[Insight-users] 3D bspline deformable registration works for example data but gives exception for breast mri data

Luis Ibanez luis.ibanez at kitware.com
Sun Oct 17 12:36:00 EDT 2004 


Hi Sachin,

A new example has been committed in the repository in order
to address the type of registration that you are facing.

This new examples was configured by Dr. Lydia Ng by replacing
the vnl_lbfgs optimizer with the itkLBFGSBOptimizer and by
replacing the MeanSquares metric with the MattesMutualInformation
metric.


You will find this new example under:


      Insight/Examples/Registration/
                 DeformableRegistration8.cxx



You will have to update your CVS checkout in order to get
the new file.


You may still need to fine tune the parameters of the optimizer
to make them fit to the characteristics of your imagse.


Please let us know if you have further questions,


     Thanks,


       Luis



-----------------------------
Sachin Jambawalikar wrote:

> Hi  Luis,
> 
> thanks for your response. i will  log a bug entry in the bug tracker.
> 
> neways wanted to know what  is my best bet now to do  registration  for
> contrast enhanced breast MRI images??
> 
> thanks again,
> 
> Regards
> --Sachin
> 
> 
> On Tue, 12 Oct 2004 09:11:48 -0400, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
>>Hi Sachin,
>>
>>We were able to reproduce the error that you reported.
>>
>>Could you please log a bug entry in the bug tracker:
>>
>>                http://www.itk.org/Bug/
>>
>>You can create your own account by just providing your
>>email address as user Id.
>>
>>Please let us know if you encounter any problem while
>>logging this bug entry.
>>
>>
>>   Thanks
>>
>>     Luis
>>
>>---------------------------
>>Sachin Jambawalikar wrote:
>>
>>>Hi Luis ,
>>
>>
>>>The only thing needed to modify for deformable registration using
>>>Bspline for  3D  breast MRI data   was image dimension.
>>>
>>>this code works weel for Brain web simulated data  but  gives me
>>>following error for my data sets (
>>>http://www.ic.sunysb.edu/Stu/sjambawa/b_images/volumes.tar.gz )
>>>
>>>  I   NFN    FUNC        GNORM       STEPLENGTH
>>> IFLAG= -1. LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN
>>>  OF LINE SEARCH: INFO=3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE  INCORRECT OR
>>> INCORRECT TOLERANCESvnl_lbfgs: ** EEEK **
>>> ExceptionObject caught !
>>>
>>> itk::ExceptionObject (00F2FB80)
>>> Location: "Unknown"
>>> File: g:\itk_vtk\itk\insighttoolkit-1.6.0\code\common\itkBSplineDeformableTransf
>>> orm.txx
>>> Line: 232
>>> Description: itk::ERROR: BSplineDeformableTransform(003337D0):
>>>Mismatched betwee
>>> n parameters size and region size
>>>
>>>Breast MRI  data=512 x 512 x 60 (0.68x0.68x3)
>>>BrainWeb Data   =181x217x180(1x1x1)
>>>
>>>=======================
>>>Code  for deformable registration
>>>========================
>>>
....  // code was here....
>>>
>>>
>>>
>>>Is  there something I'm doign wrong here ??
>>>
>>>regards
>>>--Sachin
>>>On Sat, 2 Oct 2004 18:33:42 -0400, Sachin Jambawalikar
>>><sachinjam at gmail.com> wrote:
>>>
>>>
>>>>Hi Luis ,
>>>>Even when I try running from command line   the exe
>>>>deformabelregistration4 and deformableregistration6 (after compiling
>>>>itk with examples and no modifications )  I get the same errors for my
>>>>datasets . But If  I use  Brain web simulated datasets they work .
>>>>is it because of the size of my data  512 x 512 x 60 (0.68x0.68x3)
