https://public.kitware.com/Wiki/api.php?action=feedcontributions&user=Romain.blatrix&feedformat=atomKitwarePublic - User contributions [en]2024-03-29T00:04:15ZUser contributionsMediaWiki 1.38.6https://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34877TubeTK/Events/2010.11.232010-11-23T22:30:07Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya , Strata(has Mac and PC free trial; not tested) : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**[http://www.3dsom.com/cgi-bin/trialsurvey2_1.cgi 3dsom] free trial on Windows(again!) license code : XysqzHIKLiRv<br />
**[http://rosset.org/graphix/anaglyph/zanag_en.htm Z-Anaglyph] for Windows --. not good, only to create 3D images you can see with blue and red googles<br />
**[http://www.microsoft.com/getsilverlight/get-started/install/default.aspx Microsoft Silverlight] for Windows --> I have no idea how it is working but doesn't seem to be really important<br />
**[http://www.imodeller.com/en/ iModeller] for Windows and Mac --> looks pretty nice (the pdf file shows exactly the kind of stuff we want) BUT it is only a Demo<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34873TubeTK/Events/2010.11.232010-11-23T20:44:14Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya , Strata(has Mac and PC free trial; not tested) : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**[http://www.3dsom.com/cgi-bin/trialsurvey2_1.cgi 3dsom] free trial on Windows(again!) license code : XysqzHIKLiRv<br />
**[http://rosset.org/graphix/anaglyph/zanag_en.htm Z-Anaglyph] for Windows<br />
**[http://www.microsoft.com/getsilverlight/get-started/install/default.aspx Microsoft Silverlight] for Windows<br />
**[http://www.imodeller.com/en/ iModeller] for Windows and Mac<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34872TubeTK/Events/2010.11.232010-11-23T20:33:22Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya , Strata(has Mac and PC free trial; not tested) : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**[http://www.3dsom.com/cgi-bin/trialsurvey2_1.cgi 3dsom] free trial on Windows(again!) license code : XysqzHIKLiRv<br />
**[http://rosset.org/graphix/anaglyph/zanag_en.htm Z-Anaglyph] for Windows<br />
**[http://www.microsoft.com/getsilverlight/get-started/install/default.aspx Microsoft Silverlight] for Windows<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34871TubeTK/Events/2010.11.232010-11-23T19:44:21Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya , Strata(has Mac and PC free trial; not tested) : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**[http://www.3dsom.com/cgi-bin/trialsurvey2_1.cgi 3dsom] free trial on Windows(again!) license code : XysqzHIKLiRv<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34870TubeTK/Events/2010.11.232010-11-23T19:36:00Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya , Strata(Mac and PC free trials not tested) : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**[http://www.3dsom.com/cgi-bin/trialsurvey2_1.cgi 3dsom] free trial on Windows(again!) license code : XysqzHIKLiRv<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34869TubeTK/Events/2010.11.232010-11-23T19:35:19Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya , Strata(Mac and PC free trials not tested) : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : looks really great, don't know how to get it ---> to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**[http://www.3dsom.com/cgi-bin/trialsurvey2_1.cgi 3dsom] free trial on Windows(again!) license code : XysqzHIKLiRv<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34868TubeTK/Events/2010.11.232010-11-23T19:22:07Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya , Strata : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : looks really great, don't know how to get it ---> to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34866TubeTK/Events/2010.11.232010-11-23T18:58:09Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
*A list of commercial and non commercial softwares is available [http://biocomp.stanford.edu/3dreconstruction/software/index.html here]<br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : looks really great, don't know how to get it ---> to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34865TubeTK/Events/2010.11.232010-11-23T18:50:37Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**CMVS (includes PMVS) : couldn't install but is definitely worth trying [http://grail.cs.washington.edu/software/cmvs/ CMVS] : I recommend you try it on Windows first because the installation was really really painful on my machine :)<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
