[Insight-users] deformable registration 3D
Luis Ibanez
luis.ibanez at kitware.com
Wed, 28 Apr 2004 19:50:00 -0400
Hi Christoph,
Please be nice and send us your modified .cxx file :-)
It is hard to make autopsies from only pictures
of the dead body...
Thanks,
Luis
--------------------------
Christoph Albrecht wrote:
> Hi Luis,
>
> I added these two lines (typedef::itk...) to the source code in
> deformableregistration1.cxx, direclty before the part of writing (around
> line 265). Unfortunately, this changed nothing. The output is still 8
> bit, the same as before.
>
> Also deleting the resampling part did not work. I deleted lines 230-260,
> rescale and histogram. Now there is an error as the following:
>
> --------------------------------------------------------
> Microsoft Visual C++ Debug Library
> Debug Error!
> Program: DeformableRegistration1.exe
> abnormal program termination
> (Press Retry to debug the application)
> Cancel Retry Ignore
> --------------------------------------------------------
>
> Hitting Retry leads to
>
> -------------------------------------------------------------
> unknown software exception (0x80000003)
> --------------------------------------------------------------
>
> and
>
> --------------------------------------------------------------------------------
> Call to Userdefined Stop in Source Code at 0x1020b1f3
> --------------------------------------------------------------------------------
>
> If the 16 bit output does not work, I have the idea of registering the
> original image to itself to get exactly the same file format. But the
> rescaling kills the substraction, the most important part of the work.
> Once again I have to ask for your help, especially with the rescaling.
>
> Best regards
> Christoph
>
>
>
>
>
>
> ----- Original Message -----
> *From:* Luis Ibanez <mailto:luis.ibanez at kitware.com>
> *To:* Christoph Albrecht <mailto:christoph.albrecht at hamburg.de>
> *Cc:* Insight-users at itk.org <mailto:Insight-users at itk.org>
> *Sent:* Wednesday, April 28, 2004 4:07 PM
> *Subject:* Re: [Insight-users] deformable registration 3D
>
>
> Hi Christoph
>
> Thanks for letting us know that the
> registration is now working for you.
>
> About the output:
>
> if you want to get image files in 16bit/pixel
> You should simply instantiate the writers as
>
>
> typedef itk::Image< unsigned short, Dimension > OutputImageType;
> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>
>
> Note that the image that you connect to the writer in SetInput()
> *must* be of pixel type "unsigned short". If you need a
> conversion you could to casting with:
>
> CastImageFilter
> RescaleIntensityImageFilter
> IntensityWindowingImageFilter
>
> or any of the other filters described in Section 6.2
> "Casting and Intensity Mapping", pdf-page 146 on the
> SoftwareGuide.
>
> http://www.itk.org/ItkSoftwareGuide.pdf
>
>
> Feel free to delete the resampling part. If you want to
> do subtraction you may want to use the SquaredDifference
> image filter. You will find examples on the use of this
> filter the follwing files:
>
> Insight/Examples/Registration/
> DeformableRegistration4.cxx
> ImageRegistration1.cxx
> ImageRegistration10.cxx
> ImageRegistration5.cxx
> ImageRegistration6.cxx
> ImageRegistration7.cxx
> ImageRegistration8.cxx
> ImageRegistration9.cxx
>
>
> Regards,
>
>
> Luis
>
>
> ----------------------------
> Christoph Albrecht wrote:
>
> > Dear Luis,
> >
> > Many Thanks. I changed all file types to the correspondend 3D
> types, now it
> > works fine. The relative path was no problem anymore.
> > Now I have one more thing:
> > The input files are 16 bit files, ANALYZE format. The output
> files are also
> > ANALYZE, but only 8 bit. Can I change the output somewhere to 16
> bit? In the
> > internet I found the information that it is short integer.
> > I was also thinking of deleting the whole rescaling part, because
> after the
> > registration I want to substract the original, fixed image from
> the result
> > to see a distribution of a contrast medium.
