<div dir="ltr"><div><div><div>Hi, Bilal and R?mulo<br><br></div><span style="font-family:arial,sans-serif;font-size:12.571428298950195px">Thanks for your quick reply, v</span>ery glad to know my two</div><div> problems have been discussed previously. <br>
<br></div>Now I am able to create landmark points with the <font size="4"><b>space bar</b></font>,<br>
</div><div>and save them. I will try to work on landmark point sets for<br>both fixed and moving images.<br></div><div><br></div><div>For the <span style="font-family:arial,sans-serif;font-size:12.571428298950195px">clitk suite, wonder if a binary version of vv may include </span></div>
<div><span style="font-family:arial,sans-serif;font-size:12.571428298950195px">it or I have to compile by myself. Any simple document for the</span></div><div><span style="font-family:arial,sans-serif;font-size:12.571428298950195px">clitk suite?</span></div>
<div><span style="font-family:arial,sans-serif;font-size:12.571428298950195px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:12.571428298950195px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:12.571428298950195px">Tian</span></div>
<div><font face="arial, sans-serif"><span style="font-size:12.571428298950195px">Singapore Bioimaging Consortium (SBIC)</span></font></div><div><font face="arial, sans-serif"><span style="font-size:12.571428298950195px">Singapore</span></font></div>
<div><div><div><div><div></div></div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Oct 2, 2013 at 2:14 AM, <span dir="ltr"><<a href="mailto:vv-request@creatis.insa-lyon.fr" target="_blank">vv-request@creatis.insa-lyon.fr</a>></span> wrote:<br>
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Today's Topics:<br>
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1. Use vv as a landmark annotation/comparison tool? (qi tian)<br>
2. Re: Use vv as a landmark annotation/comparison tool? (Bilal Tahir)<br>
3. Re: Use vv as a landmark annotation/comparison tool?<br>
(R?mulo Pinho)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 1 Oct 2013 18:14:44 +0800<br>
From: qi tian <<a href="mailto:tianqig@gmail.com">tianqig@gmail.com</a>><br>
To: <a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a><br>
Subject: [Vv] Use vv as a landmark annotation/comparison tool?<br>
Message-ID:<br>
<<a href="mailto:CAMTCV5sVVTu2bUm9M9nTQngD51-PPZf2oN%2BMcssK5fvbW0ytSg@mail.gmail.com">CAMTCV5sVVTu2bUm9M9nTQngD51-PPZf2oN+McssK5fvbW0ytSg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi,<br>
<br>
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>
in two files, I could not find any documentation<br>
on how this can be done with vv.<br>
<br>
<br>
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>
landmark points can be compared with ones<br>
of a target image. This way it helps to to assess<br>
registration performance.<br>
<br>
Wonder if this can be done with vv?<br>
<br>
Thanks<br>
<br>
Tian<br>
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<br>
Message: 2<br>
Date: Tue, 1 Oct 2013 18:57:06 +0100<br>
From: Bilal Tahir <<a href="mailto:b.tahir@sheffield.ac.uk">b.tahir@sheffield.ac.uk</a>><br>
To: "<a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a>" <<a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a>><br>
Subject: Re: [Vv] Use vv as a landmark annotation/comparison tool?<br>
Message-ID:<br>
<CAFZ9P6GRq4Bu94xD0rbsM-yCzKjZ8i=<a href="mailto:RtEP3nOXLZDHMt7AgeA@mail.gmail.com">RtEP3nOXLZDHMt7AgeA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Tian,<br>
<br>
For question 2 above, I had asked this previously and below is the answer I<br>
received from Stephan Klein, one of the developers of Elastix:<br>
<br>
*"I would do it like this:<br>
1) ask your radiologists to click corresponding points in the ORIGINAL<br>
fixed and moving images. This gives you two files: fixedpoints.txt and<br>
movingpoints.txt.<br>
2) Run elastix: elastix -f fixed -m moving -p parameterfile -out outdir<br>
