[Insight-users] Re: 3d multi-modality registration
Karthik Krishnan
Karthik.Krishnan at kitware.com
Wed May 31 10:29:04 EDT 2006
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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>------------------------------------------------------------------------
>>>
>>>
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>>>>>>Insight-users at itk.org
>>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>>
>>>>>>
>>>>>
>>>>>
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>>>
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