[Insight-users] gantry tilt compensation

[Luis Ibanez]

Hi Zsolt,


It probably makes more sense to first correct the geometric
distortions in your image before undertaking a segmentation
process.  Otherwise you will end up having to apply a geometrical
correction to the segmentation itself.

If you use a BSpline interpolator in the resampling process,
you probably will obtain resampled images with quality suitable
for a segmentation process.

Please read the resampling chapter on the ITK Software Guide

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

For a description of the segmentation methods available in ITK,
please look at the Tutorials

     http://www.itk.org/HTML/Tutorials.htm

in particular to

http://www.itk.org/CourseWare/Training/SegmentationMethodsOverview.pdf

and to the Segmentation chapter on the ITK SoftwareGuide.

For methods for converting ITK images into VTK images
Please look at the tutorial

http://www.itk.org/CourseWare/Training/GettingStarted-II.pdf

Once you have a VTK image, you can apply any variant of the
vtkContour filter.



   Regards,



      Luis



--------------------
Erő Zsolt wrote:

> Hi, Luis
> 
> Thank you for the informations, it was really what I needed. Just
> have an other question, what is the best time to do the segmentation
> in the reconstruction process. Typically for non-tilted slices, I do
> the segmentation before any transformation, just on the filtered
> source images, but here, you said it is good to resample the result,
> but for me any resampling did a terrible work when the aim was to get
> a binary mask. What is the case here? Do the segmentation (1.) on the
> original sheared volume and do the affine transform (2.) after, and the
> resampling (3.) (is it needed for a good binary mask?) after (1-2-3), or maybe
> it is better to do the affine transform on a resampled volume (1-3-2)
> or just compute the matrix of the cross product of a resampling and
> shearing and use this (1-23)? The purpose of the binary mask is to be
> converted later to a 3D polygon object in VTK.
> 
> Thanks,
> Zsolt Ero
> 
> --
> Monday, August 23, 2004, 5:40:34 AM,  Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
> 
> LI> Hi Zsolt,
> 
> LI> The gantry tilt will be equivalent to a Shearing
> LI> in the Affine Transform.  A typical shearing effect
> LI> in a 2D transform will generate a matrix of the form
> 
> 
> LI>      1  A
> LI>      0  1
> 
> LI> or
> 
> LI>      1   0
> LI>      B   1
> 
> 
> LI> Where "A", and "B" will be shearing factors and can
> LI> be positive or negative.
> 
> LI> The AffineTransform in ITK
> LI> http://www.itk.org/Insight/Doxygen/html/classitk_1_1AffineTransform.html
> LI> doesn't have an explicit method for setting shearing factors.
> LI> You can however setup your matrix and then pass it to the
> LI> transform with the SetMatrix() method.
> 
> LI> Once you configure your Affine transform, you may want to
> LI> use the ResampleImageFilter
> LI> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ResampleImageFilter.html
> LI> in order to resample your image into a rectilinear grid.
> 
> LI> You are strongly encouraged to read the chapter on image
> LI> resampling from the ITK SoftwareGuide
> 
> LI>      http://www.itk.org/ItkSoftwareGuide.pdf
> 
> 
> 
> LI>    Regards,
> 
> 
> LI>      Luis
> 
> 
> 
> LI> -------------------
> LI> Erő Zsolt wrote:
> 
>>>I am trying to write a small program that transforms a volume of
>>>slices made with tilted CT head into a standard (rectangular) volume
>>>array, because no algorithms support such type of volumes in ITK or
>>>VTK (as long as I know). I know, there is an affine transform in ITK,
>>>but don't know what to do with it. Could you help me how to use it
>>>(not for coding but mathematically)? I know the tilt angle from the
>>>DICOM file, but don't know how can I reverse-transform on the
>>>transformed volume. Any web resource could be useful, I looked up
>>>google, but found nothing usable.
>>>
>>>Thanks,
>>>Zsolt Ero
>>>
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>>
> 
> 
> 
> 
> 
> 
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