[Insight-users] Insight-users Digest, Vol 52, Issue 4
Gokhan Uzunbas
uzunbas at su.sabanciuniv.edu
Mon Aug 4 12:26:26 EDT 2008
Hi everyone,
I am trying to use itkSmilarity3DTransform to do registration. But it
does not make scaling.
Which transform type shall I use to make registration in 3D with
scaling translation and rotation ?
Thank you very much for your helps..
Gokhan
On Aug 4, 2008, at 7:00 PM, insight-users-request at itk.org wrote:
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> Today's Topics:
>
> 1. Re: Some problems about
> MattesMutualInformationImageToImageMetric.txx (Luis Ibanez)
> 2. Multi-Threading of Resample Filter (Ranjan, Sohan (GE,
> Research))
> 3. Re: Multi-Threading of Resample Filter (Karthik Krishnan)
> 4. Landmark tracking (Yoav Levy)
> 5. Re: Does "InPlace" filters really work "In Place"?
> (Yulia.Arzhaeva at csiro.au)
> 6. about the image border when using ResampleImageFilter (Jun
> Xiong)
> 7. The BrainWeb images (William Whartenby)
> 8. Re: The BrainWeb images (Luis Ibanez)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 03 Aug 2008 19:21:40 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] Some problems about
> MattesMutualInformationImageToImageMetric.txx
> To: ??? <wytwyt218 at hotmail.com>
> Cc: insight-users at itk.org
> Message-ID: <48963D84.4040201 at kitware.com>
> Content-Type: text/plain; charset=GB2312
>
>
> Hi ??? ,
>
>
> Please read the paper
>
> Viola, P. and Wells III, W. (1997).
> "Alignment by Maximization of Mutual Information"
> International Journal of Computer Vision, 24(2):137-154
>
>
> Regards,
>
>
> Luis
>
>
> --------------
> ??? wrote:
>> Hello,
>> I met some problems reading the codes in
>> MattesMutualInformationImageToImageMetric.txx.
>> What does the "bin of the histogram" and "parzen window index"
>> mean?
>> And would you please briefly explain the structure or the key
>> points
>> in this document?
>> Thanks a lot!
>> Best regards.
>>
>> Micheal
>>
>> ---------------------------------------------------------------------
>> ---
>> ????? Windows Live Messenger ???????? ?????
>> <http://im.live.cn/>
>>
>>
>> ---------------------------------------------------------------------
>> ---
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
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>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 4 Aug 2008 03:59:45 +0530
> From: "Ranjan, Sohan (GE, Research)" <sohan.ranjan at ge.com>
> Subject: [Insight-users] Multi-Threading of Resample Filter
> To: <insight-users at itk.org>
> Message-ID:
> <05F13D92C49FB84691B84BA7E7BE4067055FB898 at BANMLVEM05.e2k.ad.ge.com>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Resampling seems to be a perfect candidate for Multi=Threading.
> Is there any multi-threaded version of the Resample Filter?
>
> Sohan
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 03 Aug 2008 23:28:26 -0400
> From: Karthik Krishnan <karthik.krishnan at kitware.com>
> Subject: Re: [Insight-users] Multi-Threading of Resample Filter
> To: "Ranjan, Sohan (GE, Research)" <sohan.ranjan at ge.com>
> Cc: insight-users at itk.org
> Message-ID: <4896775A.9020605 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Sohan:
>
> The existing resample filter (itk::ResampleImageFilter) is threaded.
>
> Ranjan, Sohan (GE, Research) wrote:
>>
>> Resampling seems to be a perfect candidate for Multi=Threading.
>> Is there any multi-threaded version of the Resample Filter?
>>
>> Sohan
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>>
> Regards
>
> --
> Karthik Krishnan
> R & D Engineer,
> Kitware Inc,
> Ph: 518 371 3971 x119
> Fax: 518 371 3971
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 4 Aug 2008 02:24:50 -0700 (PDT)
> From: Yoav Levy <yoav.itk at gmail.com>
> Subject: [Insight-users] Landmark tracking
> To: insight-users at itk.org
> Message-ID: <18808112.post at talk.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> What kind of registration can be used (and how ...) in order track
> a small
> fixed volume (a patch containing a landmark) in a larger volume
> (the moving
> image)?
> --
> View this message in context: http://www.nabble.com/Landmark-
> tracking-tp18808112p18808112.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 4 Aug 2008 19:32:22 +1000
> From: <Yulia.Arzhaeva at csiro.au>
> Subject: Re: [Insight-users] Does "InPlace" filters really work "In
> Place"?
> To: <insight-users at itk.org>
> Message-ID:
> <1414235E09BCE744B013B1EB05BD2C9F08D95A at exbackup.nexus.csiro.au>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Indeed, there is no problem with running an "InPlace" filter with
> provided example images. However, there are no examples of tif
> images in
> the Examples\Data folder, and the runtime error I described in an
> earlier email happens when I run a ThresholdImageFilter test with some
> tif images.
>
> I found out that the crash has nothing to do with filtering but with
> writing an output image in a file. Although, it's not possible to
> catch
> it as an exception - the error happens because a null pointer is
> addressed within one of the functions called inside
> TIFFImageIO::Read().
