[Insight-users] Description: itk::ERROR: MattesMutualInformationImageToImageMetric(0x1db9020): Joint PDF summed to zero
Luis Ibanez
luis.ibanez at kitware.com
Fri Oct 9 13:08:30 EDT 2009
Hi John,
Thanks for letting us know that you found the solution to
the problem.
Luis
----------------------------
On Fri, Oct 9, 2009 at 12:35 PM, John Drozd <john.drozd at gmail.com> wrote:
> Hi Luis,
>
> Thank you very much for your help. The images were not overlapping because
> my two images were too different. One image was ours and the other I got
> from the internet from a 3D Slicer workshop. This time, I used dicom series
> from two different brain subjects that were from the same database. These
> subjects wer from two different people. This time, the
> DeformableRegistration8.cxx program was able to successfully register them.
>
> thanks again,
> john
>
> On Thu, Oct 8, 2009 at 9:08 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>
>> Hi John,
>>
>> Typical suspects are:
>>
>> 1) Your readers are failing to load the DICOM images correctly.
>>
>> 2) The images intensities are not interpreted correctly.
>>
>> 3) The images are not overlapping with the current parameters
>> of the transform.
>>
>>
>> I would suggest you to test for (1) and (2) first.
>>
>>
>> This can easily be done by connecting Writers to the two readers
>> that you are using for loading the DICOM images. Then save
>> those images in a format such as MHD, that can be easily load
>> in many applications (Slicer, VV, ITK-SNAP, VolView, Paraview).
>>
>> BTW, Why is that the other command line arguments do not
>> have extensions ?
>>
>> Are they intended to be directory names ?
>>
>>
>> Please let us know what you find.
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> ----------------------------------------------
>> On Thu, Oct 8, 2009 at 6:00 PM, John Drozd <john.drozd at gmail.com> wrote:
>> > Hello,
>> >
>> > I ran DeformableRegistration8.cxx using the following command:
>> > (I altered the reading of files suitable for DICOM)
>> >
>> > ./DeformableRegistration8 subjectout.dcm atlasout.dcm outputImagefile
>> > differenceOutputfile differenceBeforeRegistration deformationField
>> >
>> > Starting Registration
>> > ExceptionObject caught !
>> >
>> > itk::ExceptionObject (0x4f51fd0)
>> > Location: "void
>> > itk::MattesMutualInformationImageToImageMetric<TFixedImage,
>> > TMovingImage>::GetValueAndDerivative(const typename
>> > itk::ImageToImageMetric<TFixedImage, TMovingImage>::ParametersType&,
>> > typename itk::ImageToImageMetric<TFixedImage,
>> > TMovingImage>::MeasureType&,
>> > typename itk::ImageToImageMetric<TFixedImage,
>> > TMovingImage>::DerivativeType&) const [with TFixedImage =
>> > itk::Image<short
>> > int, 3u>, TMovingImage = itk::Image<short int, 3u>]"
>> > File:
>> >
>> > /trumpet/downloads/3DSlicer/Slicer3-lib/Insight/Code/Review/itkOptMattesMutualInformationImageToImageMetric.txx
>> > Line: 1034
>> > Description: itk::ERROR:
>> > MattesMutualInformationImageToImageMetric(0x1db9020): Joint PDF summed
>> > to
>> > zero
>> >
>> > Does anyone know what this error means?
>> >
>> > john
>> >
>> >
>> > On Thu, Oct 8, 2009 at 5:19 PM, John Drozd <john.drozd at gmail.com> wrote:
>> >>
>> >> Sorry, my oversight. The parameters file was for
>> >> DeformableRegistration1.cxx.
>> >> The parameters file just happened to be listed in the ITK Software
>> >> Guide
>> >> directly after the code listing for DeformableRegistration8.cxx, and
>> >> that's
>> >> why I thought a parameter file was needed for
>> >> DeformableRegistration8.cxx.
>> >> Looking at the code for DeformableRegistration8.cxx, I see that only a
>> >> fixedImageFile, movingImageFile and outputImageFile are required.
