[Insight-users] Reg Deformabale Reg 6

[Dalal, Dhaval]

 Hi Luis
 Thanx for your help regarding analyze format.
 I have some more questions to ask 
- I can specify the 2  .img files on the command line (my .hdr files are
stored in the same directory) and specify the output file as .img . IS this
correct? 
- In DeformableRegistration6.cxx, I just changed 
    const    unsigned int    ImageDimension = 3 (for 3D datasets).
  My datasets are 256*256*512 Mri Images. When i run the exe file
  it says "Starting resolution with low resolution transform", but just
hangs in there and nothing seems to happen,I changed from
DeformableRegistration4.cxx to DeformableRegistration6.cxx to incorporate
multi-resolution scheme but it still seems to be very slow.
Any suggestions on how can i increase the speed, like should i reduce the
Bspline grid size.
- My goal is to to replace the itkMeanSquaresImageToImageMetric.h with 
  Mattes implementation of MI cause i will be registering different modality
images, for doing this 
#include "itkMeanSquaresImageToImageMetric.h"
needs to be replaced with 
#include "itkMattesMutualInformationImageToImageMetric.h"
and 
typedef itk::MeanSquaresImageToImageMetric< 
                                    FixedImageType, 
                                    MovingImageType >    MetricType;
on line 116 needs to be replaced with 
typedef itk::MattesMutualInformationImageToImageMetric< 
                                          FixedImageType, 
                                          MovingImageType >   MetricType;
IS that all?
I did run the example Imageregistration11.cxx to get an idea about this
metric by changing the no. of histogram bins and no. of spatial samples.
But i tested it for 2D data.
Kindly reply back. Any help will be greatly appreciated.
Thanx
Regards
Dhaval

-----Original Message-----
From: Luis Ibanez
To: Dalal, Dhaval
Cc: Insight-users at itk.org
Sent: 9/12/2004 12:48 PM
Subject: Re: how to read analyze files


Hi Dhaval,

Regarding your questions on DeformableRegistration4.cxx

1) "How to change the code for 3D images?"

   A) Just edit the file, go to line 106, and replace

         "const unsigned int Dimension = 2;"

      with

         "const unsigned int Dimension = 3;"


   B)  in line 208 add the third component of the initial
       parameters (for the Z axis)

   initialParameters[0] = 0.0;  // Initial offset in mm along X
   initialParameters[1] = 0.0;  // Initial offset in mm along Y
   initialParameters[2] = 0.0;  // Initial offset in mm along Z


               Then recompile...




2)  "How do i change the code in there to read analyze files?"

            You have not done your homework !

from the previous email:

 > You don't need anything especial for reading Analyze
 > images. The Analyze reader is used by default by the
 > ImageIO factory.
 >
 > You just need to instantiate an ImageFileReader and
 > to pass the filename of your image to the reader.
 > The image file and header must be located in the
 > same directory. ITK will expect your header file to
 > have extension ".hdr".
 >
 > Please read the IO Chapter from the ITK Software Guide
 >
 >      http://www.itk.org/ItkSoftwareGuide.pdf
 >
 > Chapter 7, pdf-page 219-240.
 >
 >

    If you do your homework, there will be no need for
    repeating the same question over and over again.




Regards,



     Luis


-------------------
Dalal, Dhaval wrote:

>  Hi Luis
>  Thanx so much for your reply.
> I want to use Deformable regitration4 example based on bsplines.
> I have successfully tested the algorithm for 2D .tif files, running
the
> executables from ms-dos.
> Can you please tell me
> - How to change the code for 3D images
> - How do i change the code in there to read analyze files
> i am not fluent in C++ so i am confused regarding which specific class
to
> intantiate.
> PLease let me know.
> thanx
> Dhaval
> 
> -----Original Message-----
> From: Luis Ibanez
> To: Dalal, Dhaval
> Cc: Insight-users at itk.org
> Sent: 9/10/2004 5:45 PM
> Subject: Re: how to read analyze files
> 
> 
> Hi Dalal,
> 
> 
> Please read the IO Chapter from the ITK Software Guide
> 
>      http://www.itk.org/ItkSoftwareGuide.pdf
> 
> Chapter 7, pdf-page 219-240.
> 
> ---
> 
> You don't need anything especial for reading Analyze
> images. The Analyze reader is used by default by the
> ImageIO factory.
> 
> You just need to instantiate an ImageFileReader and
> to pass the filename of your image to the reader.
> The image file and header must be located in the
> same directory. ITK will expect your header file to
> have extension ".hdr".
> 
> --
> 
> Most of the examples in ITK are designed to be run
> from the command line. There are not intended to be
> GUI applications. You need to run them from an MS_DOS
> command window or from a Cygwin shell.
> 
> Please read the ITK software guide, all the examples
> are described there.
> 
> 
> If you are interested in GUI applications, you could
> try the ones in the InsightApplications module.
> 
> However, it will be much more efficient for you to
> first get familiar with ITK by reading the software
> guide and by looking at the Tutorial sessions.
> 
>      http://www.itk.org/HTML/Tutorials.htm
> 
> 
> 
> Regards,
> 
> 
>     Luis
> 
> ---------------------
> Dalal, Dhaval wrote:
> 
> 
>> 
>>
>>Hi Luis
>>I DOn't now how to read in analyze file format, i did not see any
> 
> examples
> 
>>on this and even the software guide does not explain this.
>>can you tell me which files to use, so that i can write the cmake.txt
> 
> file
> 
>>with the included libraries.
>>also shuld my image files and header files should be stored in the
> 
> same
> 
>>directory.
>>I am not so fluent in C++, also whenever i run any exe file(generated
> 
> from
> 
>>buildiing examples), the exe file just appears on the screen and
> 
> disappears,
> 
>>how can i see the output? or do i have to add some getc statement in
> 
> the c++
> 
>>code and generate the build again?
>>i am sorry for asking such questions..
>>thanx in advance for yr help.
>>Dhaval  
>>
> 
> 
> 
> 
>