3) Run transformix to transform the FIXED points: transformix -def<br>
fixedpoints.txt -tp outdir/TransformParameters.0.txt -out outdir<br>
4) now compare the transformed fixed points (which are stored in<br>
outdir/outputpoints.txt) to the original moving points.<br>
<br>
Instead of using the custom elastix input and output point formats (see<br>
elastix manual, section on transformix), you could also use .vtk (in legacy<br>
asci vtk format).<br>
<br>
Since the transformation is defined as a mapping from the fixed image<br>
domain to the moving image domain, you can only directly transform points<br>
from fixed to moving image."*<br>
*<br>
*<br>
For calculation of target registration error, I don't think you can do that<br>
in VV. However, I'm sure one of the members on this mailbase has a bash<br>
script for this that they could share with us specifically for Elastix. You<br>
could also use Matlab.<br>
*<br>
*<br>
For your first question, you can identify landmarks in VV with the space<br>
bar. However, unless it has recently been improved, when I looked into it<br>
there were a number of problems using VV for this including being unable to<br>
edit a landmark once identified. One of the developers can provide<br>
more information on this. As it is open source you can always edit it.<br>
<br>
Best wishes,<br>
<br>
Bilal<br>
<br>
<br>
On 1 October 2013 11:14, qi tian <<a href="mailto:tianqig@gmail.com">tianqig@gmail.com</a>> wrote:<br>
<br>
> Hi,<br>
><br>
> 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>
> in two files, I could not find any documentation<br>
> on how this can be done with vv.<br>
><br>
><br>
> 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>
> landmark points can be compared with ones<br>
> of a target image. This way it helps to to assess<br>
> registration performance.<br>
><br>
> Wonder if this can be done with vv?<br>
><br>
> Thanks<br>
><br>
> Tian<br>
><br>
> _______________________________________________<br>
> vv mailing list<br>
> <a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a><br>
> <a href="http://www.creatis.insa-lyon.fr/mailman/listinfo/vv" target="_blank">http://www.creatis.insa-lyon.fr/mailman/listinfo/vv</a><br>
><br>
><br>
<br>
<br>
--<br>
Bilal Tahir,<br>
James Morrison Researcher in Radiotherapy Imaging,<br>
Department of Clinical Oncology,<br>
University of Sheffield<br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 01 Oct 2013 15:13:51 -0300<br>
From: R?mulo Pinho <<a href="mailto:romulopinho@yahoo.com.br">romulopinho@yahoo.com.br</a>><br>
To: <a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a><br>
Subject: Re: [Vv] Use vv as a landmark annotation/comparison tool?<br>
Message-ID: <<a href="mailto:524B10DF.2030608@yahoo.com.br">524B10DF.2030608@yahoo.com.br</a>><br>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br>
<br>
Hello, Tian and Bilal,<br>
<br>
For question 1, you can indeed add landmarks with the space bar. They<br>
are placed at the current cursor position and appear in the Landmarks<br>
tab, on the left side of the main window. In the latest version of the<br>
program I had contact with, you couldn't edit the landmarks, as Bilal<br>
pointed out. Still, you can double click on one landmark in the<br>
Landmarks tab and it is immediately displayed on the image. You can<br>
remove a single landmark using the buttons on the GUI and add a new<br>
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<br>
is a large set of command line tools on which much of VV's functionality<br>
is also based. There you'll find clitkCalculateTRE, where you provide<br>
the reference points, the motion vectors obtained in the registration<br>
(or bspline coefficients of the transformation), and the transformed<br>
points. The app takes care of transforming the points and calculating<br>
the TRE (average and std) before and after registration. To compile the<br>