>> >>
>> >> Thanks,
>> >> john
>> >>
>> >> On Thu, Oct 8, 2009 at 3:14 PM, John Drozd <john.drozd at gmail.com>
>> >> wrote:
>> >>>
>> >>> Hello,
>> >>>
>> >>> I have two brain volumes, that I successfully loaded into ITK from two
>> >>> different sets of dicom series, namely,
>> >>>
>> >>> image 1 data: (header info that I obtained when I saved my first
>> >>> volume
>> >>> as a nrrd file in Slicer)
>> >>> type: short
>> >>> dimension: 3
>> >>> space: left-posterior-superior
>> >>> sizes: 256 256 124
>> >>> space directions: (0,0.9375,0) (0,0,-0.9375) (-1.3,0,0)
>> >>> kinds: domain domain domain
>> >>> endian: little
>> >>> encoding: gzip
>> >>> space origin: (-79.9,-125.9,121.8)
>> >>>
>> >>> image 2 data: (header info that I obtained when I saved my second
>> >>> volume
>> >>> as a nrrd file in Slicer)
>> >>> type: unsigned short
>> >>> dimension: 3
>> >>> space: left-posterior-superior
>> >>> sizes: 256 256 166
>> >>> space directions: (0,0,-0.93905) (0,0.93905,0) (1.2024,0,0)
>> >>> kinds: domain domain domain
>> >>> endian: little
>> >>> encoding: gzip
>> >>> space origin: (198.396,-0,-0)
>> >>>
>> >>> I want to use a deformable registration such that I will deform the
>> >>> first
>> >>> image into the the second image. Because the images will have
>> >>> different
>> >>> modalities, I am planning to use a modified version of either
>> >>> DeformableRegistration8.cxx (which uses
>> >>> itk::BSplineDeformableTransform,
>> >>> itk::MattesMutualInformationImageToImageMetric with the LBFGSB
>> >>> Optimizer).
>> >>> I may also try using DeformableRegistration14.cxx which uses a
>> >>> gradientsteepestdescent optimizer. As a final refinement, maybe a
>> >>> multiresolution scheme of these routines to speed up the computation.
>> >>>
>> >>> I noticed that in the parameter file for DeformableRegistration8.cxx,
>> >>> only one size Nx, Ny, Nz is specified for both images, but my images
>> >>> have
>> >>> different sizes and different space directions, and different space
>> >>> origins
>> >>> as listed in the nrrd headers above for these images.
>> >>>
>> >>> I will try on my own, but I was wondering if someone has some helpful
>> >>> insight or hints as to whether there are many modifications that I
>> >>> have to
>> >>> do, to refine DeformableRegistration8.cxx or
>> >>> DeformableRegistration14.cxx
>> >>> and their associated classes to make this workable for my situation.
>> >>>
>> >>> Any suggestions are welcome.
>> >>>
>> >>> Thank you.
>> >>>
>> >>> john
>> >>>
>> >>> --
>> >>> John Drozd
>> >>> Postdoctoral Fellow
>> >>> Imaging Research Laboratories
>> >>> Robarts Research Institute
>> >>> Room 1256
>> >>> 100 Perth Drive
>> >>> London, Ontario, Canada
>> >>> N6A 5K8
>> >>> (519) 661-2111 ext. 25306
>> >>
>> >>
>> >>
>> >> --
>> >> John Drozd
>> >> Postdoctoral Fellow
>> >> Imaging Research Laboratories
>> >> Robarts Research Institute
>> >> Room 1256
>> >> 100 Perth Drive
>> >> London, Ontario, Canada
>> >> N6A 5K8
>> >> (519) 661-2111 ext. 25306
>> >
>> >
>> >
>> > --
>> > John Drozd
>> > Postdoctoral Fellow
>> > Imaging Research Laboratories
>> > Robarts Research Institute
>> > Room 1256
>> > 100 Perth Drive
>> > London, Ontario, Canada
>> > N6A 5K8
>> > (519) 661-2111 ext. 25306
>> >
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>
>
>
> --
> John Drozd
> Postdoctoral Fellow
> Imaging Research Laboratories
> Robarts Research Institute
> Room 1256
> 100 Perth Drive
> London, Ontario, Canada
> N6A 5K8
> (519) 661-2111 ext. 25306
>
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