[Insight-users] DeformableModel1 bug

Wang, Liqin Wang.Liqin at mayo.edu
Fri May 4 16:43:22 EDT 2007 

 
Hi, All,

I saw there is a bug reported related to this program and the bug number is #1317. The staus for this one is closed.

However, when I run this program by using the itk-3.2.0, I still get the same errors as:

[lxw06 at radlab3 working]$ DeformableModel1 T1_ax1.hdr T1_mask.hdr testout.hdr
The gradient map created!
Creating mesh...
Mesh (0x9046e18)
  RTTI typeinfo:   itk::Mesh<double, 3u, itk::DefaultStaticMeshTraits<double, 3u, 3u, float, float, double> >
  Reference Count: 2
  Modified Time: 554
  Debug: Off
  Observers:
    none
  Source: (0x9047260)
  Source output index: 0
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 545
  UpdateMTime: 555
  Number Of Points: 0
  Requested Number Of Regions: 1
  Requested Region: 0
  Buffered Region: 0
  Maximum Number Of Regions: 1
  Number Of Points: 0
  Number Of Cell Links: 0
  Number Of Cells: 0
  Size of Cell Data Container: 0
  Number of explicit cell boundary assignments: 3
  CellsAllocationMethod: 3
Deformable mesh created using Marching Cube!
Segmentation fault

Thanks for any help.

Liqin



-----Original Message-----
From: insight-users-bounces+wang.liqin=mayo.edu at itk.org [mailto:insight-users-bounces+wang.liqin=mayo.edu at itk.org] On Behalf Of insight-users-request at itk.org
Sent: Thursday, May 03, 2007 5:38 PM
To: insight-users at itk.org
Subject: Insight-users Digest, Vol 37, Issue 10

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Today's Topics:

   1. Re: Mutual Information with Mask (Karthik Krishnan)
   2. Subtracting two binary dicome 3D Volum Image (Alireza Salamy)
   3. Re: 3D deformable registration (Luis Ibanez)
   4. Re: Inspecting images and result (Lars Nygard)
   5. Re: Inspecting images and result (Karthik Krishnan)
   6. Re: Inspecting images and result (Lars Nygard)
   7. ANNOUNCE : ITK 3.4 : Selection of paper from the	INSIGHT
      JOURNAL (Luis Ibanez)
   8. DeformabeModel1 (Wang, Liqin)


----------------------------------------------------------------------

Message: 1
Date: Thu, 3 May 2007 14:18:40 -0400
From: "Karthik Krishnan" <karthik.krishnan at kitware.com>
Subject: Re: [Insight-users] Mutual Information with Mask
To: "Xabier Artaechevarria Artieda" <xabiarta at unav.es>
Cc: insight-users at itk.org
Message-ID:
	<9ddb27260705031118s4dc29demd0c922895a4588d5 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Please send me a minimal test case with the images (off the list, or it'll
bounce) so we can reproduce the issue.

On 5/3/07, Xabier Artaechevarria Artieda <xabiarta at unav.es> wrote:
>
> I think the problem is in the way I set the mask, because:
>   1. I get no errors if I do not set it.
>   2. The error comes out even if I try to calculate the metric between
> an image and itself.


Didi you initialize the transform to identity before starting the
registration ?

  3. I have also checked the mask by writing it to a file, and it looks ok.


DId you ensure that the origin / spacing etc do match.. Remember the
fixed/moving images, the mask, transform etc work in physical coordinates.

Thanks
-- 
Karthik Krishnan
R&D Engineer,
Kitware Inc.
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Message: 2
Date: Thu, 3 May 2007 11:45:51 -0700 (PDT)
From: Alireza Salamy <alireza_sal2000 at yahoo.com>
Subject: [Insight-users] Subtracting two binary dicome 3D Volum Image
To: luis.ibanez at kitware.com, insight-users at itk.org
Message-ID: <40240.98271.qm at web33302.mail.mud.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

hi 
  I have try to subtract two binary dicome 3D volume image and I use image calculatorTest,but when it try to write the output image,I got an error:
  Reading 1st Image...testb1.dcm
Reading image.... open1.dcm
Before write...sub1.dcm
Exception Object caught:
  itk::ExceptionObject (019BCBF0)
Location: "void __thiscall itk::GDCMImageIO::Write(const void *)"
File: ..\..\..\Code\IO\itkGDCMImageIO.cxx
Line: 993
Description: itk::ERROR: GDCMImageIO(02090F48): DICOM does not support this comp
onent type
   
  my command line is as follow:
  C:\2>"C:\InsightApplications-3.2.0\InsightApplicationb\ImageCalculator\debug\Ima
geCalculatorTests.exe" ImageCalculatorTest -in testb1.dcm open1.dcm -d 3 -out su
b1.dcm -sub
  Can anybody let me know what is wrong with that?
  Thanks alot
   

