[Vv] Use vv as a landmark annotation/comparison tool?
Rômulo Pinho
romulopinho at yahoo.com.br
Tue Oct 1 21:52:46 CEST 2013
Hello, Bilal,
Try adding "-v" to the cmd line.
As for the initial rigid transformation, the app assumes the alignment
has already been made, as far as I can remember (I don't have the source
code here with me right now).
Regarding the file type, there's an option (--type, I think) with which
you specify the landmarks' format. But in any case its either .pts or
the .txt used by VV. It's .pts by default.
Best,
Rômulo
On 01/10/2013 16:09, Bilal Tahir wrote:
> 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
> <mailto: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
>> <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 <mailto: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 <mailto:rpinho at tecgraf.puc-rio.br>
> http://www.tecgraf.puc-rio.br/~rpinho/ <http://www.tecgraf.puc-rio.br/%7Erpinho/>
>
>
> _______________________________________________
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/vv/attachments/20131001/d4b46cb9/attachment-0001.html>
More information about the vv
mailing list