[Insight-users] RE: Reg Deformabale Reg 6
Luis Ibanez
luis.ibanez at kitware.com
Thu Sep 23 11:13:23 EDT 2004
Hi Dalal,
In order to read Analyze images, please specify the
input filename as the one with extension .hdr
Thanks
Luis
------------------------
Dalal, Dhaval wrote:
> Thanx Luis,
> What should the output image be specified as, .img or .hdr?
> Thanx
> Dhaval Dalal
>
> -----Original Message-----
> From: Luis Ibanez
> To: Dalal, Dhaval
> Cc: 'Insight-users at itk.org '
> Sent: 9/19/2004 8:14 PM
> Subject: Re: Reg Deformabale Reg 6
>
>
> Hi Dalal,
>
> 1) You should specify the filenames with extensions .hdr
> as the input in the command line of this example.
> The associated .img files must be in the same directory
> as the .hdr files.
>
> 2) The program is not hanging...
> it is simply consuming a lot of CPU time, because the
> operation that you are requesting is *extremely* time
> consuming. If you are in Unix you can check the CPU
> consumption with the command "top", if you are using
> windows, you can use CPU usage with the "Task Manager".
>
> 3) The Multi-resolution scheme in DeformableRegistration6
> is applyed to the BSpline Grid, not to the image. You
> still should use a multi-resolution scheme for the image
> itself.
>
> 4) Replacing the image type is the most important step,
> however you still have to add the settings for the
> parameters of the Mattes mutual information class.
> Please look at the Software Guide for a description
> of the parameters needed by the Mattes metric.
>
> 5) Before you do too far,... did you already applied an
> Affine (or at least a rigid) registration to your pair
> of images ?
>
> If there is any misregistration at the Affine transform
> level, you don't want to try to solve it using a deformable
> transform such as the BSplines, it will take a long time
> for the BSpline to converte to that correction. Please
> reserve the BSpline for very local and small correction
> that remain after an Affine transform registration.
>
>
>
>
> Regards,
>
>
>
> Luis
>
>
> ---------------------
> Dalal, Dhaval wrote:
>
>
>> 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
>>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
>
>
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