<div dir="ltr"><div>Many thanks <span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Rômulo,</span></div><div><br></div><div>For the following:</div><div>fixed point file: 50.pts</div><div>moving point file: 00.pts</div>
<div>deformation field: deform.nii.gz/deform.mhd</div><div><br></div><div>Would the following command be correct?</div><div>clitkCalculateTRE --ref=50.pts --input=00.pts --vf=deformation.nii.gz</div><div><br></div><div>I tried this but got no output.</div>
<div><br></div><div>Also, how does the clitkCalculateTRE command account for initial rigid/affine pre-alignment of fixed and moving images?</div><div><br></div><div>I also assume that only the .pts file are accepted and not .csv (comma separated)?</div>
<div>E.g:</div><div><div>39.0621 -117.187 -6.5</div><div>47.8512 50.7814 35.5</div><div>-114.258 -120.117 -92.5<br></div></div><div>etc...</div><div><br></div><div>Best wishes,</div><div><br></div><div>Bilal</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 1 October 2013 19:13, Rômulo Pinho <span dir="ltr"><<a href="mailto:romulopinho@yahoo.com.br" target="_blank">romulopinho@yahoo.com.br</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hello, Tian and Bilal,<br>
<br>
For question 1, you can indeed add landmarks with the space bar.
They are placed at the current cursor position and appear in the
Landmarks tab, on the left side of the main window. In the latest
version of the program I had contact with, you couldn't edit the
landmarks, as Bilal pointed out. Still, you can double click on one
landmark in the Landmarks tab and it is immediately displayed on the
image. You can remove a single landmark using the buttons on the GUI
and add a new landmark where you want. This is a workaround for the
editing functionality.<br>
<br>
For question 2, you can use the clitk suite that comes along with
VV. It is a large set of command line tools on which much of VV's
functionality is also based. There you'll find clitkCalculateTRE,
where you provide the reference points, the motion vectors obtained
in the registration (or bspline coefficients of the transformation),
and the transformed points. The app takes care of transforming the
points and calculating the TRE (average and std) before and after
registration. To compile the clitk suite, you have to enable the
BUILD_CLITK_* flags in VV's cmake and then run make. <br>
<br>
I hope this is useful.<br>
<br>
Best,<br>
Rômulo<div><div class="h5"><br>
<br>
<br>
<div>On 01/10/2013 14:57, Bilal Tahir wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Tian,
<div><br>
</div>
<div>For question 2 above, I had asked this previously and below
is the answer I received from Stephan Klein, one of the
developers of Elastix: </div>
<div><br>
</div>
<div><i><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">"I
would do it like this:</span><br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<span style="font-family:arial,sans-serif;font-size:12.727272033691406px">1)
ask your radiologists to click corresponding points in the
ORIGINAL fixed and moving images. This gives you two
files: fixedpoints.txt and movingpoints.txt. </span><br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<span style="font-family:arial,sans-serif;font-size:12.727272033691406px">2)
Run </span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">elastix</span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">: </span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">elastix</span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"> -f
fixed -m moving -p parameterfile -out outdir</span><br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<span style="font-family:arial,sans-serif;font-size:12.727272033691406px">3)
Run transformix to transform the FIXED points: transformix
-def fixedpoints.txt -tp outdir/TransformParameters.0.</span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">txt
-out outdir</span><br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<span style="font-family:arial,sans-serif;font-size:12.727272033691406px">4)
now compare the transformed fixed points (which are stored
in outdir/outputpoints.txt) to the original moving
points. </span><br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Instead
of using the custom </span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">elastix</span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"> input
and output point formats (see </span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">elastix</span><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"> manual,
section on transformix), you could also use .vtk (in
legacy asci vtk format). </span><br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<br style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Since
the transformation is defined as a mapping from the fixed
image domain to the moving image domain, you can only
directly transform points from fixed to moving image."</span></i><br>
</div>
<div><i><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br>
</span></i></div>
<div><font face="arial, sans-serif">For calculation of target
registration error, I don't think you can do that in VV.
However, I'm sure one of the members on this mailbase has a
bash script for this that they could share with us
specifically for Elastix. You could also use Matlab.</font></div>
<div><i><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br>
</span></i></div>
<div><font face="arial, sans-serif">For your first question, you
can identify landmarks in VV with the space bar. However,
unless it has recently been improved, when I looked into it
there were a number of problems using VV for this including
being unable to edit a landmark once identified. One of the
developers can provide more information on this. As it is
open source you can always edit it.</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Best wishes,</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Bilal</font></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 1 October 2013 11:14, qi tian <span dir="ltr"><<a href="mailto:tianqig@gmail.com" target="_blank">tianqig@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Hi,<br>
<br>
</div>
<div>I have two questions related to landmark
points:<br>
<br>
1. Can vv be used for clinicians by clicking <br>
landmark points for a given image?<br>
Ideally these landmark points can be stored<br>
</div>
</div>
in two files, I could not find any documentation<br>
on how this can be done with vv.<br>
</div>
<br>
<br>
</div>
<div>2. Can a transform be applied to a set <br>
of landmark points to create a new set of landmark<br>
points in vv? For instance, this set of landmark<br>
points is from a moving image, the transform <br>
is estimated with elastix, then the transformed <br>
</div>
<div>landmark points can be compared with ones<br>
</div>
<div>
of a target image. This way it helps to to assess<br>
registration performance.<br>
<br>
</div>
<div>Wonder if this can be done with vv?<br>
</div>
<div><br>
</div>
<div>Thanks<span><font color="#888888"><br>
<br>
</font></span></div>
<span><font color="#888888">
<div>Tian<br>
</div>
</font></span></div>
</div>
<br>
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<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">Bilal Tahir,
<div>James Morrison Researcher in Radiotherapy Imaging,</div>
<div>Department of Clinical Oncology,</div>
<div>University of Sheffield</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
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</pre>
</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><pre cols="72">--
Rômulo Pinho
R&D Software Engineer
TecGraf - PUC-Rio
<a href="mailto:rpinho@tecgraf.puc-rio.br" target="_blank">rpinho@tecgraf.puc-rio.br</a>
<a href="http://www.tecgraf.puc-rio.br/~rpinho/" target="_blank">http://www.tecgraf.puc-rio.br/~rpinho/</a></pre>
</font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Bilal Tahir,<div>James Morrison Researcher in Radiotherapy Imaging,</div><div>Department of Clinical Oncology,</div><div>University of Sheffield</div>
</div>
</div>