[Insight-users] 3D image registration

Fri Sep 16 12:10:35 EDT 2005

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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> >>>
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>
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