[Vv] Use vv as a landmark annotation/comparison tool?
qi tian
tianqig at gmail.com
Wed Oct 2 16:27:07 CEST 2013
Hi, Bilal and R?mulo
Thanks for your quick reply, very glad to know my two
problems have been discussed previously.
Now I am able to create landmark points with the *space bar*,
and save them. I will try to work on landmark point sets for
both fixed and moving images.
For the clitk suite, wonder if a binary version of vv may include
it or I have to compile by myself. Any simple document for the
clitk suite?
Tian
Singapore Bioimaging Consortium (SBIC)
Singapore
On Wed, Oct 2, 2013 at 2:14 AM, <vv-request at creatis.insa-lyon.fr> wrote:
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> Today's Topics:
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> 1. Use vv as a landmark annotation/comparison tool? (qi tian)
> 2. Re: Use vv as a landmark annotation/comparison tool? (Bilal Tahir)
> 3. Re: Use vv as a landmark annotation/comparison tool?
> (R?mulo Pinho)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 1 Oct 2013 18:14:44 +0800
> From: qi tian <tianqig at gmail.com>
> To: vv at creatis.insa-lyon.fr
> Subject: [Vv] Use vv as a landmark annotation/comparison tool?
> Message-ID:
> <
> CAMTCV5sVVTu2bUm9M9nTQngD51-PPZf2oN+McssK5fvbW0ytSg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I have two questions related to landmark points:
>
> 1. Can vv be used for clinicians by clicking
> landmark points for a given image?
> Ideally these landmark points can be stored
> in two files, I could not find any documentation
> on how this can be done with vv.
>
>
> 2. Can a transform be applied to a set
> of landmark points to create a new set of landmark
> points in vv? For instance, this set of landmark
> points is from a moving image, the transform
> is estimated with elastix, then the transformed
> landmark points can be compared with ones
> of a target image. This way it helps to to assess
> registration performance.
>
> Wonder if this can be done with vv?
>
> Thanks
>
> Tian
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> Message: 2
> Date: Tue, 1 Oct 2013 18:57:06 +0100
> From: Bilal Tahir <b.tahir at sheffield.ac.uk>
> To: "vv at creatis.insa-lyon.fr" <vv at creatis.insa-lyon.fr>
> Subject: Re: [Vv] Use vv as a landmark annotation/comparison tool?
> Message-ID:
> <CAFZ9P6GRq4Bu94xD0rbsM-yCzKjZ8i=
> RtEP3nOXLZDHMt7AgeA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Tian,
>
> 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:
>
> *"I would do it like this:
> 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.
> 2) Run elastix: elastix -f fixed -m moving -p parameterfile -out outdir
> 3) Run transformix to transform the FIXED points: transformix -def
> fixedpoints.txt -tp outdir/TransformParameters.0.txt -out outdir
> 4) now compare the transformed fixed points (which are stored in
> outdir/outputpoints.txt) to the original moving points.
>
> Instead of using the custom elastix input and output point formats (see
> elastix manual, section on transformix), you could also use .vtk (in legacy
> asci vtk format).
>
> 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."*
> *
> *
> 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.
> *
> *
> 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.
>
> Best wishes,
>
> Bilal
>
>
> On 1 October 2013 11:14, qi tian <tianqig at gmail.com> wrote:
>
> > Hi,
> >
> > I have two questions related to landmark points:
> >
> > 1. Can vv be used for clinicians by clicking
> > landmark points for a given image?
> > Ideally these landmark points can be stored
> > in two files, I could not find any documentation
> > on how this can be done with vv.
> >
> >
> > 2. Can a transform be applied to a set
> > of landmark points to create a new set of landmark
> > points in vv? For instance, this set of landmark
> > points is from a moving image, the transform
> > is estimated with elastix, then the transformed
> > landmark points can be compared with ones
> > of a target image. This way it helps to to assess
> > registration performance.
> >
> > Wonder if this can be done with vv?
> >
> > Thanks
> >
> > Tian
> >
> > _______________________________________________
> > vv mailing list
> > vv at creatis.insa-lyon.fr
> > http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
> >
> >
>
>
> --
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging,
> Department of Clinical Oncology,
> University of Sheffield
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> ------------------------------
>
> Message: 3
> Date: Tue, 01 Oct 2013 15:13:51 -0300
> From: R?mulo Pinho <romulopinho at yahoo.com.br>
> To: vv at creatis.insa-lyon.fr
> Subject: Re: [Vv] Use vv as a landmark annotation/comparison tool?
> Message-ID: <524B10DF.2030608 at yahoo.com.br>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hello, Tian and Bilal,
>
> 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.
>
> 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.
>
> I hope this is useful.
>
> Best,
> R?mulo
>
>
> On 01/10/2013 14:57, Bilal Tahir wrote:
> > Hi Tian,
> >
> > 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:
> >
> > /"I would do it like this:
> > 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.
> > 2) Run elastix: elastix -f fixed -m moving -p parameterfile -out outdir
> > 3) Run transformix to transform the FIXED points: transformix -def
> > fixedpoints.txt -tp outdir/TransformParameters.0.txt -out outdir
> > 4) now compare the transformed fixed points (which are stored in
> > outdir/outputpoints.txt) to the original moving points.
> >
> > Instead of using the custom elastix input and output point formats
> > (see elastix manual, section on transformix), you could also use .vtk
> > (in legacy asci vtk format).
> >
> > 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."/
> > /
> > /
> > 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.
> > /
> > /
> > 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.
> >
> > Best wishes,
> >
> > Bilal
> >
> >
> > On 1 October 2013 11:14, qi tian <tianqig at gmail.com
> > <mailto:tianqig at gmail.com>> wrote:
> >
> > Hi,
> >
> > I have two questions related to landmark points:
> >
> > 1. Can vv be used for clinicians by clicking
> > landmark points for a given image?
> > Ideally these landmark points can be stored
> > in two files, I could not find any documentation
> > on how this can be done with vv.
> >
> >
> > 2. Can a transform be applied to a set
> > of landmark points to create a new set of landmark
> > points in vv? For instance, this set of landmark
> > points is from a moving image, the transform
> > is estimated with elastix, then the transformed
> > landmark points can be compared with ones
> > of a target image. This way it helps to to assess
> > registration performance.
> >
> > Wonder if this can be done with vv?
> >
> > Thanks
> >
> > Tian
> >
> > _______________________________________________
> > vv mailing list
> > vv at creatis.insa-lyon.fr <mailto:vv at creatis.insa-lyon.fr>
> > http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
> >
> >
> >
> >
> > --
> > Bilal Tahir,
> > James Morrison Researcher in Radiotherapy Imaging,
> > Department of Clinical Oncology,
> > University of Sheffield
> >
> >
> > _______________________________________________
> > vv mailing list
> > vv at creatis.insa-lyon.fr
> > http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>
> --
> R?mulo Pinho
> R&D Software Engineer
> TecGraf - PUC-Rio
> rpinho at tecgraf.puc-rio.br
> http://www.tecgraf.puc-rio.br/~rpinho/
>
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