[Insight-users] bug in the example configuration file of DeformableRegistration1.cxx?

[Luis Ibanez]

Hi Changhua,


Thanks for posting your parameter file.


The problem is that you modified the parameter file and
put a number "2" in the Nz (number of slices along Z).


This example is not registering 3D images.
It is intended to register two 2D slices.


The fixed  image is "RatLungSlice1.mha" which is a 2D image,
The moving image is "RatLungSlice2.mha" which is another 2D image.


If you put a number different than 0 in the Nz field,
the application would assume that you are loading 3D images.




Please change your parameter file to:




% ----------------------------------
% Information about the image inputs
% ----------------------------------
128     % Nx (image x dimension)
128     % Ny (image y dimension)
0       % Nz (image z dimension - not used if 2D)
../../InsightToolkit-1.6.0/Examples/Data/RatLungSlice1.mha
../../InsightToolkit-1.6.0/Examples/Data/RatLungSlice2.mha




    Regards,



       Luis




========================================
----------------------
Changhua Wu wrote:
> Hi Luis,
> 
> Thank you so much for your kind help. I am able to
> read and write volume file now.
> 
> I did not use any special character in  my
> configuration file. Actually I just copied it from the
> pdf file and modify the directory of reference and
> target file name to 
> ../../InsightToolkit-1.6.0/Examples/Data/RatLungSlice1.mha
> % ReferenceFileName
> ../../InsightToolkit-1.6.0/Examples/Data/RatLungSlice2.mha
> % TargetFileName
> 
> No other change was made. Attached is the
> configuration file. Would you have a look?
> 
> Changhua 
> 
> --- Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
> 
>>Hi Changhua,
>>
>>Did you put the filenames of your images in the
>>configuration file ?
>>
>>Does the path to your images contain spaces or
>>special characters ?
>>
>>
>>    Luis
>>
>>
>>
>>--------------------
>>Changhua Wu wrote:
>>
>>
>>>Hi,
>>>
>>>I tried to run DeformableRegistration1.cxx found
>>
>>in
>>
>>>the example of ITK 1.6.0. I used the configuration
>>>file found on page 295 - 296 in
>>
>>ItkSoftwareGuide.pdf. 
>>
>>>However, I got this output:
>>>
>>>Reading config file...parameter.txt
>>>Example configured. E 0 rho 0
>>> reading moving
>>> reading fixed
>>>Exception caught during reference file reading
>>> 
>>>itk::ImageFileReaderException (0x813fd38)
>>>Location: "Unknown"
>>>File:
>>>
>>
> /home/wch/ITK-VTK/InsightToolkit-1.6.0/Code/IO/itkImageFileReader.txx
> 
>>>Line: 91
>>>Description: FileName must be specified
>>> 
>>>It seems the program failed to read the names of
>>
>>the
>>
>>>fixed and moving volumes. is there a bug in the
>>>configuration file given in ItkSoftwareGuide.pdf?
>>>Thanks.
>>>
>>>Changhua Wu
>>>
>>>
>>>
>>>	
>>>		
>>>__________________________________ 
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>>>
>>>
>>
>>
>>
>>
> 
> 
> 		
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> 
> ------------------------------------------------------------------------
> 
> % Configuration file #1 for DeformableRegistration1.cxx
> %
> % This example demonstrates the setup of a basic registration
> % problem that does NOT use multi-resolution strategies. As a
> % result, only one value for the parameters between
> % (# of pixels per element) and (maximum iterations) is necessary.
> % If you were using multi-resolution, you would have to specify
> % values for those parameters at each level of the pyramid.
> %
> % Note: the paths in the parameters assume you have the traditional
> % ITK file hierarchy as shown below:
> %
> % ITK/Insight/Examples/Registration/DeformableRegistration1.cxx
> % ITK/Insight/Examples/Data/RatLungSlice*
> % ITK/Insight-Bin/bin/DeformableRegistration1
> %
> % ---------------------------------------------------------
> % Parameters for the single- or multi-resolution techniques
> % ---------------------------------------------------------
> 1       % Number of levels in the multi-res pyramid (1 = single-res)
> 1       % Highest level to use in the pyramid
>  11             % Scaling at lowest level of pyramid
>  4              % Number of pixels per element
>  1.e4           % Elasticity (E)
>  1.e4           % Density x capacity (RhoC)
>  1              % Image energy scaling (gamma) - sets gradient step size
>  2              % NumberOfIntegrationPoints
>  1              % WidthOfMetricRegion
>  20             % MaximumIterations
> % -------------------------------
> % Parameters for the registration
> % -------------------------------
> 0 0.99 % Similarity metric (0=mean sq, 1 = ncc, 2=pattern int, 3=MI, 5=demons)
> 1.0     % Alpha
> 0       % DescentDirection (1 = max, 0 = min)
> 0       % DoLineSearch (0=never, 1=always, 2=if needed)
> 1.e1    % TimeStep
> 0.5     % Landmark variance
> 0       % Employ regridding / enforce diffeomorphism ( >= 1 -> true)
> % ----------------------------------
> % Information about the image inputs
> % ----------------------------------
> 128     % Nx (image x dimension)
> 128     % Ny (image y dimension)
> 2       % Nz (image z dimension - not used if 2D)
> ../../InsightToolkit-1.6.0/Examples/Data/RatLungSlice1.mha % ReferenceFileName
> ../../InsightToolkit-1.6.0/Examples/Data/RatLungSlice2.mha % TargetFileName
> % -------------------------------------------------------------------
> % The actions below depend on the values of the flags preceding them.
> % For example, to write out the displacement fields, you have to set
> % the value of WriteDisplacementField to 1.
> % -------------------------------------------------------------------
> 0       % UseLandmarks? - read the file name below if this is true
> -       % LandmarkFileName
> ./RatLung_result                       % ResultsFileName (prefix only)
> 1       % WriteDisplacementField?
> ./RatLung_disp                         % DisplacementsFileName (prefix only)
> 0       % ReadMeshFile?
> -                                      % MeshFileName
> END