**Rhino , Maya : NOT FREE<br />
** [http://www.gatan.com/products/software/3D_Reconstruction.php Gatan products] : looks really great, don't know how to get it ---> to be tried on Windows (.exe files) :[http://www.gatan.com/resources/scripting/demo/index.php downloads]<br />
**<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34863TubeTK/Events/2010.11.232010-11-23T17:58:33Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**pmvs : impossible to install!<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter )<br />
<br />
== Danielle ==<br />
* 80% finished Slicer CLI - need to check over + make sure testing is ok<br />
* Discovered bug introduced in last week's changes, due to regression testing on deformation fields and not transformed moving images<br />
* Fixed bug introduced in last week's changes =)<br />
* Helping Luis out with handling vector images in ITK's itkTestMain.h</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34858TubeTK/Events/2010.11.232010-11-23T17:02:07Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**pmvs : impossible to install!<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard] --> only working for stacks of images<br />
**java3D on ImageJ : trouble with the installation<br />
**code in ITK/Example/IO ---> not tested yet ( itkImageSeriesReader + itkImageFileWriter ) --> haven't tried it yet</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.23&diff=34857TubeTK/Events/2010.11.232010-11-23T16:56:23Z<p>Romain.blatrix: Created page with "== Romain == # failed at reconstruction --> terrible week trying to run some codes # I think to get the reconstruction we need more information on the pictures (position of the ..."</p>
<hr />
<div>== Romain ==<br />
# failed at reconstruction --> terrible week trying to run some codes <br />
# I think to get the reconstruction we need more information on the pictures (position of the camera for each photograph,etc...)<br />
# softwares tried : <br />
**OpenCV : I think a script is writable if we have more informations but it could take a long long time <br />
**pmvs : impossible to install!<br />
**hugin : correspondence points between photos failed<br />
**[http://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages code from Pierre Fillard]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events_and_Meetings&diff=34856TubeTK/Events and Meetings2010-11-23T16:48:43Z<p>Romain.blatrix: /* Weekly Meeting Notes */</p>
<hr />
<div>=Events=<br />
* 2009.09.23 MICCAI 2009 - Planning Meeting<br />
* 2009.09.23 BrainLAB - Goals and tasks<br />
* [[NeuralNav/Meetings/2009.12.21-TCon | 2009.12.21 Planning Meeting ]]<br />
* 2010.01.10 NAMIC AHM, Salt Lake City<br />
* [[NeuralNav/Meetings/2010.02.23-Visit | 2010.02.23 Visit to Duke ]]<br />
* 2010.06.21 NAMIC AHM, Boston<br />
<br />
= Weekly meetings =<br />
* Kitware<br />
** Tuesday, 11am-Noon, KRS Conference Room<br />
** Attendees: Stephen Aylward, Casey Goodlett, Andinet Enquobahrie, Patrick Reynolds, Hua Yang<br />
* BWH/Kitware TCon<br />
** Tuesdays, 2:30-3:30<br />
** Attendees: Stephen and Sandy (and Tina)<br />
<br />
== Weekly Meeting Notes ==<br />
* [[TubeTK/Events/2010.02.09 | Feb. 9, 2010]]<br />
* [[TubeTK/Events/2010.02.23 | Feb. 23, 2010]]<br />
* [[TubeTK/Events/2010.06.14 | June 14, 2010]]<br />
* [[TubeTK/Events/2010.07.12 | July 12, 2010]]<br />
* [[TubeTK/Events/2010.07.26 | July 26, 2010]]<br />
* [[TubeTK/Events/2010.08.17 | Aug 17, 2010]]<br />
* [[TubeTK/Events/2010.09.01 | Sept 1, 2010]]<br />
* [[TubeTK/Events/2010.09.07 | Sept 7, 2010]]<br />
* [[TubeTK/Events/2010.09.14 | Sept 14, 2010]]<br />
* [[TubeTK/Events/2010.09.21 | Sept 21, 2010]]<br />
* [[TubeTK/Events/2010.09.28 | Sept 28, 2010]]<br />
* [[TubeTK/Events/2010.10.12 | Oct 12, 2010]]<br />
* [[TubeTK/Events/2010.10.14 | Oct 14, 2010]]<br />
* [[TubeTK/Events/2010.10.19 | Oct 19, 2010]]<br />
* [[TubeTK/Events/2010.10.26 | Oct 26, 2010]]<br />
* [[TubeTK/Events/2010.11.02 | Nov 2, 2010]]<br />
* [[TubeTK/Events/2010.11.09 | Nov 9, 2010]]<br />
* [[TubeTK/Events/2010.11.16 | Nov 16, 2010]]<br />
* [[TubeTK/Events/2010.11.16-Planning | Nov 16, 2010 - Project Planning]]<br />
* [[TubeTK/Events/2010.11.23 | Nov 23, 2010]]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.16&diff=34325TubeTK/Events/2010.11.162010-11-16T16:45:51Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Danielle =<br />
* Submitted ISBI paper<br />
* Cleaned up sliding organ registration code:<br />
** tests on smaller images = smaller data to be distributed + faster tests<br />
** clean up logic - don't compute things unnecessarily when using no regularization or gaussian regularization = faster execution<br />
** boundary conditions<br />
** fixed dashboard warnings<br />
** style<br />
** started web documentation - need workflow description<br />
* TODO:<br />
