> Hello All,
>>
>> Using Insight Applications 3.12.0 on windows, Curves2DExtractor does
>> nothing when I run it. (No error messages show up in the CMD box and no
>> gui appears.) I used fltk-1.1.7 and built it with CMake and Eclipse
>>
>> The build output is attached. It seemed to build with no errors.
>>
>> Any help is appreciated
>>
>> -Rick
>>
>>
>> ------------------------------------------------------------------------
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 10 Mar 2009 05:06:01 -0700
> From: Rick Giuly <rgiuly at gmail.com>
> Subject: Re: [Insight-users] Curves2DExtractor not working
> To: Luis Ibanez <luis.ibanez at kitware.com>
> Cc: insight users <insight-users at itk.org>
> Message-ID: <49B657A9.9020603 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Luis,
>
> As I understand it, running Curve2DExtractor should bring up a GUI where
> an image can be chosen. But, the GUI is not coming up, so I'm not able
> to pick an image file for input.
>
> -Rick
>
> Luis Ibanez wrote:
>>
>> Hi Rick,
>>
>> Could you post to a public web site the image that you are using
>> as input to the Curve2DExtractor ?
>>
>>
>> (Please do not send executables to the mailing list).
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> ------------------
>> Rick Giuly wrote:
>>> Hello All,
>>>
>>> Using Insight Applications 3.12.0 on windows, Curves2DExtractor does
>>> nothing when I run it. (No error messages show up in the CMD box and
>>> no gui appears.) I used fltk-1.1.7 and built it with CMake and Eclipse
>>>
>>> The build output is attached. It seemed to build with no errors.
>>>
>>> Any help is appreciated
>>>
>>> -Rick
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.itk.org/mailman/listinfo/insight-users
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 10 Mar 2009 13:48:46 +0100
> From: Marta <t_s_80 at gmx.de>
> Subject: Re: [Insight-users] Validation of deformable registration
> To: Marta <t_s_80 at gmx.de>
> Cc: insight-users at itk.org
> Message-ID: <3673490C-8CA3-48E9-97E2-788ED017E944 at gmx.de>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hello once again,
>
> I still have the questions below, but I also have a new one that
> bothers me to the topic.
>
> What is a good way to find data for my synthetic deformation field? I
> mean, it isn't enough to deform the image "anyhow", it's important to
> have a realistic deformation, right? How can I imitate that? Are there
> any tools to create an synthetic deformation field?
>
> Thanks for any comments to my questions! It's important for my master
> thesis.
>
> Best regards,
> Marta
>
>
> Am 05.03.2009 um 17:38 schrieb Marta:
>
>> Hi,
>>
>> I try to validate my deformable registration method and I do already
>> know that there is no standard for it.
>> Anyway, I found in older posts a way to do it by generating an
>> artificially deformation field and compare it with the result
>> deformation field.
>> Luis told (e.g.) so in
>> http://www.itk.org/pipermail/insight-users/2006-July/018634.html
>> :
>>
>> "The common approach is to artificially generate a
>> deformation field by using ThinPlateSplines, use this artificial
>> deformation field in order to create a deformed version of your image.
>> Then use your registration method between the original and the
>> deformed image, and finally compare the artificial deformation field
>> against the one that
>> you produced with the registration method."
>>
>> However, I'm not sure what is the best way to compare the
>> deformation fields. Can I also use a squared image difference?
>> Or are there any better ways?
>>
>> Would be happy for any suggestions!
>>
>> Best regards,
>> Marta
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
>
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>
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