       
---------------------------------
Ahhh...imagining that irresistible "new car" smell?
 Check outnew cars at Yahoo! Autos.
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Message: 3
Date: Thu, 03 May 2007 15:03:57 -0400
From: Luis Ibanez <luis.ibanez at kitware.com>
Subject: Re: [Insight-users] 3D deformable registration
To: vijay kumar <desivij at yahoo.com>
Cc: insight-users at itk.org
Message-ID: <463A321D.9070001 at kitware.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Hi Vijay,

If you are interested in a 3D version of the FEM deformable
registration example, you may want to look at the example:

         Insight/Examples/Registration/
                DeformableRegistration11.cxx

and the associated input file:


          Insight/Examples/Data/
                FiniteElementRegistration3.txt


The example: DeformableRegistration11.cxx is the 3D version
              DeformableRegistration1.cxx



The pixel dimensions (pixel spacing) are taken from the
meta information of the image. There is no need for you
to put it in the parameters file.



The values of Elasticity and RhoC must be found through
experimentation.

As a rule of Thumb, high elasticity implies that a very
strong force applied to the material will produce very
small deformations.  Therefore, you could start running
experiments with large values of elasticity. If you find
that the deformation field has vectors with very small
magnitudes, then you know that the Elasticity can be
reduced. If you find that the deformation vectors are too
large (e.g. the anatomical tissue gets displaced too far)
then you will know that the Elasticity is too low.

Note that you may have to play with the orders of magnitude
of the Elasticity.


The RhoC factor is used for computing the Mass matrix,
and its final effect is to multiply the forces applied
to the model. Therefore, large values of RhoC will result
on larger deformations, while small values of Rhoc will
result in smaller deformations.




    Regards,



       Luis



------------------
vijay kumar wrote:
> Hi,
> I would like to register two 3D images that are of different sizes ([nx1 
> ny1 nz1] & [nx1 ny2 nz2] voxels) and different voxel dimensions. I 
> modified DeformableRegistration1.cxx to accept 3D images, but I have 
> questions about the parameters file 
> (FiniteElementRegistrationParameters1.txt):
>  
> 1. How do I specify the sizes of both images? The section - Information 
> about image inputs has the option to specify only one set of sizes. How 
> do I specify the second set?
>  
> 2. How do I include voxel dimensions? Or, will the program get this 
> info from the image header?
>  
> 3. How do we determine appropriate E, RhoC and Alpha values? Are there 
> some guidelines for their choice?
>  
> Thanks,
> Vijay
>  
>  
> 
> ------------------------------------------------------------------------
> Ahhh...imagining that irresistible "new car" smell?
> Check out new cars at Yahoo! Autos. 
> <http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users


------------------------------

Message: 4
Date: Thu, 3 May 2007 13:05:38 -0700 (PDT)
From: Lars Nygard <lnygard at yahoo.com>
Subject: Re: [Insight-users] Inspecting images and result
To: Luis Ibanez <luis.ibanez at kitware.com>
Cc: insight-users at itk.org
Message-ID: <37589.67843.qm at web50204.mail.re2.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Louis,
Thanks a lot for the proposals. The LandmarkInitializedMutualInformationRegistration
tool sounds good for my purposes but I can't find it. If it's the ImageRegistrationTool.exe
than the link is not working.
regards,
Lars 

----- Original Message ----
From: Luis Ibanez <luis.ibanez at kitware.com>
To: Lars Nygard <lnygard at yahoo.com>
Cc: insight-users at itk.org
Sent: Thursday, May 3, 2007 7:34:38 PM
Subject: Re: [Insight-users] Inspecting images and result


Hi Lars,

You may want to try:


1) ImageViewer : source code available with InsightApplications
                  and binaries for Windows are available at:

     http://public.kitware.com/pub/itk/InsightApplicationsBin/


2) Slicer:   You can download both source code and binaries
              from http://www.slicer.org


3) The LandmarkInitializedMutualInformationRegistration
    program (also in Insight Applications) is a very good
    application for looking a two registered images. It
    uses color blending in order to compare both images.