** documentation<br />
** Slicer CLI<br />
** then get back to research<br />
** NAMIC UCLA/MSV<br />
<br />
<br />
=Romain =<br />
# SPIE Conference Website<br />
# Started looking at MetaIO issues with CLANG [http://www.cdash.org/CDash/viewBuildError.php?type=1&buildid=727319 Dashboard] but can't find the files to be modified to silence the warnings :-|</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.16&diff=34323TubeTK/Events/2010.11.162010-11-16T16:35:12Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Danielle =<br />
* Submitted ISBI paper<br />
* Cleaned up sliding organ registration code:<br />
** tests on smaller images = smaller data to be distributed + faster tests<br />
** clean up logic - don't compute things unnecessarily when using no regularization or gaussian regularization = faster execution<br />
** boundary conditions<br />
** fixed dashboard warnings<br />
** style<br />
** started web documentation - need workflow description<br />
* TODO:<br />
** documentation<br />
** Slicer CLI<br />
** then get back to research<br />
** NAMIC UCLA/MSV<br />
<br />
<br />
=Romain =<br />
# SPIE Conference Website<br />
# Started looking at MetaIO issues with CLANG [http://www.cdash.org/CDash/viewBuildError.php?type=1&buildid=727319 Dashboard]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.16&diff=34321TubeTK/Events/2010.11.162010-11-16T16:34:02Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Danielle =<br />
* Submitted ISBI paper<br />
* Cleaned up sliding organ registration code:<br />
** tests on smaller images = smaller data to be distributed + faster tests<br />
** clean up logic - don't compute things unnecessarily when using no regularization or gaussian regularization = faster execution<br />
** boundary conditions<br />
** fixed dashboard warnings<br />
** style<br />
** started web documentation - need workflow description<br />
* TODO:<br />
** documentation<br />
** Slicer CLI<br />
** then get back to research<br />
** NAMIC UCLA/MSV<br />
<br />
<br />
=Romain =<br />
# SPIE Conference Website<br />
# Started looking at MetaIO issues with CLANG [[http://www.cdash.org/CDash/viewBuildError.php?type=1&buildid=727319]Dashboard]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.16&diff=34320TubeTK/Events/2010.11.162010-11-16T16:33:32Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Danielle =<br />
* Submitted ISBI paper<br />
* Cleaned up sliding organ registration code:<br />
** tests on smaller images = smaller data to be distributed + faster tests<br />
** clean up logic - don't compute things unnecessarily when using no regularization or gaussian regularization = faster execution<br />
** boundary conditions<br />
** fixed dashboard warnings<br />
** style<br />
** started web documentation - need workflow description<br />
* TODO:<br />
** documentation<br />
** Slicer CLI<br />
** then get back to research<br />
** NAMIC UCLA/MSV<br />
<br />
<br />
=Romain =<br />
# SPIE Conference Website<br />
# Started looking at MetaIO issues with CLANG [http://www.cdash.org/CDash/viewBuildError.php?type=1&buildid=727319]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.16&diff=34316TubeTK/Events/2010.11.162010-11-16T16:20:47Z<p>Romain.blatrix: /* Danielle */</p>
<hr />
<div>= Danielle =<br />
* Submitted ISBI paper<br />
* Cleaned up sliding organ registration code:<br />
** tests on smaller images = smaller data to be distributed + faster tests<br />
** clean up logic - don't compute things unnecessarily when using no regularization or gaussian regularization = faster execution<br />
** boundary conditions<br />
** fixed dashboard warnings<br />
** style<br />
** started web documentation - need workflow description<br />
* TODO:<br />
** documentation<br />
** Slicer CLI<br />
** then get back to research<br />
** NAMIC UCLA/MSV<br />
<br />
<br />
=Romain =<br />
# SPIE Conference Website<br />
# Started looking at MetaIO issues with CLANG</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.09&diff=34023TubeTK/Events/2010.11.092010-11-09T17:26:20Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Danielle =<br />
* XCAT validation with MeshValmet (+ scripts for preprocessing and interpreting MeshValmet results)<br />
[[File:2011_11_09_XCATValidationResults.png]]<br />
* Haussdorf distance not informative<br />
* Finished writing paper<br />
* Next priorities - similar to last week:<br />
** some code cleanup<br />
** register CT data<br />
** implement improvements from Marc's suggestions + discussion with Stephen (coarse to fine, normals as matrices to handle corners)<br />
** documentation on TubeTK wiki<br />
<br />
<br />
==Romain==<br />
