[Insight-users] 3d multi-modality registration

Tue May 30 15:20:41 EDT 2006

Hi there,

I found that after the 3D rigid registration is perform, I still need to do
this:
currTransform->Scale((double)fSpacing[0]/mSpacing[0],(double)fSpacing[1]/mSp
acing[1], (double)fSpacing[2]/mSpacing[2]);

to scale the movig image to make the corresponding slices in the fixed and
the moving images matched.

Also, I found that even though the physical attributes of the input images
are quite different.

(Original Moving Image:  Origin = -141.902 -178.097 -109.268 , Spacing =
1.17188 1.17188 5.50000

Original Fixed Image:  Origin = 110.361 -147.531 -49.3294,  Spacing =
0.937500 0.937500 5.00000)

The registration program still works quite well even if I use the whole
volumes....I just need to calculate the overlapping slices to matches the
slices.  The program works even when the initializer's option  is set to
MomentOn( ) (instead of the GeometryOn( )).

Can anyone tell me if I am on the right track?  Thanx!

Grace

----- Original Message ----- 
From: "Grace Chen" <Grace.Chen at swri.ca>
To: <insight-users at itk.org>
Cc: "Karthik Krishnan" <Karthik.Krishnan at kitware.com>
Sent: Monday, May 29, 2006 11:58 AM
Subject: [Insight-users] 3d multi-modality registration

> Hi there,
>
> My moving image looks smaller than the fixed image on screen.  (These two
> input images have different spacing.)  And because it's 3D multi-modality
> registration, so only translation and rotation are involved in the
> registration process.  Is this why the registered moving image still look
> smaller than the fixed image and the slices of the moving images don't
match
> that of the fixed image?
>
> Thanx a lot!
>
> Grace
>
>
> ----- Original Message ----- 
> From: "Grace Chen" <Grace.Chen at swri.ca>
> To: <Karthik.Krishnan at kitware.com>
> Cc: <insight-users at itk.org>
> Sent: Friday, May 26, 2006 6:00 PM
> Subject: Re: [Insight-users] 3d multi-modality registration
>
>
> > Hi Karthik,
> >
> > Thanx for your help!
> >
> > However, my program needs this process to be made automatic....  So, I
> > extracted the volume of interest from the moving image, making sure that
> the
> > moving image covers the whole fixed image but yet is not too big.  The
> > registration program can correct the movement in the x and y direction.
> And
> > I can see the program translates the slices (in z direction) too.
> However,
> > because the moving image has smaller spacing, so within the same volume
of
> > interest, the moving image has more slices.  The program doesn't seem to
> > interpolate the moving image well so the subsequent slices of the
> registered
> > moving image matches the corresponding slices of the fixed image.
> >
> > Any idea why? or is there a bug in my understanding??
> >
> > Thanx again!!
> >
> > 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, May 26, 2006 3:11 PM
> > Subject: Re: [Insight-users] 3d multi-modality registration
> >
> >
> > > Hi Grace,
> > >
> > > The correct use of image registration is to bring it close to final
> > > solution and expect image registration to take it from there. I you
> > > provide two volumes with vastly differnt extents and a poor
> > > initialization, it wouldn't be surprising if registration failed to
> > > achieve results.
> > >
> > > In a clinincal workflow, I don't think any radiologist/clinician would
> > > perform registration using command line tools and proceed to the next
> > > step without validating the quality of the registration. This is why
its
> > > usually done using GUI tools. For instance
> > > InsightApplications/LandmarkInitializedMutualInformation (have you
tried
> > > this application for your datasets ?) allows you to place landmarks on
> > > the source and target image, so you can roughly overlay the images
> > > (usually within 0-5 mm of each other) and then allow registration to
> > > fine tune it. If the overlay looks good, you are happy.
> > >
> > > Please give this application a try first :
> > >
> > > 1. Specify a landmark on the fixed and moving image. Pick  anatomical
> > > correspondances. For an MRI of the brain, you could pick the tips of
the
> > > splenium of the corpuscallosum on a sagittal/coronal acquistion (you
can
> > > see it very clearly in
Insight/Examples/Data/BrainMidSagittalSlice.png).
> > > For an axial MRI, you could pick the tips of the ventricles.
> > >
> > > 2. Initialize using landmarks. (it should be one of the options on the
> > > initialization menu).
> > >
> > > 3. Register
> > >
> > > Does this work for you ?
> > >
> > > HTH
> > > karthik
> > >
> > > On Fri, 2006-05-26 at 12:26 -0400, Grace Chen wrote:
> > > > Hi Luis,  Thanx a lot for your inputs!
> > > >
> > > > I've been struggling with this one for a longest time....  The
problem
> > is
> > > > that I have two 3D brain images and one brain image has greater
> physical
> > > > extents in z.  The information of the two volumes are as follows:
> > > >
> > > > Fixed image:
> > > >   origin = [-120, -135.805, -29.7683]
> > > >   spacing = [0.9375,  0.9375,  7]
> > > >   extent = [256,256, 7]
> > > >
> > > > Moving image:
> > > >   origin = [-142.5, -170.488, -84.8781]
> > > >   spacing = [1.17188, 1.17188, 5.5]
> > > >   extent = [256,256, 28]
> > > >
> > > > For these two brain volumes, the fixed image matches a section in
the
> > moving
> > > > image...I tried registered them using the whole volume, the first
> slice
> > of
> > > > the registered moving image doesn't looked like that of the fixed
> image
> > at
> > > > all...Then, I tried extracting a section from the moving slice and
> > > > registered them together....but the middle slices of the the
> registered
> > > > image does not match the corresponding slices in the fixed image.
> > What's
> > > > going on??  Is there prerequisite on the input data for performing
> > > > mullti-modality registration using ITK?
> > > >
> > > > Please help!!  I am in deperate need to really nail this this time!!
> > Thanx
> > > > a million!!
> > > >
> > > > 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: Thursday, May 25, 2006 9:58 PM
> > > > Subject: Re: [Insight-users] 3d multi-modality registration
> > > >
> > > >
> > > > >
> > > > > Hi Grace,
> > > > >
> > > > > In principle, that's true,
> > > > >
> > > > > but in practice it may not happen if the spatial extension
> > > > > of the moving image doesn't fully overlap with the fixed
> > > > > image.
> > > > >
> > > > > Have you checked the other slices ?
> > > > >
> > > > > Do they overlap well ?
> > > > >
> > > > >
> > > > >      Luis
> > > > >
> > > > >
> > > > > ===================
> > > > > Grace Chen wrote:
> > > > > > Hi there,
> > > > > >
> > > > > > My program performs the 3D multi-modality registration for two
> > volumes.
> > > > > > After the registration has been performed, is it true that the
> first
> > > > > > slice of the registered moving image should look like the first
> > slice of
> > > > > > the fixed image?
> > > > > >
> > > > > > Grace
> > > > > >
> > > > > >
> > > > >
> >
> ------------------------------------------------------------------------
> > > > > >
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