> >
> > Best regards
> > Christoph
> >
> >
> >
> >
> >
> >
> > ----- Original Message -----
> > From: "Luis Ibanez" <luis.ibanez at kitware.com
> <mailto:luis.ibanez at kitware.com>>
> > To: "Christoph Albrecht" <chrisalb at upvnet.upv.es
> <mailto:chrisalb at upvnet.upv.es>>
> > Cc: <insight-users at itk.org <mailto:insight-users at itk.org>>
> > Sent: Monday, April 26, 2004 7:00 PM
> > Subject: Re: [Insight-users] deformable registration 3D
> >
> >
> >
> >>Hi Christoph,
> >>
> >>Did you changed the Dimension from 2 to 3
> >>in the .cxx file and recompiled ?
> >>
> >>The error message is sayikng that the
> >>image filename was not found.
> >>
> >>You are writing a relative path in the
> >>specification of the input Moving and
> >>Fixed image files.
> >>
> >>Could you please try with an absolute
> >>path ?
> >>
> >>Please let us know if that works or not.
> >>
> >>
> >> Thanks
> >>
> >>
> >> Luis
> >>
> >>
> >>----------------------------
> >>Christoph Albrecht wrote:
> >>
> >>
> >>>Hello,
> >>>
> >>>I tried to use the example "deformableregistration1" for a 3D
> problem
> >
> > instead of the given 2D problem.
> >
> >>>The result was always 2D, the first slice of my ANALYZE data
> registered.
> >>>In an old post I found this problem solved by adding a third 1
> to the
> >
> > "scaling at lowest level of pyramid", but this leads to the error
> message:
> >
> >>>%---------------------------------------------------
> >>>Exception caught during reference file reading
> >>>
> >>>itk::ImageFileReaderException (010DFB2C)
> >>>Location: "Unknown"
> >>>File: ......\IO\itkImageFileReader.txx
> >>>Line: 91
> >>>Description: FileName must be specified
> >>>%----------------------------------------------------
> >>>
> >>>My configuration file looks like the following, I have only
> changed the
> >
> > dimensions, the file names and the third 1:
> >
> >>>% ---------------------------------------------------------
> >>>1 % Number of levels in the multi-res pyramid (1 = single-res)
> >>>1 % Highest level to use in the pyramid
> >>> 1 1 1 % Scaling at lowest level of pyramid
> >>> 4 % Number of pixels per element
> >>> 1.e4 % Elasticity (E)
> >>> 1.e4 % Density x capacity (RhoC)
> >>> 1 % Image energy scaling (gamma) - sets gradient step size
> >>> 2 % NumberOfIntegrationPoints
> >>> 1 % WidthOfMetricRegion
> >>> 20 % MaximumIterations
> >>>
> >>>0 0.99 % Similarity metric (0=mean sq, 1 = ncc, 2=pattern int,
> 3=MI,
> >
> > 5=demons)
> >
> >>>1.0 % Alpha
> >>>0 % DescentDirection (1 = max, 0 = min)
> >>>0 % DoLineSearch (0=never, 1=always, 2=if needed)
> >>>1.e1 % TimeStep
> >>>0.5 % Landmark variance
> >>>0 % Employ regridding / enforce diffeomorphism ( >= 1 -> true)
> >>>
> >>>512 % Nx (image x dimension)
> >>>512 % Ny (image y dimension)
> >>>24 % Nz (image z dimension - not used if 2D)
> >>>./___FEM/000000310000001x01.hdr % ReferenceFileName
> >>>./___FEM/000000310000001x02.hdr % TargetFileName
> >>>
> >>>0 % UseLandmarks? - read the file name below if this is true
> >>>- % LandmarkFileName
> >>>./___FEM/RatLung_result % ResultsFileName
> (prefix
> >
> > only)
> >
> >>>1 % WriteDisplacementField?
> >>>./___FEM/RatLung_disp %
> DisplacementsFileName
> >
> > (prefix only)
> >
> >>>0 % ReadMeshFile?
> >>>- % MeshFileName
> >>>END
> >>>%-----------------------------------------------------------------------
> >>>
> >>>
> >>>I would be glad if somebody could help me with this.
> >>>
> >>>Many thanks
> >>> Christoph Albrecht
> >>>
> >>>_______________________________________________
> >>>Insight-users mailing list
> >>>Insight-users at itk.org
> >>>http://www.itk.org/mailman/listinfo/insight-users
> >>>
> >>
> >>
> >>
> >
> >
>
>