*done<br />
# Grassroots data on Slicer ---> fail [https://www.kitware.com/KWWiki/index.php/Medical_Imaging/Grassroots Grassroots kitware]<br />
# Compute Tortuosity documentation on the wiki [http://public.kitware.com/Wiki/TubeTK/ComputeTortuosity ComputeTortuosity wiki]<br />
# XHTML/CSS Tutorials + reproduction of the SPIE Medical Imaging Computer-Aided Diagnosis Workshop website on my machine<br />
*to do<br />
#get the informations about the conference to put on the web site<br />
#get access to the kitware website to host the conference site<br />
# what else?</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.09&diff=34022TubeTK/Events/2010.11.092010-11-09T17:20:21Z<p>Romain.blatrix: /* Danielle */</p>
<hr />
<div>= Danielle =<br />
* XCAT validation with MeshValmet (+ scripts for preprocessing and interpreting MeshValmet results)<br />
[[File:2011_11_09_XCATValidationResults.png]]<br />
* Haussdorf distance not informative<br />
* Finished writing paper<br />
* Next priorities - similar to last week:<br />
** some code cleanup<br />
** register CT data<br />
** implement improvements from Marc's suggestions + discussion with Stephen (coarse to fine, normals as matrices to handle corners)<br />
** documentation on TubeTK wiki<br />
<br />
<br />
==Romain==<br />
# Grassroots data on Slicer ---> fail [https://www.kitware.com/KWWiki/index.php/Medical_Imaging/Grassroots Grassroots kitware]<br />
# Compute Tortuosity documentation on the wiki [http://public.kitware.com/Wiki/TubeTK/ComputeTortuosity ComputeTortuosity wiki]<br />
#</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33975TubeTK/Documentation/ComputeTortuosity2010-11-08T20:32:14Z<p>Romain.blatrix: /* Documentation */</p>
<hr />
<div>== Documentation ==<br />
*Command line to measure the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
<br />
== Parameters ==<br />
# input data : .tre files = files containing the successive 3D positions of the centerline of the tubes (example : tubeTK/Data/Branch-truth.tre)<br />
# mask : image specifying the ROI. Pixel intensity is 0 outside the ROI and ≠0 inside the ROI (example : tubeTK/Data/Branch.n010.mha)<br />
# Methods<br />
## Distance Metric (flag = d, default = true)<br />
## Inflection Count Metric (flag = i, default = false)<br />
## Sum Of Angles Metric (flag = s, default = false)<br />
<br />
== Tests ==<br />
[[File:Screenshot-9.png|1200px]]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33974TubeTK/Documentation/ComputeTortuosity2010-11-08T20:28:09Z<p>Romain.blatrix: /* Tests */</p>
<hr />
<div>== Documentation ==<br />
*Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
<br />
== Parameters ==<br />
# input data : .tre files = files containing the successive 3D positions of the centerline of the tubes (example : tubeTK/Data/Branch-truth.tre)<br />
# mask : image specifying the ROI. Pixel intensity is 0 outside the ROI and ≠0 inside the ROI (example : tubeTK/Data/Branch.n010.mha)<br />
# Methods<br />
## Distance Metric (flag = d, default = true)<br />
## Inflection Count Metric (flag = i, default = false)<br />
## Sum Of Angles Metric (flag = s, default = false)<br />
<br />
== Tests ==<br />
[[File:Screenshot-9.png|1200px]]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:Screenshot-9.png&diff=33973File:Screenshot-9.png2010-11-08T20:26:07Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33972TubeTK/Documentation/ComputeTortuosity2010-11-08T20:25:44Z<p>Romain.blatrix: /* Parameters */</p>
<hr />
<div>== Documentation ==<br />
*Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
<br />
== Parameters ==<br />
# input data : .tre files = files containing the successive 3D positions of the centerline of the tubes (example : tubeTK/Data/Branch-truth.tre)<br />
# mask : image specifying the ROI. Pixel intensity is 0 outside the ROI and ≠0 inside the ROI (example : tubeTK/Data/Branch.n010.mha)<br />
# Methods<br />
## Distance Metric (flag = d, default = true)<br />
## Inflection Count Metric (flag = i, default = false)<br />
## Sum Of Angles Metric (flag = s, default = false)<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33971TubeTK/Documentation/ComputeTortuosity2010-11-08T20:20:09Z<p>Romain.blatrix: /* Parameters */</p>
<hr />
<div>== Documentation ==<br />
*Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
<br />
== Parameters ==<br />
# input data : .tre files = files containing the successive 3D positions of the centerline of the tubes (example : tubeTK/Data/Branch-truth.tre)<br />
# mask : image specifying the ROI. Pixel intensity is 0 outside the ROI and ≠0 inside the ROI (example : tubeTK/Data/Branch.n010.mha)<br />
# Methods<br />
## Distance Metric (flag = d, default = true)<br />
## Inflection Count Metric (flag = i, default = false)<br />
## Sum Of Angles Metric (flag = s, default = false)<br />
<br />
