[Insight-users] How to register MRI/fMRI?

[Luis Ibanez]

Hi Yu,

If the two volumes are from the same subject you *DO NOT* need
to do any rescaling.


ITK performs registration in physical space, not in pixel space,
therefore all the transformations are relative to millimeters,
not pixels.

You *MUST* verify that your images have correct values for pixel
spacing and origin. Once you verify that, you can proceed to
register them.

Note that even if the images are from different subjects, human
variability is such that the size of heads from adult specimens
are not too different. If you ever need to register brains from
different subjects, the scaling factors should be *VERY* close
to 1.0.

When talking about "volume size", make sure that you are not
confusing "Number of Pixels", with "Image Resolution" or with
"Image Extent".


You *MUST* read the resampling chapter from the ITK Software Guide:


    http://www.itk.org/ItkSoftwareGuide.pdf



  Regards,



     Luis


----------------
Yu Qi wrote:

> Hi Luis,
> I solved this problem. Thank you!
>  
> But I have another question.
> As the two volumes have different size, do I have to rescale one of them?
> Or I need a affine transformation?
> Thank you!
>  
> Best regards,
>  
> Yu Qi
> 
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
> 
> 
>     Hi Yu,
> 
>      From your description it is not possible to
>     know what the problem is with your code.
> 
>     Please post your code the list.
> 
> 
>     Thanks,
> 
> 
>     Luis
> 
> 
>     --------------
>     Yu Qi wrote:
> 
>      > Hi Luis,
>      > Thank you!
>      >
>      > I am now writing my code. I have
>      > a MRI image, .img 256X256X256
>      > and a EPI image, .img 64X64X28
>      > I use
>      > itkMultiResolutionImageRegistrationMethod
>      > itkMattesMutualInformationImageToImageMetric
>      > itkLinearInterpolateImageFunction
>      > itkMultiResolutionPyramidImageFilter
>      > itkVersorRigid3DTransform
>      > itkVersorRigid3DTransformOptimizer
>      >
>      >
>      > And I do this:
>      > 1.read fixed and moving files(succeed)
>      > 2.cast image into float type (succeed)
>      > 3.initialize parameters: spacing,origin, transformation, optimizer,
>     &! gt; metric,pyramid
>      > 4.try to register
>      > 5.resample moving image
>      > 6.write resampled image
>      >
>      > If I skip step4 and 5, I can read images and cast them and then
>     rewrite
>      > as a new image.
>      >
>      > But I can not register them. I copy the code of Command observer, but
>      > no data displayed when running the program. It seems that the
>      > registration didn't start.
>      >
>      > I think I missed something.
>      > Do you know what is the problem?
>      >
>      > Best Regards,
>      > Yu Qi
>      >
>      >
>      > */Luis Ibanez /* wrote:
>      >
>      >
>      >
>      > Hi Yu,
>      >
>      > Mutual information is an appropriate Metric for registering
>      > MRI to fMRI. Please read the Image Registration chapter
>      > from the ITK Software Guide:
>      >
>      > http://www.itk.org/ItkSoftwareGuide.pdf
>      >
>      > You will find examples on 3D registration in
>      >
>      >
>      > Insight/Examples/Registration
>      >
>      > as well as some 3D multi-modality image registration
>      > applications in
>      >
>      > InsightApplications
>      >
>      >
>      >
>      > Regards,
>      >
>      >
>      > Luis
>      >
>      >
>      > ------------------
>      > Yu Qi wrote:
>      >
>      > > Hi, everybody,
>      > >
>      > > I have 3D MRI and fMRI from the same subject.
>      > > And I want to align these two volumes through ITK+VC6.0.
>      > > I think I should use mutual information method.
>      > > What do you think?
>      > > Can you give me some suggestions about the
>      > > metric, optimizer, interpolator and other filters?
>      > >
>      > > Thank you!
>      > >!
>      > > Have a nice day!
>      > >
>      > >
>      > >
>      > > *Best Regards!*
>      > > **
>      > > *Yu Qi*
>      > >
>      > >
>      > >
>      > >
>      > >
>      >
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