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Hello, Bilal,<br>
Try adding "-v" to the cmd line.<br>
As for the initial rigid transformation, the app assumes the
alignment has already been made, as far as I can remember (I don't
have the source code here with me right now).<br>
Regarding the file type, there's an option (--type, I think) with
which you specify the landmarks' format. But in any case its either
.pts or the .txt used by VV. It's .pts by default.<br>
Best,<br>
Rômulo<br>
<br>
<br>
<div class="moz-cite-prefix">On 01/10/2013 16:09, Bilal Tahir wrote:<br>
</div>
<blockquote
cite="mid:CAFZ9P6Gx-_bBNVjH3i3jzbKo=dksqJ0sxc9Dz4HwGoiH+TNW_A@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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
moz-do-not-send="true"
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>
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<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>
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<span class="HOEnZb"><font color="#888888">
<pre cols="72">--
Rômulo Pinho
R&D Software Engineer
TecGraf - PUC-Rio
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<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>
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