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

Bilal Tahir b.tahir at sheffield.ac.uk
Tue Oct 1 19:57:06 CEST 2013


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
>
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> vv at creatis.insa-lyon.fr
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>
>


-- 
Bilal Tahir,
James Morrison Researcher in Radiotherapy Imaging,
Department of Clinical Oncology,
University of Sheffield
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