in the meantime, you can try the "clitkAffineTransform" command line tool in the vv source code (turn ON "CLITK_BUILD_TOOLS" option, then 'make clitkAffineTransform', then wait the looooong compilation time, and you can use it to turn your image). It is a temporary solution but could work. <br>
<br>We definitively will work on this orientation stuff soon.<br><br>David<br><br><div class="gmail_quote">On Wed, Feb 9, 2011 at 09:08, <span dir="ltr"><<a href="mailto:a.mans@nki.nl">a.mans@nki.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear vv team,<br>
<br>
for the moment, my only problem is that I cannot view my unregistered data in vv. The output of the registration package i'm using (elastix) is using the same orientation as the 'fixed' image. Reviewing registrations therefore works fine.<br>
<br>
When you need scans for testing, you can contact me.<br>
And say hello to Simon (old NKI collegue).<br>
<br>
Anton<br>
________________________________<br>
Van: <a href="mailto:david.sarrut@gmail.com">david.sarrut@gmail.com</a> [<a href="mailto:david.sarrut@gmail.com">david.sarrut@gmail.com</a>] namens David Sarrut [<a href="mailto:David.Sarrut@creatis.insa-lyon.fr">David.Sarrut@creatis.insa-lyon.fr</a>]<br>
Verzonden: woensdag 9 februari 2011 8:17<br>
Aan: Anton Mans<br>
CC: vv<br>
Onderwerp: Re: [Vv] Transformation matrix ?!<br>
<div class="im"><br>
Hello Anton,<br>
<br>
as Vivien found in the sources, Simon has indeed implemented some technique which will allow to take orientation (and any affine transformation) into account in vv.<br>
<br>
However, it is currently disabled due to robustness reason (and potential memory leak). We plan to include it near future. When Simon will be back from his trip, we will discuss about that and may contact you if you will to participate with us to this feature.<br>
<br>
sincerely,<br>
David<br>
<br>
</div><div class="im">On Tue, Feb 8, 2011 at 18:09, Vivien Delmon <<a href="mailto:vivien.delmon@creatis.insa-lyon.fr">vivien.delmon@creatis.insa-lyon.fr</a><mailto:<a href="mailto:vivien.delmon@creatis.insa-lyon.fr">vivien.delmon@creatis.insa-lyon.fr</a>>> wrote:<br>
On 02/07/2011 10:27 AM, <a href="mailto:a.mans@nki.nl">a.mans@nki.nl</a><mailto:<a href="mailto:a.mans@nki.nl">a.mans@nki.nl</a>> wrote:<br>
Dear vv team,<br>
<br>
another small question:<br>
does vv correctly use the 'global' transformation information in the image header?<br>
<br>
My case: MR and CT scans have different orientations, which is compensated for by the transformation matrix in the .mhd image header.<br>
CT: TransformMatrix = 1 0 0 0 1 0 0 0 1<br>
MR: TransformMatrix = 0 1 0 0 0 -1 -1 0 0<br>
<br>
In FSLview the images are correctly aligned. In vv, however, it seems that the transformation is not applied. Also when I modify the header file, vv still shows the same orientations.<br>
<br>
Regards, Anton<br>
<br>
VV doesn't take into account the direction part of the image when it converts an ITK image to a VTK image.<br>
<br>
The problem should be fixed in these files :<br>
<br>
common/vvFromITK.h<br>
common/vvImage.txx<br>
<br>
I am not sure I will have time to correct this bug soon.<br>
<br>
Kind Regards,<br>
<br>
<br>
--<br>
Vivien Delmon<br>
PhD student at CREATIS, Lyon<br>
Supported by ANRT and ELEKTA<br>
<a href="http://www.creatis.insa-lyon.fr/rio" target="_blank">http://www.creatis.insa-lyon.fr/rio</a><br>
<br>
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<br>
<br>
<br>
--<br>
David Sarrut, Phd<br>
Chargé de recherche CNRS<br>
Laboratoire CREATIS, UMR CNRS 5220, Inserm U 1044<br>
Centre de lutte contre le cancer Léon Bérard<br>
28 rue Laënnec, 69373 Lyon cedex 08<br>
Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
<a href="http://www.creatis.insa-lyon.fr/rio" target="_blank">http://www.creatis.insa-lyon.fr/rio</a><br>
_________________________________<br>
"2 + 2 = 5, for extremely large values of 2"<br>
_________________________________<br>
<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>David Sarrut, Phd<br>Chargé de recherche CNRS<br>Laboratoire CREATIS, UMR CNRS 5220, Inserm U 1044<div>Centre de lutte contre le cancer Léon Bérard<br>28 rue Laënnec, 69373 Lyon cedex 08<br>
Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/rio" target="_blank">http://www.creatis.insa-lyon.fr/rio</a><br>_________________________________<br> "2 + 2 = 5, for extremely large values of 2"<br>
_________________________________</div><br>