/home/romain/Projects/TubeTK/tubetk/Applications/CLI/ComputeTortuosity/Testing/tre_files/Sick_A_c_upsamp--new.tre /home/romain/Projects/TubeTK/tubetk/Applications/CLI/ComputeTortuosity/Testing/masks/Branch.n010.mha<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33970TubeTK/Documentation/ComputeTortuosity2010-11-08T20:19:03Z<p>Romain.blatrix: /* Parameters */</p>
<hr />
<div>== Documentation ==<br />
*Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
<br />
== Parameters ==<br />
# input data : .tre files = files containing the successive 3D positions of the centerline of the tubes (example : tubeTK/Data/Branch-truth.tre)<br />
# mask : image specifying the ROI. Pixel intensity is 0 outside the ROI and ≠0 inside the ROI (example : tubeTK/Data/Branch.n010.mha)<br />
# Methods<br />
## Distance Metric (flag = d)<br />
## Inflection Count Metric (flag = i)<br />
<br />
/home/romain/Projects/TubeTK/tubetk/Applications/CLI/ComputeTortuosity/Testing/tre_files/Sick_A_c_upsamp--new.tre /home/romain/Projects/TubeTK/tubetk/Applications/CLI/ComputeTortuosity/Testing/masks/Branch.n010.mha<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33969TubeTK/Documentation/ComputeTortuosity2010-11-08T20:18:16Z<p>Romain.blatrix: /* Use cases */</p>
<hr />
<div>== Documentation ==<br />
*Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
<br />
== Parameters ==<br />
# input data : .tre files = files containing the successive 3D positions of the centerline of the tubes (example : tubeTK/Data/Branch-truth.tre)<br />
# mask : image specifying the ROI. Pixel intensity is 0 outside the ROI and ≠0 inside the ROI (example : tubeTK/Data/Branch.n010.mha)<br />
# Methods<br />
## Distance Metric (flag = d)<br />
##<br />
<br />
/home/romain/Projects/TubeTK/tubetk/Applications/CLI/ComputeTortuosity/Testing/tre_files/Sick_A_c_upsamp--new.tre /home/romain/Projects/TubeTK/tubetk/Applications/CLI/ComputeTortuosity/Testing/masks/Branch.n010.mha<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33959TubeTK/Documentation/ComputeTortuosity2010-11-08T20:07:56Z<p>Romain.blatrix: /* Documentation */</p>
<hr />
<div>== Documentation ==<br />
*Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
<br />
== Use cases ==<br />
<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33958TubeTK/Documentation/ComputeTortuosity2010-11-08T20:06:50Z<p>Romain.blatrix: /* Documentation */</p>
<hr />
<div>== Documentation ==<br />
*Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
*For more informations about the methods, please visit [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images] (Informations about the methods used to measure the tortuosity of the blood vessels are on pages 4-5)<br />
*Parameters<br />
# input data : .tre files = files containing the successive 3D positions of the centerline of the tubes (example : tubeTK/Data/Branch-truth.tre)<br />
# mask : image specifying the ROI. Pixel intensity is 0 outside the ROI and ≠0 inside the ROI (example : tubeTK/Data/Branch.n010.mha)<br />
<br />
== Use cases ==<br />
<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33955TubeTK/Documentation/ComputeTortuosity2010-11-08T19:47:28Z<p>Romain.blatrix: /* Documentation */</p>
<hr />
<div>== Documentation ==<br />
Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
For more informations about the methods, please read [http://www.kitware.com/publications/item/view/1123 Measuring Tortuosity of the Intracerebral Vasculature from MRA Images].<br />
<br />
== Use cases ==<br />
<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33954TubeTK/Documentation/ComputeTortuosity2010-11-08T19:46:00Z<p>Romain.blatrix: /* Documentation */</p>
<hr />
<div>== Documentation ==<br />
Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
Right now, only the distance metric method is implemented.<br />
[[http://www.kitware.com/publications/item/view/1123]]Measuring Tortuosity of the Intracerebral Vasculature from MRA Images<br />
<br />
== Use cases ==<br />
<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33953TubeTK/Documentation/ComputeTortuosity2010-11-08T19:27:24Z<p>Romain.blatrix: /* Documentation */</p>
<hr />
<div>== Documentation ==<br />
Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
[[http://www.kitware.com/publications/item/view/1123]]Measuring Tortuosity of the Intracerebral Vasculature from MRA Images<br />
<br />
== Use cases ==<br />
<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33952TubeTK/Documentation/ComputeTortuosity2010-11-08T18:21:12Z<p>Romain.blatrix: /* Documentation */</p>
<hr />
<div>== Documentation ==<br />
