When using itksnap , Is the final image resampled or has the same resolution as the original ?<br><br>If resampled I think you add the resampling as a translation to the matrix transform.<br><br>Regards<br>Darshan<br><br><div class="gmail_quote">
On Tue, May 25, 2010 at 10:03 AM, Scott Johnson <span dir="ltr"><<a href="mailto:Scott.Johnson@neuwave.com">Scott.Johnson@neuwave.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Thanks Jothy,</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">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.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">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?</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">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.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Thanks</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> --
Scott</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; padding: 3pt 0in 0in;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> Jothy
[mailto:<a href="mailto:jothybasu@gmail.com" target="_blank">jothybasu@gmail.com</a>] <br>
<b>Sent:</b> Monday, May 24, 2010 4:58 PM<div><div></div><div class="h5"><br>
<b>To:</b> Scott Johnson<br>
<b>Cc:</b> VTK<br>
<b>Subject:</b> Re: [vtkusers] Segment Import from itksnap</div></div></span></p>
</div><div><div></div><div class="h5">
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;">Scott, I hope you are aware of
the coordinate conventions between imaging and RT/IEC. Z and Y are
interchanged.<br>
<br>
Jothy </p>
<div>
<p class="MsoNormal">On Mon, May 24, 2010 at 10:52 PM, Scott Johnson <<a href="mailto:Scott.Johnson@neuwave.com" target="_blank">Scott.Johnson@neuwave.com</a>>
wrote:</p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Thanks Jothy, now I can shift the ROI,
but I’m still trying to figure out the mathematical relationship between
the 2 coordinate systems. </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">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?</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">
-- Scott</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-color: -moz-use-text-color;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> Jothy
[mailto:<a href="mailto:jothybasu@gmail.com" target="_blank">jothybasu@gmail.com</a>]
<br>
<b>Sent:</b> Monday, May 24, 2010 4:20 PM</span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 10pt;"><br>
<b>To:</b> Scott Johnson<br>
<b>Cc:</b> VTK<br>
<b>Subject:</b> Re: [vtkusers] Segment Import from itksnap</span></p>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;">Will
vtkTransformPolyDataFilter help? Of course, you should know the vector to
shift.<br>
<br>
Jothy</p>
<div>
<p class="MsoNormal">On
Mon, May 24, 2010 at 10:00 PM, Scott Johnson <<a href="mailto:Scott.Johnson@neuwave.com" target="_blank">Scott.Johnson@neuwave.com</a>>
wrote:</p>
<div>
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">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.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">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.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Thanks</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">
-- Scott</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-color: -moz-use-text-color;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> Jothy
[mailto:<a href="mailto:jothybasu@gmail.com" target="_blank">jothybasu@gmail.com</a>]
<br>
<b>Sent:</b> Monday, May 24, 2010 3:56 PM<br>
<b>To:</b> Scott Johnson<br>
<b>Cc:</b> VTK<br>
<b>Subject:</b> Re: [vtkusers] Segment Import from itksnap</span></p>
</div>
<div>
<div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;">I think
you should set the appropriate ImageOrigin.<br>
<br>
Jothy</p>
<div>
<p class="MsoNormal">On
Mon, May 24, 2010 at 9:52 PM, Scott Johnson <<a href="mailto:Scott.Johnson@neuwave.com" target="_blank">Scott.Johnson@neuwave.com</a>>
wrote:</p>
<div>
<div>
<p class="MsoNormal">Hi
Folks,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">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.)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">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.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">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?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thanks</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
-- Scott</p>
<p class="MsoNormal"> </p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><br>
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