[Insight-users] problems on deformable registration 8

Sean lee kevinseanlee at live.com
Thu Jul 9 09:22:59 EDT 2009 

Hi, Luis,
Thanks for your reply.
> A) Did you make *any* changes to the source code
> of the DeformableRegistration8.cxx example ?
I believe I did not.
> B) How are you reading your images ?
> Are they DICOM files ?
> Are you using a Series Reader ?They are raw data with mhd or mha header files and I used following filter to read them.	VolumeReaderType::Pointer fixVolumeReader = VolumeReaderType::New();	fixVolumeReader->SetFileName(fixVolumeFileName);	fixVolumeReader->Update();
> C) How *exactly* have you been removing slices from them.
My original volume are 512X512. First I down-sampled them to 256X256 with itk::ResampleImageFilter and thenrun itk::ExtractImageFilter with following setting	Input3DImageType::RegionType sliceRegion;	Input3DImageType::IndexType sliceStartPoint;	sliceStartPoint[0] = 0;	sliceStartPoint[1] = 0;	sliceStartPoint[2] = 0;	Input3DImageType::SizeType NewVolumeSize;	NewVolumeSize[0]=fixVolumeSize[0];	NewVolumeSize[1]=fixVolumeSize[1];	NewVolumeSize[2]=59; //or 60  !!!!! here is the way I selecting the number of slices !!!!!	sliceRegion.SetSize(NewVolumeSize);	sliceRegion.SetIndex(sliceStartPoint);It is my understanding that the volume size should not affect the results that much. But like what I experienced earlier, changing that number could result in reaching "Convergence: function tolerance reached." without a good result. I hope it can always reach "Convergence: gradient tolerance reached." 
Thanks.
Sean
> Date: Wed, 8 Jul 2009 18:08:48 -0400
> From: luis.ibanez at kitware.com
> To: kevinseanlee at live.com
> CC: insight-users at itk.org
> Subject: Re: [Insight-users] problems on deformable registration 8
> 
> 
> Hi Sean,
> 
> 
> The Exception
> 
>               itk::InvalidRequestedRegionError
> 
> 
> doesn't seem to be related to the registration process.
> 
> 
> A) Did you make *any* changes to the source code
>     of the DeformableRegistration8.cxx example ?
> 
> 
> B) How are you reading your images ?
>     Are they DICOM files ?
>     Are you using a Series Reader ?
> 
> 
> C) How *exactly* have you been removing slices from them.
> 
> 
> D) 2Gb of RAM should be enough for registering two images of
>     64 slices with 256x256 pixels each.
> 
> 
> 
> 
> Something else is going on here....
> 
> 
> 
>     Please let us know about (A),(B) and (C)
> 
> 
> 
>        Thanks
> 
> 
> 
>          Luis
> 
> 
> 
> 
> 
> ------------------
> Sean lee wrote:
> > Hi, Luis,
> > 
> > Thank you for your reply.
> > 
> > I have 2GB RAM. Here is the error message if I run more than 62 slices: 
> > Unhandled exception at 0x7c812afb in RegTest.exe: Microsoft C++ 
> > exception: itk::InvalidRequestedRegionError at memory location 0x0013fbbc..
> > 
> > My CT volumes are liver images from two different phases. 
> > 
> > I also did another test on these two volumes by switch them (switch 
> > fixed and moving volumes). If I run 62 slices,, it would come with same 
> > memory problem (see above error message). This time if I run 60 slices, 
> > it would reach "CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH" after 
> > one iteration; but it seems 59 slices allow me to run 34 iterations and 
> > gave me a good result.
> > 
> > So, it seems the good results came with "reach Projected Gradient 
> > Tolerance". If it reaches "CONVERGENCE: REL_REDUCTION_OF_F <= 
> > FACTR*EPSMCH" first, it come with a "bad" result. How can I control this 
> > situation?
> > 
> > Thanks.
> > 
> > Sean
> > 
> >  > Date: Wed, 8 Jul 2009 17:39:25 -0400
> >  > From: luis.ibanez at kitware.com
> >  > To: kevinseanlee at live.com
> >  > CC: insight-users at itk.org
> >  > Subject: Re: [Insight-users] problems on deformable registration 8
> >  >
> >  >
> >  > Hi Sean,
> >  >
> >  > This is very suspicious.
> >  >
> >  >
> >  > A) your images do not seem to be that big...
> >  >
> >  > One image of:
> >  >
> >  > 64 slices of 256 x 256 in 16bits
> >  >
> >  > will take 8 Mb
> >  >
> >  >
> >  > How much RAM do you have ?
> >  >
> >  >
> >  > B) Just removing one slice (out of 60) from your
> >  > dataset shouldn't lead the registration to
> >  > behave differently.
> >  >
> >  >
> >  > Unless...
> >  >
> >  > There is some special content in that slice...
> >  >
> >  > Are any objects in Slice 60 that have very
> >  > different intensities to those objects visible
> >  > in slice 59 ?
> >  >
> >  >
> >  > ...and...
> >  >
> >  >
> >  > C) How are you removing that slice ?
> >  >
> >  > Are you using a region of interest extraction first ?
> >  >
> >  >
> >  >
> >  >
> >  > Please let us know,
> >  >
> >  >
> >  > Thanks
> >  >
> >  >
> >  >
> >  > Luis
> >  >
> >  >
> >  >
> >  > ---------------
> >  > Sean lee wrote:
> >  > > Hello,
> >  > >
> >  > > I am trying to use the example of deformable registration 8 on two ct
> >  > > image volumes (64 256X256 slices). The problem is If i use more 
> > than 62
> >  > > slices, I would have memory problem; I run 60 slice, I got a perfect
> >  > > results with 20 iterations; but if I run 59 slices, it only run one
> >  > > iteration and reaches "CONVERGENCE: REL_REDUCTION_OF_F <= 
> > FACTR*EPSMCH".
> >  > > I tried to reduce the Cost Function Convergence Factor to 1e+1 and it
> >  > > still comes same results. What could be the problem and any suggested
> >  > > solutions? Thanks. Sean
> >  > > >
> >  > >
> >  > > 
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