[Insight-users] Description: itk::ERROR: MattesMutualInformationImageToImageMetric(0x1db9020): Joint PDF summed to zero
Luis Ibanez
luis.ibanez at kitware.com
Fri Oct 9 13:11:45 EDT 2009
Hi John,
The .mhd extensions are not required. However, ITK expects "some"
extension in the filename, since the IO factory uses the filename
extension to select the actual ImageIO class that will be used for
saving the file.
It is interesting (and maybe suspicious) that the image is appearing
flipped when you turn off the meta data dictionary.
You may want to double check on what is the correct behavior,
specially if you are developing code for clinical purposes.
What program are you using as a Image Viewer for verifying
the orientation of the images ?
Please let us know,
Thanks
Luis
----------------------------------------------
On Fri, Oct 9, 2009 at 12:40 PM, John Drozd <john.drozd at gmail.com> wrote:
> Hi Luis (again),
>
> Also, I forgot to mention that also this time I used ".mhd" extensions on
> the output files. I did not know that extensions were required. BTW, if I
> used a .dcm extension for the output files, I had to set the writer to:
> writer->UseInputMetaDataDictionaryOff(), otherwise the images came out
> flipped. Maybe it's because my original input files were dicom series.
>
> thanks again,
> john
>
> 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
>
>
>
> --
> 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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