[Insight-users] Re: 3d multi-modality registration

Grace Chen Grace.Chen at swri.ca
Wed May 31 10:56:05 EDT 2006 

 Hi Karthik,

 Do you mean I should apply scalling (as in the following line) after
applying the registration transformation to make corresponding slices of
both images matched??

currTransform->Scale((double)fSpacing[0]/mSpacing[0],(double)fSpacing[1]/mSp
acing[1], (double)fSpacing[2]/mSpacing[2]);

Thank you so much!

 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, May 31, 2006 10:29 AM
> Subject: Re: 3d multi-modality registration
>
>
> >
> > Grace Chen wrote:
> >
> > >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?
> > >
> > >
> > This happens often in multi-modality registration, where CT, MR PET
> > datasets have very different resolutions. If you use the registration
> > framework in ITK, the moving image is resampled to the grid of the fixed
> > image. In otherwords your resampled/transformed moving image should,
> > after registration have the same meta-data (spacing, origin) as the
> > fixed image.  You definitely want to do this so you evaluate the
> > registatration using an overlay or checkerboard.
> >
> > >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
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> >
>
>>>------------------------------------------------------------------------
> > >>>
> > >>>
> > >>>>>>_______________________________________________
> > >>>>>>Insight-users mailing list
> > >>>>>>Insight-users at itk.org
> > >>>>>>http://www.itk.org/mailman/listinfo/insight-users
> > >>>>>>
> > >>>>>>
> > >>>>>
> > >>>>>
> > >>>>_______________________________________________
> > >>>>Insight-users mailing list
> > >>>>Insight-users at itk.org
> > >>>>http://www.itk.org/mailman/listinfo/insight-users
> > >>>>
> > >>>>
> > >>>_______________________________________________
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> > >>>
> > >>>
> > >>>
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> > >>
> > >>
> > >>
> > >
> > >
> > >
> > >
> >
>

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