Fw: [Insight-users] different spacing
Grace Chen
Grace.Chen at swri.ca
Wed Jan 4 15:33:16 EST 2006
Hi all,
My program is now working, and the trick seems to be that I have to use
image paramid for multi-modality registration. However, the program seems
to be doing better without using image paramid when two volumes are of the
same type.
Grace
----- Original Message -----
From: "Karthik Krishnan" <Karthik.Krishnan at kitware.com>
To: "Grace Chen" <Grace.Chen at swri.ca>
Cc: <insight-users at itk.org>
Sent: Wednesday, January 04, 2006 1:13 PM
Subject: Re: Fw: [Insight-users] different spacing
> Can you check if
> InsightApplications/LandmarkInitializedMutualInformationRegistration
> works for you ?
>
> You can apply an initial misalignment with landmarks and then register
> the two volumes. The registration in the application there allows a
> VersorRigid3DTransform along with the MattesMI metric. Maybe this is all
> you need.
>
> bye
> -karthik
>
> Grace Chen wrote:
>
> >Hi Karthik,
> >
> >Thanx for your help! However, the spacing for my data is about 1mm. so a
> >movement (5, -25, 0) is only about 25 pixels away in y direction, is that
> >still too much for the program to handle? Also, I noticed that
registration
> >doesn't work well only when I feed the program with data acquiring from
> >different modality. If I simulate the same movement in the same image
data,
> >the program will correct the movement pretty nicely.
> >
> >Grace
> >
> >
> >----- Original Message -----
> >From: "Karthik Krishnan" <Karthik.Krishnan at kitware.com>
> >To: "Grace Chen" <Grace.Chen at swri.ca>
> >Cc: <insight-users at itk.org>
> >Sent: Friday, December 30, 2005 10:39 PM
> >Subject: Re: Fw: [Insight-users] different spacing
> >
> >
> >
> >
> >>On Fri, 2005-12-30 at 16:45 -0500, Grace Chen wrote:
> >>
> >>
> >>>Hi there,
> >>>
> >>>After struggling for so long trying to make the multi-modality version
> >>>
> >>>
> >of my
> >
> >
> >>>program to work using ITK, I think it's not working after all. Is it
> >>>because that I am using VersorRigid3DTransform and the
> >>>VersorRigid3DTransformOptimizer?
> >>>
> >>>Grace
> >>>
> >>>----- Original Message -----
> >>>From: "Grace Chen" <Grace.Chen at swri.ca>
> >>>To: "Luis Ibanez" <luis.ibanez at kitware.com>
> >>>Cc: <insight-users at itk.org>
> >>>Sent: Wednesday, December 28, 2005 2:36 PM
> >>>Subject: Re: [Insight-users] different spacing
> >>>
> >>>
> >>>
> >>>
> >>>>Hi Luis,
> >>>>
> >>>>Sorry, I should have explained a little more.
> >>>>
> >>>>My program has several levels. The input images were first stored as
> >>>>vtkImageData. I moved the fixed image using a vtkTransform object.
> >>>>
> >>>>
> >Then,
> >
> >
> >>>I
> >>>
> >>>
> >>>>used a lower level program which converts these vtkImageData to
> >>>>
> >>>>
> >ImageData
> >
> >
> >>>in
> >>>
> >>>
> >>>>ITK and perform registration using ITK.
> >>>>
> >>>>The ouput of the optimizer seems to improve the image. I use
> >>>>MattesMutualInformationImageToImageMetric. And the ouput of the first
> >>>>
> >>>>
> >and
> >
> >
> >>>>last 10 interations are listed as followed:
> >>>>
> >>>>
> >>>>[optimizer->GetCurrentIteration() , optimizer->GetValue() ,
> >>>>optimizer->GetCurrentPosition()]
> >>>>0 -0.180789 [-0.00372431, -0.00216522, -0.00342151,
> >>>>
> >>>>
> >0.0378279, -0.24234,
> >
> >
> >>>>0.763643]
> >>>>
> >>>>
> >>[snip]
> >>
> >>What I would do is to
> >>
> >>1. Set the scales for the Versor transform so that it effectively does
> >>only translation. Once I am satisfied that it does a decent job of
> >>correcting the translations, I would reduce the scales for the rotation
> >>too. For instance see the following example
> >>
> >>
> >>
>
>http://www.itk.org/cgi-bin/viewcvs.cgi/Examples/Registration/ImageRegistrat
ion8.cxx?rev=1.34&root=Insight&view=markup
> >
> >
> >>The larger the scale, the more it curbs any optimization of that
> >>parameter.
