[Insight-users] 3D image registration

Grace Chen Grace.Chen at swri.ca
Fri Sep 16 14:00:39 EDT 2005 

Hi Karthik,  Thanx for your help!

In the example code in itk software guide, instead of using GetMatrix( ),
it's GetRotationMatrix( ).  So, I was using that function, and it didn't
work correctly!

Thanx again for your help!

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, September 16, 2005 12:54 PM
Subject: Re: [Insight-users] 3D image registration


> For *any* transform that derives from MatrixOffsetTransformBase, (such
> as the VersorRigid3D transform ) you should be able to get the
> equivalent 3x3 affine matrix and the offset via the
>
> GetMatrix() and GetOffset() methods.
>
> The 4x4 matrix is just the [  R  | O ]
>
> HTH
> karthik
>
>
> Grace Chen wrote:
>
> >Hi Luis,
> >
> >Thanx for your help!  However, while the formula for converting between
> >Quaternion to matrix is readily available, I still don't know how to use
> >those 6 parameters that VersorRigid3DTransform returns to compute the
> >transformation matrix.  Is there a formula that does it?  thanx!!
> >
> >Grace
> >
> >
> >----- Original Message ----- 
> >From: "Luis Ibanez" <luis.ibanez at kitware.com>
> >To: "Grace Chen" <Grace.Chen at swri.ca>
> >Cc: "Insight Users" <insight-users at itk.org>
> >Sent: Thursday, September 15, 2005 9:55 PM
> >Subject: Re: [Insight-users] 3D image registration
> >
> >
> >
> >
> >>Hi Grace,
> >>
> >>The reason why a Versor has only three components,
> >>while a Quaternion has four, is that Quaternions
> >>can describe rotations and scaling.
> >>
> >>When you use quaternions for describing only rotations,
> >>you must use unit quaternions.  A versor is simply a
> >>unit quaternion.
> >>
> >>So... when people talk about using Quaternions, they
> >>usually mean (or think) of Versors, even though they
> >>don't call them that way.
> >>
> >>Versor is the original name the Hamilton used for this
> >>concept when he introduced Quaternions in 1866.
> >>
> >>You will find more information about Versors in the ITK
> >>Software Guide
> >>
> >>
> >>     http://www.itk.org/ItkSoftwareGuide.pdf
> >>
> >>
> >>
> >>   Regards,
> >>
> >>
> >>      Luis
> >>
> >>
> >>
> >>-------------------
> >>Grace Chen wrote:
> >>
> >>
> >>>Hi Luis,
> >>>
> >>>Thank you for your help!
> >>>
> >>>I don't know why the technicians choosed the low frequency scan rate.
> >>>
> >>>
> >Given
> >
> >
> >>>such a data with thick spacing between slice, I can only do my best to
> >>>correct the movement...
> >>>
> >>>Since our data is MR scan on brain, we can be sure that it's a 3D rigid
> >>>movement.  I found in the ITK user manual about how to use
> >>>VersorRigid3DTransform.  However, my question is, since there are four
> >>>
> >>>
> >parts
> >
> >
> >>>constituting a quaternion, how come the class has only 3 parameters for
> >>>
> >>>
> >the
> >
> >
> >>>rotation?
> >>>
> >>>Thanx a lot!
> >>>
> >>>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, September 08, 2005 6:53 PM
> >>>Subject: Re: [Insight-users] 3D image registration
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>Hi Grace,
> >>>>
> >>>>The registration framework of ITK will manage images with
non-isotropic
> >>>>spacing. The registration process is fully done in physical
coordinates,
> >>>>so it is immune to the various spacings of your datasets.
> >>>>
> >>>>You may want to read details on this in the Image Registration Chapter
> >>>>of the ITK Software Guide
> >>>>
> >>>>        http://www.itk.org/ItkSoftwareGuide.pdf
> >>>>
> >>>>and the Tutorial on registration
> >>>>
> >>>>http://www.itk.org/CourseWare/Training/RegistrationMethodsOverview.pdf
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>Each one of the datasets may have different spacings along X, Y and Z,
> >>>>and different from the other dataset. The datasets can also have
> >>>>different number of pixels along each dimension.
> >>>>
> >>>>
> >>>>
> >>>>Than being said....
> >>>>
> >>>>Acquiring datasets with large inter-slice spacing is just
> >>>>*BAD-ENGINEERING* ...  very very bad engineering.
> >>>>
> >>>>Doing this is to let Claude Shannon die in vain,
> >>>>(along with his sampling theorem).
> >>>>
> >>>>The practice of acquiring datasets with hight in-plane resolution
> >>>>and large inter-slice spacing is a bad legacy from the tendency of
> >>>>clinicians to still look at the datasets slice by slice and fool
> >>>>themselves with the illusion that the dataset looks great.
> >>>>
> >>>>Each member of the medical image processing community has the
> >>>>moral responsibility of educating her/his fellow clinicians on
> >>>>how bad is to acquire dataset in such poor configurations.
> >>>>The easiest way to provide that education is to show them how
> >>>>bad a dataset look like when viewed in an orthogonal view, where
> >>>>the pixels have anisotropic ratios of 10:1.
> >>>>
> >>>>
> >>>>
> >>>>   Regards,
> >>>>
> >>>>
> >>>>      Luis
> >>>>
> >>>>
> >>>>-----------------
> >>>>Grace Chen wrote:
> >>>>
> >>>>
> >>>>
> >>>>><> Hi all,   I post my question a few days ago and didn't get any
> >>>>>feedback.  So, I post my question again in the next pargraph hoping
> >>>>>someone today will be able to help me with this problelm.  I am a new
> >>>>>ITK user, so my question should be trivial for those who use ITK's
> >>>>>registration tools.  Please help!! :>  Thanx!!   ----- Original
Message
> >>>>>----- *From:* Grace Chen <mailto:Grace.Chen at swri.ca> *To:*
> >>>>>insight-users at itk.org <mailto:insight-users at itk.org> *Sent:*
Thursday,
> >>>>>September 01, 2005 12:00 PM *Subject:* [Insight-users] 3D image
> >>>>>registration
> >>>>>Hi there,  Good day!   We are using ITK for registering 2D images for
> >>>>>our current project.  It's working very nicely for correcting most of
> >>>>>the misalignment in our data.  However, we noticed out-of-plant
> >>>>>
> >>>>>
> >movement
> >
> >
> >>>>>in our image data, so we want to extend our project to perform 3D
> >>>>>rigid registration.  The data I have is the MR scan for the brain.
The
> >>>>>dimension of the image is (256, 256, 8), and the spacing is (0.93mm,
> >>>>>0.93mm, 7mm).
> >>>>>So, our problem is: since the space between neighbor slices is so
> >>>>>distant, can the ITK
> >>>>>registration program perform 3D registration properly on this type of
> >>>>>data? ...or do we have to
> >>>>>use some additional VTK/ITK tools to cope with that?   If we can use
> >>>>>
> >>>>>
> >ITK
> >
> >
> >>>>>to register our data, can you recommand the registration component
good
> >>>>>for our data?   Any help is greatly appreciated!! :>   Have a great
> >>>>>
> >>>>>
> >day!
> >
> >
> >>>>> 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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> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >
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> >
> >
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