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

[Bilal Tahir]

Many thanks Rômulo,

For the following:
fixed point file: 50.pts
moving point file: 00.pts
deformation field: deform.nii.gz/deform.mhd

Would the following command be correct?
clitkCalculateTRE --ref=50.pts --input=00.pts --vf=deformation.nii.gz

I tried this but got no output.

Also, how does the clitkCalculateTRE command account for initial
rigid/affine pre-alignment of fixed and moving images?

I also assume that only the .pts file are accepted and not .csv (comma
separated)?
E.g:
39.0621 -117.187 -6.5
47.8512 50.7814 35.5
-114.258 -120.117 -92.5
etc...

Best wishes,

Bilal


On 1 October 2013 19:13, Rômulo Pinho <romulopinho at yahoo.com.br> wrote:

>  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> 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
>
>
> _______________________________________________
> vv mailing listvv at creatis.insa-lyon.frhttp://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>
>
> --
> Rômulo Pinho
> R&D Software Engineer
> TecGraf - PUC-Riorpinho at tecgraf.puc-rio.brhttp://www.tecgraf.puc-rio.br/~rpinho/
>
>
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>
>


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