[Insight-users] problems on deformable registration 8
Sean Lee
kevinseanlee at live.com
Thu Jul 9 13:53:39 EDT 2009
Hi, Luis,
I am trying to provide more information and tested it with several other numbers. Here is the results.
29, 56, 57, 58, 59 slices: 1 iteration with a bad result.
30 slices; 45 iterations with a good result. (of course, only half volume is matched)60 slices; 34 iterations with a good result.
Let me know what I can do for this issue.
Thanks.
Sean
From: kevinseanlee at live.com
To: luis.ibanez at kitware.com
Date: Thu, 9 Jul 2009 08:22:59 -0500
CC: insight-users at itk.org
Subject: Re: [Insight-users] problems on deformable registration 8
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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