[Insight-users] 3D image registration

Fri Sep 16 12:54:52 EDT 2005

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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>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>------------------------------------------------------------------------
>>>>        
>>>>
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>>>>>          
>>>>>
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>>>>        
>>>>
>>>
>>>
>>>      
>>>
>>    
>>
>
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>