[Insight-users] 3d multi-modality registration

Grace Chen Grace.Chen at swri.ca
Thu Jun 1 10:40:07 EDT 2006 

Hi Karthik,  Good morning!

Even though the registration program does scale the registered moving image.
The registered image still does not look the same size as the fixed
image....  Do you know why?

Thanx!

Grace

----- Original Message ----- 
From: "Karthik Krishnan" <Karthik.Krishnan at kitware.com>
To: "Grace Chen" <Grace.Chen at swri.ca>; "itk"
<insight-users at public.kitware.com>
Sent: Wednesday, May 31, 2006 12:27 PM
Subject: [Insight-users] Re: 3d multi-modality registration


> No. In the end, you should not need to do this .  If you use the
> ResampleImageFilter to resample your moving image as in ,
>
>   ResampleFilterType::Pointer resample = ResampleFilterType::New();
>   resample->SetTransform( finalTransform ); // after registration
>   resample->SetInput( movingImageReader->GetOutput() );
>   resample->SetSize(
   fixedImage->GetLargestPossibleRegion().GetSize() );
>   resample->SetOutputOrigin(  fixedImage->GetOrigin() );
>   resample->SetOutputSpacing( fixedImage->GetSpacing() );
>
> Your resample filter will ensure that the moving image is resampled to
> have the same meta-data as the fixed image. Does this not work for you ?
>
>
> Try to take things one step at a time. Just resample the moving image
> first (without registration using an identity transform). Then use a
> translation transform that overlays them to a reasonable extent. Then
> register with this translation transfrom or a transform really close to
> it as the initial transform and see if your solution converges to the
> right translation transform.
>
> After you've gone through this exercise, you can dive into the other
> details of registration.
>
> HTH
> karthik
>
>
>
> Grace Chen wrote:
>
> >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]/mS
p
> >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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> >>>>>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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