[Vv] Use vv as a landmark annotation/comparison tool?

[Rômulo Pinho]

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,
Rômulo


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
>
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>
>
>
>
> -- 
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging,
> Department of Clinical Oncology,
> University of Sheffield
>
>
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> vv at creatis.insa-lyon.fr
> http://www.creatis.insa-lyon.fr/mailman/listinfo/vv

-- 
Rômulo 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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