> >>
> >>2. Use only one level for a start and try to get that right. Most of the
> >>registration should be done at the first level.
> >>
> >>[snip]
> >>
> >>
> >>>>>By looking at the result of the registration, I notice that the
> >>>>>
> >>>>>
> >>>>translation
> >>>>
> >>>>
> >>>>>>is ( 1.3884, -3.48145, 2.08022) which is not the movement I
> >>>>>>
> >>>>>>
> >simulated
> >
> >
> >>>>i.e.
> >>>>
> >>>>
> >>>>>>through the call transform->Translate(5, -25, 0).<'transform' is a
> >>>>>>vtkTransform.>
> >>>>>>
> >>>>>>
> >>Registration is usually not meant to correct for large, impractical
> >>misalignments. For instance if this were a CT image with a spacing of
> >>0.125, I would be surprised if the registration managed to correct for
> >>this misagnment (200 pixels here !). Please use reasonable test cases.
> >>
> >>[snip]
> >>
> >>
> >>>>Even if the viewer I use is a naive viewer, after I
> >>>>apply
> >>>>
> >>>>
> >>>>>>the registration transform and then I scale the image, both images
> >>>>>>
> >>>>>>
> >>>(now
> >>>
> >>>
> >>>>look
> >>>>
> >>>>
> >>>>>>approximiatly of the same size) should look aligned too, am I
> >>>>>>
> >>>>>>
> >correct?
> >
> >
> >>>>But
> >>>>
> >>>>
> >>>>>>that's not the case for me.
> >>>>>>
> >>>>>>
> >>For a start, please use
> >>InsightApplications/LandmarkInitializedMutualInformationRegistration as
> >>a viewer. You can load both images and conveniently view the overlay in
> >>3 windows and you will have crosshairs and meta-info to query position
> >>information. This is the bare-minimum viewer capability you will need
> >>for any kind of registration.
> >>
> >>Happy new year.
> >>-karthik
> >>
> >>
> >>
> >>>>
> >>>>Grace
> >>>>
> >>>>
> >>>>
> >>>>----- Original Message -----
> >>>>
> >>>>From: "Luis Ibanez" <luis.ibanez at kitware.com>
> >>>>To: "Grace Chen" <Grace.Chen at swri.ca>
> >>>>Cc: <insight-users at itk.org>
> >>>>Sent: Wednesday, December 28, 2005 2:11 PM
> >>>>Subject: Re: [Insight-users] different spacing
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>Hi Grace,
> >>>>>
> >>>>>
> >>>>> * Did your registration converged ?
> >>>>>
> >>>>>
> >>>>> * Could you please post the output of the Command/Observer
> >>>>> class that you connected to the optimizer ?
> >>>>>
> >>>>>
> >>>>> * Why is that you end up with a vtkTransform
> >>>>> if you are doing registration with ITK ?
> >>>>>
> >>>>>
> >>>>>
> >>>>>Please let us know,
> >>>>>
> >>>>>
> >>>>> Thanks
> >>>>>
> >>>>>
> >>>>> Luis
> >>>>>
> >>>>>
> >>>>>
> >>>>>-----------------
> >>>>>Grace Chen wrote:
> >>>>>
> >>>>>
> >>>>>>Hi Luis,
> >>>>>>
> >>>>>>Thanx for the reply. I know the registration should have been
> >>>>>>
> >>>>>>
> >done in
> >
> >
> >>>>the
> >>>>
> >>>>
> >>>>>>physical space. Even if the viewer I use is a naive viewer, after
> >>>>>>
> >>>>>>
> >I
> >
> >
> >>>>apply
> >>>>
> >>>>
> >>>>>>the registration transform and then I scale the image, both images
> >>>>>>
> >>>>>>
> >>>(now
> >>>
> >>>
> >>>>look
> >>>>
> >>>>
> >>>>>>approximiatly of the same size) should look aligned too, am I
> >>>>>>
> >>>>>>
> >correct?
> >
> >
> >>>>But
> >>>>
> >>>>
> >>>>>>that's not the case for me.
> >>>>>>
> >>>>>>By looking at the result of the registration, I notice that the
> >>>>>>
> >>>>>>
> >>>>translation
> >>>>
> >>>>
> >>>>>>is ( 1.3884, -3.48145, 2.08022) which is not the movement I
> >>>>>>
> >>>>>>
> >simulated
> >
> >
> >>>>i.e.