>
>
> I've done a bit of debugging and that is what I've found. In a
> pipeline,
> that connects a reader with a filter with a writer, calling
> writer->Update() causes an update of a reader, because, with
> filter->InPlaceOn(), the filter input gets released. For tif images,
> TIFFImageIO::Read() is called, which uses m_InternalImage that is
> supposed to have a non-null pointer m_Image to an allocated piece of
> memory. m_InternalImage is filled in TIFFImageIO::CanReadFile(), which
> is not called the second time, as a part of writer->Update()
> procedure.
> As a result, m_InternalImage->m_Image points to NULL, and causes the
> runtime error when addressed in TIFFImageIO::Read(). If one includes
> filter->GetOutput()->DisconnectPipeline() before calling
> writer->Update(), no error occurs because no input image update
> occurs.
>
> I guess, there might be an error in handling tif images. Could anyone
> please comment?
> Thanks.
> Yulia
>
>
> ----------
> Bill Lorensen wrote:
>
> Yulia,
>
> The example works fine for me when I add filter->InPlaceOn(). Are you
> running the example data or your own?
>
> Replace the first filter-<Update(); with
>
> try
> {
> filter->Update();
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex;
> return EXIT_FAILURE;
> }
>
> and see if you get more information.
>
> Actually, place a try/catch around each ->Update() just in case the
> problem is with reading or writing.
>
> Bill
>
> On Fri, Jul 25, 2008 at 11:07 AM, <Yulia.Arzhaeva at csiro.au> wrote:
>> Hello,
>>
>> I have just started using ITK, so I might have overlooked something..
>>
>> I have tried to use ThresholdImageFilter with "InPlace" feature ON,
> i.e. I called filter->InPlaceOn() before calling filter->Update().
> As a
> result, I got a runtime error. I played with an example code, so it
> can
> be reproducible.
>>
>> If you take an example code ThresholdImageFilter.cxx from the
> ..\Examples\Filtering folder , leave just one filter update instead of
> three updates, for simplicity, and insert filter->InPlaceOn(),
> would you
> get a runtime error as well?
>>
>> Could you explain me what's wrong, either with my way to set InPlace
> feature, or with using such a filter "In Place" at all?
>>
>> Thanks,
>> Yulia
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>>
> _______________________________________________
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>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 4 Aug 2008 21:18:52 +0800
> From: "Jun Xiong" <junxiongcn at gmail.com>
> Subject: [Insight-users] about the image border when using
> ResampleImageFilter
> To: insight-users at itk.org
> Message-ID:
> <5a5a6dd00808040618q611b5c48i2241610f57d345ac at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi all,
> I have a question about the image border interpolation question
> when using
> ResampleImageFilter. If i use itk::ResampleImageFilter to resample an
> image to a bigger size, the area around the image border (about half
> of the Spacing value), are NOT interpolated and as a result the
> borders are fade to the default pixel value of the resampling filter.
> For example, if i resample a slice(256*256) from the
> volume(size:128*128*64) in the x-z orientation(using the same
> spacing), the result image only contains 126 line effective data in
> the middle, others are default value. It seems that, the outer half
> of the image border are not interpolated and their values were set as
> the default value directly.
> If i use the PadImageFilter to pad the volume with one pixel, the
> result image contains 130 lines effective data. How can i get a result
> image containing 128 lines.
> Thank you very much!
>
> Best regards!
>
> Jun Xiong
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 4 Aug 2008 08:35:44 -0700 (PDT)
> From: William Whartenby <wwill066 at yahoo.com>
> Subject: [Insight-users] The BrainWeb images
> To: insight-users at itk.org
> Message-ID: <804822.87691.qm at web63114.mail.re1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> The users guide pg 371 refers to
> brainweb165a10f17.mha and brainweb165a10f17Rot10Tx15.mha downloaded
> from
> ?
> ftp://public.kitware.com/pub/itk/Data/BrainWeb
> I can't get to the site. Has it been moved?
> Also, I already had one of the files downloaded. it is attached.
> When I unzip it, I get a file "BrainPart1.DOWNLOAD" How do I read
> that into MATLAB?
> ?
> Finally, I also tried using some .MNC data. Does anyone have a way
> to read this data into MATLAB? Thanks!
>
>
>
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> ------------------------------
>
> Message: 8
> Date: Mon, 04 Aug 2008 11:52:29 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] The BrainWeb images
> To: William Whartenby <wwill066 at yahoo.com>
> Cc: insight-users at itk.org
> Message-ID: <489725BD.8080703 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi William,
>
> The new location of this data is:
>
> http://public.kitware.com/pub/itk/Data/BrainWeb/
>
> The file that you got:
>
> "BrainPart1.DOWNLOAD"
>
> looks like an incomplete download...
>
>
> You may want to try downloading them again using
> the address above
>
>
> Regards,
>
>
> Luis
>
>
> ------------------------
> William Whartenby wrote:
>> The users guide pg 371 refers to
>> brainweb165a10f17.mha and brainweb165a10f17Rot10Tx15.mha
>> downloaded from
>>
>> ftp://public.kitware.com/pub/itk/Data/BrainWeb
>> I can't get to the site. Has it been moved?
>> Also, I already had one of the files downloaded. it is attached.
>> When I
>> unzip it, I get a file "BrainPart1.DOWNLOAD" How do I read that
>> into MATLAB?
>>
>> Finally, I also tried using some .MNC data. Does anyone have a way to
>> read this data into MATLAB? Thanks!
>>
>>
>>
>>
>>
>>
>> ---------------------------------------------------------------------
>> ---
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
> ------------------------------
>
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>
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