   Regards,



      Luis



--------------------
Lars Nygard wrote:
> Hi,
> 
> Im working on multimodal MRI (MRT1 and MRA images) registration 
> problems and I want to view the 3D images I get back from the 
> registration algorithm.
> Does anybody has a suggestion for a good program to view the raw 3D images 
> so that i can scroll through the images?
> Im running windows XP.
> best regards,
> Lars Nygard
> 
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>


      
_________________________________________________________
Alt i én. Få Yahoo! Mail med adressekartotek, kalender og
notisblokk. http://no.mail.yahoo.com


------------------------------

Message: 5
Date: Thu, 3 May 2007 16:18:38 -0400
From: "Karthik Krishnan" <karthik.krishnan at kitware.com>
Subject: Re: [Insight-users] Inspecting images and result
To: "Lars Nygard" <lnygard at yahoo.com>
Cc: insight-users at itk.org, Luis Ibanez <luis.ibanez at kitware.com>
Message-ID:
	<9ddb27260705031318v1ad93f80pa11666cb148f9436 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

On 5/3/07, Lars Nygard <lnygard at yahoo.com> wrote:
>
> Louis,
> Thanks a lot for the proposals. The
> LandmarkInitializedMutualInformationRegistration
> tool sounds good for my purposes but I can't find it. If it's the
> ImageRegistrationTool.exe
> than the link is not working.


Yes . This is the tool we are referring to. Sorry about the broken link. Its
fixed. Please try it now.

Thanks
-- 
Karthik Krishnan
R&D Engineer,
Kitware Inc.
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Message: 6
Date: Thu, 3 May 2007 13:43:26 -0700 (PDT)
From: Lars Nygard <lnygard at yahoo.com>
Subject: Re: [Insight-users] Inspecting images and result
To: Karthik Krishnan <karthik.krishnan at kitware.com>
Cc: insight-users at itk.org, Luis Ibanez <luis.ibanez at kitware.com>
Message-ID: <726721.90877.qm at web50207.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Karthik,
Thanks, I got it. It's great, just what I was looking for.
best regards,
Lars Nygard


----- Original Message ----
From: Karthik Krishnan <karthik.krishnan at kitware.com>
To: Lars Nygard <lnygard at yahoo.com>
Cc: Luis Ibanez <luis.ibanez at kitware.com>; insight-users at itk.org
Sent: Thursday, May 3, 2007 10:18:38 PM
Subject: Re: [Insight-users] Inspecting images and result

On 5/3/07, Lars Nygard <lnygard at yahoo.com> wrote:
Louis,
Thanks a lot for the proposals. The LandmarkInitializedMutualInformationRegistration
tool sounds good for my purposes but I can't find it. If it's the ImageRegistrationTool.exe
than the link is not working. 

Yes . This is the tool we are referring to. Sorry about the broken link. Its fixed. Please try it now.


Thanks
-- 
Karthik Krishnan
R&D Engineer,
Kitware Inc.


      
_________________________________________________________
Alt i én. Få Yahoo! Mail med adressekartotek, kalender og
notisblokk. http://no.mail.yahoo.com
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Message: 7
Date: Thu, 03 May 2007 16:50:53 -0400
From: Luis Ibanez <luis.ibanez at kitware.com>
Subject: [Insight-users] ANNOUNCE : ITK 3.4 : Selection of paper from
	the	INSIGHT JOURNAL
To: Insight Users <insight-users at itk.org>
Message-ID: <463A4B2D.7030108 at kitware.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


In preparation for the release of ITK 3.4 we have
selected from the Insight Journal the papers with
higher ratings and a minimum of 3 reviews.

We anticipate to move the source code from these
papers into the Code/Review directory of the toolkit
as part of the process of releasing ITK 3.4.


The ITK 3.4 release schedule is available at:
http://www.itk.org/Wiki/ITK_Release_Schedule#Release_3.4_Schedule

The selected contributions from the Insight Journal
are listed at:
http://www.itk.org/Wiki/ITK_Release_Schedule#Contributions_5


They are:


    1. Using a Mask to Decrease Computation Time for
       SpatialObject to Image Conversions

    2. Digital Topology

    3. Computational Geometry Computation and KNN Segmentation in ITK

    4. itkEllipseBoundaryToImageFilter

    5. Implementing the Automatic Generation of 3D Statistical
       Shape Models with ITK

    6. I-DO: A Deformable Organisms framework for ITK

    7. Minimal Imposition Image Filter

    8. Binary morphological closing and opening image filter

    9. Support for "cub" image format



Please let us know if you have any questions or
suggestions regarding this selection.



      Thanks


         Luis






------------------------------

Message: 8
Date: Thu, 3 May 2007 17:37:41 -0500
From: "Wang, Liqin" <Wang.Liqin at mayo.edu>
Subject: [Insight-users] DeformabeModel1
To: <insight-users at itk.org>
Message-ID:
	<F6CF0A9FC409564C99A78DE026BBDDCE0986924E at msgarc11.mfad.mfroot.org>
Content-Type: text/plain; charset="us-ascii"


I have the similar  problem and not sure if this problem is solved or
not. Could any one help ??

Thanks a lot.