> >>>>
> >>>>
> >>>>>>through the call transform->Translate(5, -25, 0).<'transform' is a
> >>>>>>vtkTransform.>
> >>>>>>
> >>>>>>Grace
> >>>>>>
> >>>>>>----- Original Message -----
> >>>>>>From: "Luis Ibanez" <luis.ibanez at kitware.com>
> >>>>>>To: "Grace Chen" <Grace.Chen at swri.ca>
> >>>>>>Cc: <insight-users at itk.org>
> >>>>>>Sent: Wednesday, December 28, 2005 1:32 PM
> >>>>>>Subject: Re: [Insight-users] different spacing
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>Hi Grace,
> >>>>>>>
> >>>>>>>Please read with more attention the "Image Registration" Chapter
> >>>>>>>of the ITK Software Guide.
> >>>>>>>
> >>>>>>>
> >>>>>>>If the two images are taken from the same patient and the image
> >>>>>>>spacings are set correctly by the scanner, you *should not need*
> >>>>>>>to do *any scaling* when registering the images.
> >>>>>>>
> >>>>>>>
> >>>>>>>The fact that the images look of different sizes in your screen
> >>>>>>>just shows that you are using a poor image viewer.
> >>>>>>>
> >>>>>>>
> >>>>>>>You are probably comparing the images based on their number of
> >>>>>>>pixels instead of based on their physical extent in space.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>Please study Figure 8.7 in pdf-page 358.
> >>>>>>>
> >>>>>>>
> >>>>>>>The Transfrom that ITK compute is the one that maps the *physical*
> >>>>>>>space of one image into the *physical* space of the other image.
> >>>>>>>
> >>>>>>>
> >>>>>>>In that context, if the patient is the same, you shouldn't need
> >>>>>>>any scaling unless the head of the patient if physically shrinking
> >>>>>>>or expanding between the time of acquiring both scans. (hopefully
> >>>>>>>that doesn't happen in any hospital).
> >>>>>>>
> >>>>>>>
> >>>>>>>The transformations from the discrete image grid and the physical
> >>>>>>>space are done using the origin and spacing. (Transform T1 and T2
> >>>>>>>in Figure 8.7).
> >>>>>>>
> >>>>>>>
> >>>>>>>The transform that ITK computes for you is the "Space Transform".
> >>>>>>>
> >>>>>>>Please read Section 8.3, from the ITK Software Guide
> >>>>>>>
> >>>>>>>
> >>>>>>>and also read the Tutorial
> >>>>>>>
> >>>>>>>http://wiki.na-mic.org/Wiki/images/b/ba/Insight-Registration.ppt
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Regards,
> >>>>>>>
> >>>>>>>
> >>>>>>> Luis
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>------------------
> >>>>>>>Grace Chen wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>Hi there,
> >>>>>>>>
> >>>>>>>>I am trying to perform multi-modality registration for two
> >>>>>>>>
> >>>>>>>>
> >volumes.
> >
> >
> >>>>The
> >>>>
> >>>>
> >>>>>>>>two image data have different physical attributes, etc.
> >>>>>>>>different origin, spacing and dimension (so, on the screen, one
> >>>>>>>>
> >>>>>>>>
> >looks
> >
> >
> >>>>>>>>bigger than the other). I simulated a movement (e.g. a
> >>>>>>>>
> >>>>>>>>
> >translation
> >
> >
> >>>(5,
> >>>
> >>>
> >>>>>>>>-25, 0) in the fixed image. However, when the registration
> >>>>>>>>
> >>>>>>>>
> >program
> >
> >
> >>>>>>>>returns, the final transform matrix is
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>0.999951 0.00912699 -0.00371374 1.3884
> >>>>>>>>
> >>>>>>>>-0.0091721 0.999882 -0.0123175 -3.48145
> >>>>>>>>
> >>>>>>>>0.00360089 0.0123509 0.999917 2.08022
> >>>>>>>>
> >>>>>>>>0 0 0
> >>>>>>>>
> >>>>>>>>
> >1
> >
> >
> >>>>>>>>This result is wrong, isn't it? Does the registration program
> >>>>>>>>
> >>>>>>>>
> >scale
> >
> >
> >>>>the
> >>>>
> >>>>
> >>>>>>>>images before aligning them? What's going on?
> >>>>>>>>
> >>>>>>>>Thanx!
> >>>>>>>>
> >>>>>>>>Grace
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
>
>>>>------------------------------------------------------------------------
> >>>>
> >>>>
> >>>>>>>>_______________________________________________
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> >>>>>>>>
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> >>>>>>
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