Measuring the tortuosity of vessels using Distance Metric, Inflection Count Metric and Sum Of Angles Metric methods.<br />
<br />
== Use cases ==<br />
<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation/ComputeTortuosity&diff=33951TubeTK/Documentation/ComputeTortuosity2010-11-08T18:19:59Z<p>Romain.blatrix: Created page with "== Documentation == == Use cases == == Tests =="</p>
<hr />
<div>== Documentation ==<br />
<br />
<br />
== Use cases ==<br />
<br />
<br />
== Tests ==</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Documentation&diff=33950TubeTK/Documentation2010-11-08T18:06:50Z<p>Romain.blatrix: /* Applications */</p>
<hr />
<div>= Applications =<br />
# GUI Applications<br />
# Command-line (CLI) Applications<br />
#* [[TubeTK/HessianVesselness2D | Hessian Vesselness 2D]]<br />
#* [[TubeTK/ExtractCurves2D | Extract Curves 2D]]<br />
#* [[TubeTK/ComputeTortuosity | Compute Tortuosity]]<br />
<br />
= Modules =<br />
# Pre-processing<br />
#* [[TubeTK/Anisotropic Hybrid Diffusion with Continuous Switch]]<br />
# Object segmentation<br />
# Tube extraction<br />
# Data structures<br />
# Topology analysis<br />
# Editing<br />
# Export<br />
# [[TubeTK/OpenIGTLink | OpenIGTLink]]<br />
<br />
= Related Efforts =<br />
<br />
* [[TubeTK/Reference | Reference works]]<br />
* [https://musiic.lcsr.jhu.edu Medical Ultrasound Imaging and Intervention Collaboration (MUSIIC)]<br />
* [http://www.vmtk.org The Vascular Modeling Toolkit (VMTK)]</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.02&diff=33527TubeTK/Events/2010.11.022010-11-02T17:02:52Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Romain =<br />
<br />
* Implementation on the ComputeTortuosity module (only Distance Metric) ---->OK!!<br />
** With input data = Branch-truth.tre (from tubetk/Data)<br />
*** With mask covering the whole tube (Branch.n010.mha):<br />
**** Distance Metric Tortuosity for tube section 0 - 999 is 0.0524638<br />
**** Distance Metric Tortuosity for tube section 0 - 499 is 0.0656099<br />
*** With other mask (Branch.n010.sub.mha) not covering the whole scene<br />
**** Distance Metric Tortuosity for tube section 0 - 399 is 0.0811677<br />
*Future<br />
** Grassroots data visualization<br />
** Conference website<br />
** CLANG errors in metaImage<br />
<br />
*GRASSROOT<br />
**clsm-automation<br />
[[File:Tile_rgb_z1.png|800px|thumb|left|tile rgb z1]]<br />
[[File:Tile_rgb_z11.png|800px|thumb|left|tile rgb z11]]<br />
<br />
**ra-sample<br />
[[File:23805.jpg|800px|thumb|left|23805]]<br />
[[File:24267.jpg|800px|thumb|left|24267]]<br />
[[File:24189.jpg|800px|thumb|left|24189]]<br />
<br />
= Stephen =<br />
<br />
* TubeSpatialObject<br />
** Bug in ComputeTangentAndNormals<br />
** Therefore, Tube/Base/Segmentation/VTree/tubeMath.h<br />
** Pursue refactoring of itk's SpatialObject classes<br />
** Time? Funding?<br />
* RadiusEstimation<br />
** Refactoring complete, bugs remain, tests being added<br />
* Slicer integration<br />
** Next Priority<br />
* USC<br />
** Funding becoming active<br />
** Urgent need for unsupervised method<br />
* Grassroots<br />
** Received data<br />
** Romain to view in Slicer and send visualization to Danielle and Stephen<br />
** NDA signed<br />
** Meeting next week<br />
* UCLA/TBI<br />
** Received data (can't find it)<br />
** Visualizations needed (Danielle)<br />
* BWH US Machine in Eternia<br />
<br />
= Danielle =<br />
* Successfully registered XCAT images:<br />
[[File:2010_11_02_xcatRegistration.png]]<br />
* Anisotropic gives much better motion field<br />
* Gaussian does a bit of a better job than anisotropic<br />
* Currently doing last validations = mutual overlap / Haussdorf distance between surfaces (with Valmet)<br />
* Small questions:<br />
** Max filename size in ITK?<br />
** Valmet only in Windows...<br />
* Next priorities: TubeTK dashboard, some code cleanup, register CT data, then implement improvements from Marc's suggestions + discussion with Stephen on Friday (coarse to fine, normals as matrices to handle corners)<br />
* To think about: MICCAI 2011 (submission of full papers = March 11)</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:24189.jpg&diff=33526File:24189.jpg2010-11-02T17:02:16Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.02&diff=33525TubeTK/Events/2010.11.022010-11-02T17:01:32Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Romain =<br />
<br />
* Implementation on the ComputeTortuosity module (only Distance Metric) ---->OK!!<br />
