[IGSTK-Users] Needle Biopsy demonstration and display problems

[Patrick Cheng]

Hi Sophie,

I am sorry, I was a little confused about last email. So the problem is: 
The image reads fine, but they are not displayed in the correct orientation.

This problem might be because the images do not have the complete 
acquisition parameters, such as the "patient orientation direction cosine".

In igstkView2D.cxx line 56:

/** Select the orientation of the View */
void View2D::RequestSetOrientation( const OrientationType & orientation )
{
   igstkLogMacro( DEBUG, "igstk::View2D::RequestSetOrientation called 
....\n");

   m_Orientation = orientation;

   double focalPoint[3];
   double position[3];

   for ( unsigned int cc = 0; cc < 3; cc++)
     {
     focalPoint[cc] = 0.0;
     position[cc]   = focalPoint[cc];
     }

   const double distanceToFocalPoint = 1000;

   switch( m_Orientation )
     {
     case Sagittal:
       {
       position[0] += distanceToFocalPoint;
       m_Camera->SetViewUp (     0,  0,  1 );
       break;
       }
     case Coronal:
       {
       position[1] -= distanceToFocalPoint;
       m_Camera->SetViewUp (     0,  0,  1 );
       break;
       }
     case Axial:
       {
       position[2] -= distanceToFocalPoint;
       m_Camera->SetViewUp (     0,  -1,  0 );
       break;
       }
     }

   m_Camera->SetPosition (   position );
   m_Camera->SetFocalPoint ( focalPoint );
   m_Camera->SetClippingRange( 0.1, 100000 );
   m_Camera->ParallelProjectionOn();
}

This is where all the cameras being set up, affects the view orientation 
in the display window.

If you can't find the problem with the data. One thing you can do is to 
adjust your camera so that it's being positioned in the right way.

You can add a function in igstkView class {View class will be refactored 
to include this function in the future}:

   /** Request to return the camera to a known position */
   void RequestSetCamera( vtkCamera * camera )
   {
     m_Camera = camera;
     this->m_Renderer->SetActiveCamera( m_Camera );
   };

You can then set up your camera in similar way and pass it on to your 
view window.

Hope this helps,

Patrick


Sophie Blestel wrote:
> Hi Patrick,
> 
> I have a dicom serie of MR images but I don't manage to read them 
> correctly with igstk (the 3D view is correct but not the 2D views, 
> because of the orientation..) Maybe because my images are not .dcm ? 
> (they come directly from the mri)
> 
> Thanks,
> 
> Sophie
> 
> 2007/4/12, Patrick Cheng <cheng at isis.georgetown.edu 
> <mailto:cheng at isis.georgetown.edu>>:
> 
>     Hi Sophie,
> 
>     IGSTK dicom reader is checking the Modality tag of dicom images
>     internally, it reads MR, CT, and XA (for Siemens DynaCT) images.
> 
>     Patrick
> 
>     Sophie Blestel wrote:
>      > Hi,
>      >
>      > I'm trying to read dicom datas with igstk but I don't manage to open
>      > them correctly. I tried with "your" dicom series and it works.
>      > What kind of dicom series does igstk read ? Only .dcm ? How can I get
>      > .dcm from my dicom series ?
>      >
>      > Thanks,
>      >
>      > Sophie
>      >
>      >
>      >
>      >  > Hi Patrick,
>      >  >
>      >  > Thank you for your data.
>      >  > I will not be able to test it during one month, but I will try
>     to use
>      > it a
>      >  > soon as I'll be back. Should the Needle Biopsy application
>     work fine
>      > with
>      >  > this data ?
>      >  >
>      >  > Thank you for your help and have a nice day.
>      >  >
>      >  > Vincent Gratsac
>      >  >
>      >  >> Hi Vincent,
>      >  >>
>      >  >> Here is a DICOM series acquired using DynaCT.
>      >  >>
>      >  >> I put it on our Data Server:
>      >  >>
>      >  >> http://isiswiki.georgetown.edu/DataServer
>      >  >>
>      >  >> Under "Temporary" directory, a file named:
>      >  >>
>      >  >> series_7_256_Nat_Manual_Bone_Smooth_[InSpace3D].zip
>      >  >>
>      >  >> Hope this will help.
>      >  >>
>      >  >> Patrick
>      >  >>
>      >  >> Vincent Gratsac wrote:
>      >  >>> Hi all,
>      >  >>> As I told you before, I'm quite new to IGSTK, and I would
>     like to do
>      >  >>> some tests on the Needle Biopsy Example.
>      >  >>> The goal would be to open a volume (DICOM for the moment),
>     to open
>      > some
>      >  >>> VTK surfaces (with my home made VtkPolyDataReader) and to
>     simulate
>      >  >>> navigation with the MouseTracker.  Unfortunately, I
>     currently don't
>      >  >>> have
>      >  >>> any DICOM data which are displayed correctly with this
>     application. In
>      >  >>> fact, the display doesn't correspond with the declared
>     Axial, Sagital
>      >  >>> and Coronal views.  Moreover, 2D and 3D views are not
>     centered on the
>      >  >>> volume.  So my question is : Do you have any DICOM data that
>     would
>      > help
>      >  >>> me to do these tests ? And do you have any idea on reasons
>     of these
>      >  >>> display problems
>      >  >>>
>      >  >>> I would be very grateful for your help.
>      >  >>>
>      >  >>> Have a nice day,
>      >  >>>
>      >  >>
>      >  >
>      >  >
>      >  >
> 
>