Liqin


----------searched from web and got the message as follow---

Hi Stephen,

Thank you very much your suggestion.  I tried it with the right file
format but still the same error.  Have you used this example
successfully?  If so, what would you recommend I use as input image and
mask (e.g. image type, dimensions, etc)?  Thank you again.

Akiko

-----Original Message-----
From: Stephen R. Aylward [mailto:HYPERLINK
"http://www.itk.org/mailman/listinfo/insight-users"aylward at unc.edu
<mailto:HYPERLINK> ] 
Sent: Wednesday, March 16, 2005 12:26 PM
To: Akiko Campbell
Cc: insight-users at itk.org
<http://www.itk.org/mailman/listinfo/insight-users> 
Subject: Re: [Insight-users] DeformableModel1.cxx problem

Hi,

One possible cause - the input image filename is "analyze.hdr" but the 
text your gave is a header in the MetaImage fileformat.

Try changing the filename for the input image to
"input.mhd" so that the IO factories will use the correct reader.

Stephen



Akiko Campbell wrote:
> I've noticed there have been some issues reported for 
> DeformableModel1.cxx and I would like to know if anyone has found the 
> solution.  My ITK is 2.0.0 from February 2005, running on Windows XP. 
> When I run this example, the code raises the following exception at: 
> deformableModelFilter->Update();
> 
>  
> 
> "Unhandled exception at 0x00473991 in DeformableModel1.exe:
0xC00000005: 
> Access violation reading location 0x00000034"
> 
>  
> 
> My inputs are:
> 
>  
> 
> * InputImage
> 
>  
> 
> analyze.hdr
> 
> NDims = 3
> 
> DimSize = 512 512 40
> 
> ElementSpacing = 0.388672 0.388672 2
> 
> Position = 0 0 0
> 
> ElementByteOrderMSB = 0
> 
> ElementType = MET_UCHAR
> 
> HeaderSize = -1
> 
> ElementDataFile = analyze.img
> 
>  
> 
> * BinaryImage
> 
>  
> 
> mask.mhd
> 
> NDims = 3
> 
> DimSize = 512 512 40
> 
> ElementSpacing = 0.388672 0.388672 2
> 
> Position = 0 0 0
> 
> ElementByteOrderMSB = 0
> 
> ElementType = MET_UCHAR
> 
> HeaderSize = -1
> 
> ElementDataFile = mask.raw
> 
>  
> 
>  
> 
> The output I get until the exception is raised is:
> 
>
************************************************************************
**************************************************************
> 
> The gradient map created!
> 
> Creating mesh...
> 
> Mesh (013B78D8)
> 
>   RTTI typeinfo:   class itk::Mesh<double,3,class 
> itk::DefaultStaticMeshTraits<double,3,3,float,float,double> >
> 
>   Reference Count: 2
> 
>   Modified Time: 424
> 
>   Debug: Off
> 
>   Observers: none
> 
>   Source: (013B53C8)
> 
>   Source output index: 0
> 
>   Release Data: Off
> 
>   Data Released: False
> 
>   Global Release Data: Off
> 
>   PipelineMTime: 415
> 
>   UpdateMTime: 425
> 
>   Number Of Points: 0
> 
>   Requested Number Of Regions: 1
> 
>   Requested Region: 0
> 
>   Buffered Region: 0
> 
>   Maximum Number Of Regions: 1
> 
>   Number Of Points: 0
> 
>   Number Of Cell Links: 0
> 
>   Number Of Cells: 0
> 
>   Size of Cell Data Container: 0
> 
>   Number of explicit cell boundary assignments: 3
> 
>   CellsAllocationMethod: 3
> 
> Deformable mesh created using Marching Cube!
> 
> Deformable mesh fitting...
> 
>    
> 
>    
> 
> If anyone could help me resolve this issue, I would really appreciate
it.
> 
>  
> 
> Akiko
> 
> 
> --
> No virus found in this outgoing message.
> Checked by AVG Anti-Virus.
> Version: 7.0.308 / Virus Database: 266.7.3 - Release Date: 2005-03-15
> 
> 
>
------------------------------------------------------------------------
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
<http://www.itk.org/mailman/listinfo/insight-users> 
> http://www.itk.org/mailman/listinfo/insight-users

-- 
===========================================================
Dr. Stephen R. Aylward
Associate Professor of Radiology
Adjunct Associate Professor of Computer Science and Surgery
http://caddlab.rad.unc.edu
aylward at unc.edu <http://www.itk.org/mailman/listinfo/insight-users> 
(919) 966-9695

-- 
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Checked by AVG Anti-Virus.
Version: 7.0.308 / Virus Database: 266.7.3 - Release Date: 2005-03-15
 

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