** With input data = Branch-truth.tre (from tubetk/Data)<br />
*** With mask covering the whole tube (Branch.n010.mha):<br />
**** Distance Metric Tortuosity for tube section 0 - 999 is 0.0524638<br />
**** Distance Metric Tortuosity for tube section 0 - 499 is 0.0656099<br />
*** With other mask (Branch.n010.sub.mha) not covering the whole scene<br />
**** Distance Metric Tortuosity for tube section 0 - 399 is 0.0811677<br />
*Future<br />
** Grassroots data visualization<br />
** Conference website<br />
** CLANG errors in metaImage<br />
<br />
*GRASSROOT<br />
**clsm-automation<br />
[[File:Tile_rgb_z1.png|800px|thumb|left|tile rgb z1]]<br />
[[File:Tile_rgb_z11.png|800px|thumb|left|tile rgb z11]]<br />
<br />
**ra-sample<br />
[[File:23805.jpg|800px|thumb|left|23805]]<br />
[[File:24267.jpg|800px|thumb|left|24267]]<br />
<br />
= Stephen =<br />
<br />
* TubeSpatialObject<br />
** Bug in ComputeTangentAndNormals<br />
** Therefore, Tube/Base/Segmentation/VTree/tubeMath.h<br />
** Pursue refactoring of itk's SpatialObject classes<br />
** Time? Funding?<br />
* RadiusEstimation<br />
** Refactoring complete, bugs remain, tests being added<br />
* Slicer integration<br />
** Next Priority<br />
* USC<br />
** Funding becoming active<br />
** Urgent need for unsupervised method<br />
* Grassroots<br />
** Received data<br />
** Romain to view in Slicer and send visualization to Danielle and Stephen<br />
** NDA signed<br />
** Meeting next week<br />
* UCLA/TBI<br />
** Received data (can't find it)<br />
** Visualizations needed (Danielle)<br />
* BWH US Machine in Eternia<br />
<br />
= Danielle =<br />
* Successfully registered XCAT images:<br />
[[File:2010_11_02_xcatRegistration.png]]<br />
* Anisotropic gives much better motion field<br />
* Gaussian does a bit of a better job than anisotropic<br />
* Currently doing last validations = mutual overlap / Haussdorf distance between surfaces (with Valmet)<br />
* Small questions:<br />
** Max filename size in ITK?<br />
** Valmet only in Windows...<br />
* Next priorities: TubeTK dashboard, some code cleanup, register CT data, then implement improvements from Marc's suggestions + discussion with Stephen on Friday (coarse to fine, normals as matrices to handle corners)<br />
* To think about: MICCAI 2011 (submission of full papers = March 11)</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:24267.jpg&diff=33524File:24267.jpg2010-11-02T16:59:58Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:23805.jpg&diff=33523File:23805.jpg2010-11-02T16:58:48Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.02&diff=33522TubeTK/Events/2010.11.022010-11-02T16:55:14Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Romain =<br />
<br />
* Implementation on the ComputeTortuosity module (only Distance Metric) ---->OK!!<br />
** With input data = Branch-truth.tre (from tubetk/Data)<br />
*** With mask covering the whole tube (Branch.n010.mha):<br />
**** Distance Metric Tortuosity for tube section 0 - 999 is 0.0524638<br />
**** Distance Metric Tortuosity for tube section 0 - 499 is 0.0656099<br />
*** With other mask (Branch.n010.sub.mha) not covering the whole scene<br />
**** Distance Metric Tortuosity for tube section 0 - 399 is 0.0811677<br />
*Future<br />
** Grassroots data visualization<br />
** Conference website<br />
** CLANG errors in metaImage<br />
<br />
*GRASSROOT<br />
**clsm-automation<br />
***[File:Tile_rgb_z1.png]]<br />
***[File:Tile_rgb_z11.png]]<br />
<br />
= Stephen =<br />
<br />
* TubeSpatialObject<br />
** Bug in ComputeTangentAndNormals<br />
** Therefore, Tube/Base/Segmentation/VTree/tubeMath.h<br />
** Pursue refactoring of itk's SpatialObject classes<br />
** Time? Funding?<br />
* RadiusEstimation<br />
** Refactoring complete, bugs remain, tests being added<br />
* Slicer integration<br />
** Next Priority<br />
* USC<br />
** Funding becoming active<br />
** Urgent need for unsupervised method<br />
* Grassroots<br />
** Received data<br />
** Romain to view in Slicer and send visualization to Danielle and Stephen<br />
** NDA signed<br />
** Meeting next week<br />
* UCLA/TBI<br />
** Received data (can't find it)<br />
** Visualizations needed (Danielle)<br />
* BWH US Machine in Eternia<br />
<br />
= Danielle =<br />
* Successfully registered XCAT images:<br />
[[File:2010_11_02_xcatRegistration.png]]<br />
* Anisotropic gives much better motion field<br />
* Gaussian does a bit of a better job than anisotropic<br />
* Currently doing last validations = mutual overlap / Haussdorf distance between surfaces (with Valmet)<br />
* Small questions:<br />
** Max filename size in ITK?<br />
** Valmet only in Windows...<br />
* Next priorities: TubeTK dashboard, some code cleanup, register CT data, then implement improvements from Marc's suggestions + discussion with Stephen on Friday (coarse to fine, normals as matrices to handle corners)<br />