>>>>for 3D  where as the brain data had size  181x 217x 180 ( 1x1x1)  or
>>>>is it because of the contrast enhancement between the images.
>>>>
>>>>You can download  two of my volumes  in meta  image format (I tried
>>>>using dicom Images 2D with just 2 2D slices  but same result ) from:
>>>>
>>>>http://www.ic.sunysb.edu/Stu/sjambawa/b_images/volumes.tar.gz
>>>>
>>>>thanks ,
>>>>
>>>>Best  Regards
>>>>
>>>>--Sachin
>>>>
>>>>
>>>>
>>>>
>>>>On Fri, 01 Oct 2004 15:00:52 -0400, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>>>
>>>>
>>>>>Hi Sachin,
>>>>>
>>>>>Did you modified the code in any way before
>>>>>applying it to your data ?
>>>>>
>>>>>If so, please post to the list the *exact* .cxx
>>>>>file that you used.
>>>>>
>>>>>It seems that the problem is related to the optimizer
>>>>>setting, and not to the number of parameters.
>>>>>
>>>>>In particular we suspect of the lines: 265-269.
>>>>>
>>>>>  optimizer->SetGradientConvergenceTolerance( 0.05 );
>>>>>  optimizer->SetLineSearchAccuracy( 0.9 );
>>>>>  optimizer->SetDefaultStepLength( 1.5 );
>>>>>
>>>>>Since the error message is comming from the optimizer
>>>>>and it is related to the convergence criteria.
>>>>>
>>>>>  Thanks
>>>>>
>>>>>    Luis
>>>>>
>>>>>--------------------------
>>>>>
>>>>>
>>>>>Sachin Jambawalikar wrote:
>>>>>
>>>>>
>>>>>
>>>>>>Hi all,
>>>>>>
>>>>>>I am using the example code DeformableRegistration4 to register   2D
>>>>>>slices of dynamci contrast breast mri data  .
>>>>>>
>>>>>>I get the following exception:
>>>>>>
>>>>>>
>>>>>>ImageRegion (0033BF04)
>>>>>> Dimension: 2
>>>>>> Index: [0, 0]
>>>>>> Size: [512, 512]
>>>>>>
>>>>>>
>>>>>>ImageRegion (0033DEA4)
>>>>>> Dimension: 2
>>>>>> Index: [0, 0]
>>>>>> Size: [512, 512]
>>>>>>
>>>>>>
>>>>>>totalGridSize: [8, 8]
>>>>>>spacing: [0.683594, 0.683594]
>>>>>>origin: [-192.401, -149.008]
>>>>>>numberOfParameters:128
>>>>>>Intial Parameters =
>>>>>>[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
>>>>>>, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
>>>>>>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
>>>>>>0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
>>>>>>, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
>>>>>>
>>>>>>Starting Registration
>>>>>>F = 18707.5, GNORM = 198.347
>>>>>>*************************************************
>>>>>>  I   NFN    FUNC        GNORM       STEPLENGTH
>>>>>>IFLAG= -1. LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN
>>>>>>OF LINE SEARCH: INFO=3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE  INCORRECT OR
>>>>>>INCORRECT TOLERANCESvnl_lbfgs: ** EEEK **
>>>>>>ExceptionObject caught !
>>>>>>
>>>>>>itk::ExceptionObject (00F2FB80)
>>>>>>Location: "Unknown"
>>>>>>File: g:\itk_vtk\itk\insighttoolkit-1.6.0\code\common\itkBSplineDeformableTransf
>>>>>>orm.txx
>>>>>>Line: 232
>>>>>>Description: itk::ERROR: BSplineDeformableTransform(003337D0): Mismatched betwee
>>>>>>n parameters size and region size
>>>>>>
>>>>>>
>>>>>>
>>>>>>Am i doing something wrong
>>>>>>
>>>>>>Regards
>>>>>>--Sachin
>>>>>>_______________________________________________
>>>>>>Insight-users mailing list
>>>>>>Insight-users at itk.org
>>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>_______________________________________________
>>
>>
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>>
>>>
>>
>>
> 
>

More information about the Insight-users mailing list