[Insight-users] Convert image's direction cosines to transform matrix

[Luis Ibanez]

Hi Dženan


Thanks a lot for sharing the solution that you found.

That's the Open Source spirit !


     Luis


------------------------------------------------------------------------
2010/4/28 Dženan Zukić <dzenanz at gmail.com>

> Hi Luis!
>
> Thanks for the provided code, but in the end it didn't really help me
> (aside from encouraging me that transformations are not that complicated). I
> re-read 3D matrix operations, did a lot of trial and error, and ended up
> with this code (it might be useful to someone):
>
> osg::ref_ptr<osg::Group> stuff=segmentInterestingStructures(...);
> //vertices have physical image coordinates
> osg::ref_ptr<osg::Group> isosurface=marchingCubesGPU(...); //accounts for
> spacing, so scaling is handled
> VisualizingImageType::DirectionType d=visualizing->GetDirection();
> d=d.GetTranspose(); //ITK matrix is in column-major format, OSG matrix is
> row major (trial and error)
>
> osg::Matrix matrix(d(0,0), d(0,1), d(0,2), 0,
>    d(1,0), d(1,1), d(1,2), 0,
>    d(2,0), d(2,1), d(2,2), 0,
>    0,   0,   0,   1);
> osg::Matrix t;
> VisualizingImageType::PointType origin=visualizing->GetOrigin();
> t.makeTranslate(origin[0], origin[1], origin[2]);
> matrix.postMult(t);
> osg::ref_ptr<osg::MatrixTransform> mt=new osg::MatrixTransform(matrix);
>
> osg::ref_ptr<Group> grp=new osg::Group;
> mt->addChild(isosurface);
> grp->addChild(mt);
> grp->addChild(stuff);
> mainForm.vis->setSceneData(grp);
>
> Regards,
> Dženan
>
> 2010/4/28 Luis Ibanez <luis.ibanez at kitware.com>
>
>
>> Hi Dženan
>>
>> This is indeed a common problem,
>> so, it is great that you bring it up.
>>
>>
>> Following the numbering of your questions:
>>
>> a) No, there is no direct way of forcing the direction
>>     matrix to be an identity. (and if there was such
>>     method we will strongly discourage you from using it)
>>
>> b)  You can change the direction matrix of the image,
>>      by using the ChangeImageInformationFilter.
>>      (but we strongly discourage you from doing so).
>>
>> c)  The RIGHT thing to do is to use the direction
>>      matrix to correct the orientation of the isosurface
>>      after you extract it.  In that way, the iso-surface
>>      will occupy the same coordinate system as the
>>      original image.
>>
>>
>> Options (a) and (b) are VERY dangerous if you are
>> dealing with real patient data.
>>
>>
>> Please find attached an example of how to do this
>> with ITK and VTK. You could directly use this example,
>> or you can probably follow the math and apply the
>> equivalent processing using OSG.
>>
>>
>> You will find the full source code at:
>>
>>                InsightApplications/Auxiliary/vtk
>>
>>
>>
>>
>>       Regards,
>>
>>
>>              Luis
>>
>>
>> ---------------------------------------------------------------------
>> 2010/4/27 Dženan Zukić <dzenanz at gmail.com>
>>
>>> Hi everybody,
>>>
>>> I guess someone has dealt with a problem similar to mine before. I am
>>> doing segmentation in a magnetic resonance image. The result of my
>>> segmentation is a polygonal model. Problem: How to visualize the resulting
>>> polygonal model along with scalar-field image?
>>>
>>> I use Qt, ITK and OpenSceneGraph. First I tried using osgVolume
>>> (ray-casting renderer) together with polygonal data in the same scene, but
>>> with that setup the depth information is lost. I resorted to using
>>> isosurface of the image instead of the image itself. It works, but I have to
>>> manage physical coordinates by myself - which is both a reinvention of the
>>> wheel and error-prone.
>>>
>>> So I decided to use ITK's physical coordinate managing routines
>>> (TransformPhysicalPointToIndex), but I ran into a problem. GetDirection does
>>> not return identity matrix for my images (at least not for sagittal ones),
>>> therefore my segmented parts end up displayed *outside* of the image.
>>> a) Is there a way to force image reading routines to load images into
>>> memory in such a way to have an identity matrix for directions?
>>> b) If not, is there a way to transform image data (using a filter) to get
>>> an image with identity matrix as "directions". Is that
>>> filter ChangeInformationImageFilter?
>>> c) What is the proper way to construct a transformation matrix to be
>>> applied to the isosurface of the image (which was generated assuming
>>> identity matrix directions) in order to bring it to same coordinates I get
>>> when using TransformIndexToPhysicalPoint? Just using matrix returned
>>> by GetDirection and adding translation to account for origin does not work.
>>>
>>> If anyone knows a better way to visualize a polygonal model alongside 3D
>>> image, I would like to hear it.
>>> Off topic question: is combining polygons with scalar fields so simple in
>>> VTK to justify a switch from OSG to VTK?
>>>
>>> Thanks to anyone who takes interest in this.
>>>
>>> Best regards,
>>> Dženan
>>>
>>
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