[Insight-users] problems on deformable registration 8
Luis Ibanez
luis.ibanez at kitware.com
Fri Jul 10 10:26:58 EDT 2009
Hi Sean,
Thanks for the details.
From your answers,
the process that you are using looks fine.
Let me get to your follow up emails...
Luis
-------------------
Sean lee wrote:
> 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 then
> run 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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