* To think about: MICCAI 2011 (submission of full papers = March 11)</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:Tile_rgb_z11.png&diff=33521File:Tile rgb z11.png2010-11-02T16:52:38Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:Tile_rgb_z1.png&diff=33520File:Tile rgb z1.png2010-11-02T16:51:37Z<p>Romain.blatrix: uploaded a new version of &quot;File:Tile rgb z1.png&quot;: Reverted to version as of 16:50, 2 November 2010</p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:Tile_rgb_z1.png&diff=33519File:Tile rgb z1.png2010-11-02T16:51:02Z<p>Romain.blatrix: uploaded a new version of &quot;File:Tile rgb z1.png&quot;</p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:Tile_rgb_z1.png&diff=33518File:Tile rgb z1.png2010-11-02T16:50:12Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.02&diff=33460TubeTK/Events/2010.11.022010-11-01T21:21:10Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Romain =<br />
<br />
* Implementation on the ComputeTortuosity module (only Distance Metric) ---->OK!!<br />
<br />
** With input data = Branch-truth.tre (from tubetk/Data)<br />
<br />
*** With mask covering the whole tube (Branch.n010.mha):<br />
**** Distance Metric Tortuosity for tube section 0 - 999 is 0.0524638<br />
**** Distance Metric Tortuosity for tube section 0 - 499 is 0.0656099<br />
<br />
*** With other mask (Branch.n010.sub.mha) not covering the whole scene<br />
**** Distance Metric Tortuosity for tube section 0 - 399 is 0.0811677<br />
<br />
<br />
*Future<br />
** obtain dimension??? make it work for every dimension??<br />
** #tube command ????<br />
** Implementation of the other 2 methods : ICM SOAM ????</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.02&diff=33459TubeTK/Events/2010.11.022010-11-01T21:14:36Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Romain =<br />
<br />
* Implementation on the ComputeTortuosity module (only Distance Metric) ---->OK!!<br />
<br />
** With input data = Branchtruth.tre (from tubetk/Data)<br />
<br />
*** With mask covering the whole tube (Branch.n010.mha):<br />
**** Distance Metric Tortuosity for tube section 0 - 999 is 0.0524638<br />
**** Distance Metric Tortuosity for tube section 0 - 499 is 0.0656099<br />
<br />
*** With other mask (Branch.n010.sub.mha) not covering the whole scene<br />
**** Distance Metric Tortuosity for tube section 0 - 399 is 0.0811677<br />
<br />
<br />
*Future<br />
** obtain dimension??? make it work for every dimension??<br />
** #tube command ????<br />
** Implementation of the other 2 methods : ICM SOAM ????</div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:Tout.png&diff=33458File:Tout.png2010-11-01T21:06:52Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=File:Sub.png&diff=33457File:Sub.png2010-11-01T21:06:05Z<p>Romain.blatrix: </p>
<hr />
<div></div>Romain.blatrixhttps://public.kitware.com/Wiki/index.php?title=TubeTK/Events/2010.11.02&diff=33456TubeTK/Events/2010.11.022010-11-01T21:01:38Z<p>Romain.blatrix: /* Romain */</p>
<hr />
<div>= Romain =<br />
<br />
* Implementation on the ComputeTortuosity module (only Distance Metric) ---->OK!!<br />
<br />
** With input data = Branchtruth.tre (from tubetk/Data)<br />
<br />
*** With mask covering the whole tube (Branch.n010.mha):<br />
[[File:sub.png|500 px]]<br />
- Starting /home/romain/Projects/TubeTK/TubeTK-build/TubeTK-Build/lib/TubeTK/Plugins/ComputeTortuosity...<br />
<filter-start><br />
<filter-name>ComputeTortuosity</filter-name><br />
<filter-comment> "ComputeTortuosity" </filter-comment><br />
</filter-start><br />
<filter-progress>0.1</filter-progress><br />
Number of children = 1<br />
Number of tubes = 2<br />
'''Distance Metric Tortuosity for tube section 0 - 999 is 0.0524638<br />
Distance Metric Tortuosity for tube section 0 - 499 is 0.0656099'''<br />
/home/romain/Projects/TubeTK/TubeTK-build/TubeTK-Build/lib/TubeTK/Plugins/ComputeTortuosity exited with code 0<br />
<br />
*** With other mask (Branch.n010.sub.mha) not covering the whole scene<br />
Starting /home/romain/Projects/TubeTK/TubeTK-build/TubeTK-Build/lib/TubeTK/Plugins/ComputeTortuosity...<br />
<filter-start><br />
<filter-name>ComputeTortuosity</filter-name><br />
<filter-comment> "ComputeTortuosity" </filter-comment><br />
</filter-start><br />
<filter-progress>0.1</filter-progress><br />
Number of children = 1<br />
Number of tubes = 2<br />
'''Distance Metric Tortuosity for tube section 0 - 399 is 0.0811677<br />
'''/home/romain/Projects/TubeTK/TubeTK-build/TubeTK-Build/lib/TubeTK/Plugins/ComputeTortuosity exited with code 0<br />
<br />
*Future<br />
** obtain dimension??? make it work for every dimension??<br />
** #tube command ????<br />
** Implementation of the other 2 methods : ICM SOAM ????</div>Romain.blatrix