[vtkusers] Segment Import from itksnap

[Darshan Pai]

When using itksnap , Is the final image resampled or has the same resolution
as the original ?

If resampled I think you add the resampling as a translation to the matrix
transform.

Regards
Darshan

On Tue, May 25, 2010 at 10:03 AM, Scott Johnson
<Scott.Johnson at neuwave.com>wrote:

>  Thanks Jothy,
>
>
>
> I am familiar with the coordinate conventions in DICOM.  What I’m trying to
> figure out is the coordinate system written by itksnap and how it maps to
> the vtk coordinate system.  Does itksnap write ITK based coordinates to the
> VTK Mesh format?  It evidently doesn’t do the conversion to the VTK
> coordinate system or it would line up with the images out of the box.
>
>
>
> If I rotate 180 degrees about the Y axis my shape looks like it has the
> correct orientation, but it isn’t in the right spot in relation to the
> images.  What point should I be rotating about?  Is the origin the top left
> corner of the origin images or the VTK origin at the bottom left corner?  Is
> there already a filter somewhere which will automatically translate ITK
> coordinates into VTK coordinates?
>
>
>
> I’ve been poking at different coordinate conventions using Paraview, but
> haven’t hit on the right combination of rotations and translations to make
> it work.  I can’t be the first person to have done this.
>
>
>
> Thanks
>
>
>
>                                 -- Scott
>
>
>
> *From:* Jothy [mailto:jothybasu at gmail.com]
> *Sent:* Monday, May 24, 2010 4:58 PM
>
> *To:* Scott Johnson
> *Cc:* VTK
> *Subject:* Re: [vtkusers] Segment Import from itksnap
>
>
>
> Scott, I hope you are aware of the coordinate conventions between imaging
> and RT/IEC. Z and Y are interchanged.
>
> Jothy
>
> On Mon, May 24, 2010 at 10:52 PM, Scott Johnson <Scott.Johnson at neuwave.com>
> wrote:
>
> Thanks Jothy, now I can shift the ROI, but I’m still trying to figure out
> the mathematical relationship between the 2 coordinate systems.
>
>
>
> I thought that it was just the differences in origin (Top/Left vs.
> bottom/left) but that doesn’t seem to be correct.  By just eyeballing it, Z
> coordinates seem to differ as well.  Maybe reversed?
>
>
>
>                                 -- Scott
>
>
>
> *From:* Jothy [mailto:jothybasu at gmail.com]
> *Sent:* Monday, May 24, 2010 4:20 PM
>
>
> *To:* Scott Johnson
> *Cc:* VTK
> *Subject:* Re: [vtkusers] Segment Import from itksnap
>
>
>
> Will vtkTransformPolyDataFilter help? Of course, you should know the vector
> to shift.
>
> Jothy
>
> On Mon, May 24, 2010 at 10:00 PM, Scott Johnson <Scott.Johnson at neuwave.com>
> wrote:
>
> It seems that my image origin is fine, but the exported segmentation origin
> is not.  If the image origin was incorrect I would have expected a different
> result in Paraview.
>
>
>
> I’m just looking for something to shift the PolyData.  The issue is by how
> much?  Right now I’m looking at shifting the vtkActor for the PolyData.
>
>
>
> Thanks
>
>
>
>                                 -- Scott
>
>
>
> *From:* Jothy [mailto:jothybasu at gmail.com]
> *Sent:* Monday, May 24, 2010 3:56 PM
> *To:* Scott Johnson
> *Cc:* VTK
> *Subject:* Re: [vtkusers] Segment Import from itksnap
>
>
>
> I think you should set the appropriate ImageOrigin.
>
> Jothy
>
> On Mon, May 24, 2010 at 9:52 PM, Scott Johnson <Scott.Johnson at neuwave.com>
> wrote:
>
> Hi Folks,
>
>
>
> I segmented a volume in itksnap, exported it to a VTK Mesh, and attempted
> to import it into my VTK application using vtkPolyDataReader.  The shape
> seems to import correctly, but it is located outside my image volume.  (To
> the left and down.)
>
>
>
> I’ve tried converting the vtp file to an XML file and imported using
> vtkXMLPolyDataReader, with the same result.  It’s also the same if I import
> to Paraview.
>
>
>
> Is this the difference between the ITK and VTK coordinate systems?  If so,
> is this only a translation issue?  What is the mathematical relationship
> between the ITK and VTK coordinate systems?
>
>
>
> Thanks
>
>
>
>                                 -- Scott
>
>
>
>
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