clitk suite, you have to enable the BUILD_CLITK_* flags in VV's cmake<br>
and then run make.<br>
<br>
I hope this is useful.<br>
<br>
Best,<br>
R?mulo<br>
<br>
<br>
On 01/10/2013 14:57, Bilal Tahir wrote:<br>
> Hi Tian,<br>
><br>
> For question 2 above, I had asked this previously and below is the<br>
> answer I received from Stephan Klein, one of the developers of Elastix:<br>
><br>
> /"I would do it like this:<br>
> 1) ask your radiologists to click corresponding points in the ORIGINAL<br>
> fixed and moving images. This gives you two files: fixedpoints.txt and<br>
> movingpoints.txt.<br>
> 2) Run elastix: elastix -f fixed -m moving -p parameterfile -out outdir<br>
> 3) Run transformix to transform the FIXED points: transformix -def<br>
> fixedpoints.txt -tp outdir/TransformParameters.0.txt -out outdir<br>
> 4) now compare the transformed fixed points (which are stored in<br>
> outdir/outputpoints.txt) to the original moving points.<br>
><br>
> Instead of using the custom elastix input and output point formats<br>
> (see elastix manual, section on transformix), you could also use .vtk<br>
> (in legacy asci vtk format).<br>
><br>
> Since the transformation is defined as a mapping from the fixed image<br>
> domain to the moving image domain, you can only directly transform<br>
> points from fixed to moving image."/<br>
> /<br>
> /<br>
> For calculation of target registration error, I don't think you can do<br>
> that in VV. However, I'm sure one of the members on this mailbase has<br>
> a bash script for this that they could share with us specifically for<br>
> Elastix. You could also use Matlab.<br>
> /<br>
> /<br>
> For your first question, you can identify landmarks in VV with the<br>
> space bar. However, unless it has recently been improved, when I<br>
> looked into it there were a number of problems using VV for this<br>
> including being unable to edit a landmark once identified. One of the<br>
> developers can provide more information on this. As it is open source<br>
> you can always edit it.<br>
><br>
> Best wishes,<br>
><br>
> Bilal<br>
><br>
><br>
> On 1 October 2013 11:14, qi tian <<a href="mailto:tianqig@gmail.com">tianqig@gmail.com</a><br>
> <mailto:<a href="mailto:tianqig@gmail.com">tianqig@gmail.com</a>>> wrote:<br>
><br>
> Hi,<br>
><br>
> 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>
> in two files, I could not find any documentation<br>
> on how this can be done with vv.<br>
><br>
><br>
> 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>
> landmark points can be compared with ones<br>
> of a target image. This way it helps to to assess<br>
> registration performance.<br>
><br>
> Wonder if this can be done with vv?<br>
><br>
> Thanks<br>
><br>
> Tian<br>
><br>
> _______________________________________________<br>
> vv mailing list<br>
> <a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a> <mailto:<a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a>><br>
> <a href="http://www.creatis.insa-lyon.fr/mailman/listinfo/vv" target="_blank">http://www.creatis.insa-lyon.fr/mailman/listinfo/vv</a><br>
><br>
><br>
><br>
><br>
> --<br>
> Bilal Tahir,<br>
> James Morrison Researcher in Radiotherapy Imaging,<br>
> Department of Clinical Oncology,<br>
> University of Sheffield<br>
><br>
><br>
> _______________________________________________<br>
> vv mailing list<br>
> <a href="mailto:vv@creatis.insa-lyon.fr">vv@creatis.insa-lyon.fr</a><br>
> <a href="http://www.creatis.insa-lyon.fr/mailman/listinfo/vv" target="_blank">http://www.creatis.insa-lyon.fr/mailman/listinfo/vv</a><br>
<br>
--<br>
R?mulo Pinho<br>
R&D Software Engineer<br>
TecGraf - PUC-Rio<br>
<a href="mailto:rpinho@tecgraf.puc-rio.br">rpinho@tecgraf.puc-rio.br</a><br>
<a href="http://www.tecgraf.puc-rio.br/~rpinho/" target="_blank">http://www.tecgraf.puc-rio.br/~rpinho/</a><br>
<br>
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</blockquote></div><br></div></div>