Difference between revisions of "User:Haehn"

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! Info ||  
 
! Info ||  
 
|- style="vertical-align:top"
 
|- style="vertical-align:top"
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|'''Daniel H&auml;hn'''<br>Student of Medical Informatics <br>University of Heidelberg, Germany<br>E-Mail: [mailto:haehn@bwh.harvard.edu haehn@bwh.harvard.edu] or [mailto:haehn@urz.uni-heidelberg.de haehn@urz.uni-heidelberg.de]<br>Expected Graduation: Summer 2009  || <center>[[Image:haehn.jpg]]</center>
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|'''Daniel Haehn'''
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http://danielhaehn.com
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|| <center>[[Image:haehn.jpg]]</center>
 
|}
 
|}
 +
  
 
=== VMTK in 3D Slicer ===
 
=== VMTK in 3D Slicer ===
  
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'''Project goal:''' Integration of VMTK in 3D Slicer<br>
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The Vascular Modeling Toolkit ([http://vmtk.org VMTK]) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. It should be very interesting to offer such techniques in 3D Slicer.
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'''Kick-Off:''' 10/15/2008
 
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'''Final Milestone 1:''' 03/31/2009
 
  
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The extraction of vessels in two­ and three­dimensional images is part of many clinical analysis tasks.
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The official project page:
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Surgical and radiology procedures often involve the visualization and quantification of vessels in order
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http://www.vmtk.org/Main/VmtkIn3DSlicer
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to perform surgical planning or diagnostics. There is no single segmentation method that can extract
 
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vessels  from  every  medical  image  modality,  but  different  approaches  and  robust  algorithms  exist.  
 
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Various  published  key  algorithms  are  available  within  an  open­source  framework  for  image­based
 
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modeling of blood vessels, referred to as the Vascular Modeling Toolkit (VMTK). <br>
 
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The library of VMTK was made available in 3D Slicer, an application providing a wide range of tools
 
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for medical image processing. This was realized using a hidden loadable module approach in order to
 
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provide a flexible way of distributing and including the library. To evaluate and verify the integration, a
 
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software module offering VMTK level set segmentation methods within 3D Slicer was created.<br>
 
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With the successful connection of the two above mentioned software solutions, processing pipelines
 
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between VMTK code and other algorithms can be established. Several techniques for three dimensional
 
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reconstruction, geometric analysis, mesh generation and surface data analysis for image­based modeling
 
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of  blood  vessels  are  now  accessible  to  the  3D  Slicer  developer.  The  reference  implementation  for
 
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accessing VMTK, as well as the created library module are available as open­source software.
 
  
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'''The NITRC project page including a SVN repository with the latest code: http://www.nitrc.org/projects/slicervmtklvlst/'''
 
  
 
More recent news on this project: <br>
 
More recent news on this project: <br>
 +
 
http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK<br>
 
http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK<br>
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http://www.na-mic.org/Wiki/index.php/Summer2009:The_Vascular_Modeling_Toolkit_in_3D_Slicer
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http://www.na-mic.org/Wiki/index.php/Summer2009:The_Vascular_Modeling_Toolkit_in_3D_Slicer<br>
 +
http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer
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http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week/The_Vascular_Modeling_Toolkit_in_3D_Slicer
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http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer
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http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:StenosisDetector
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This work is done in conjunction with Luca Antiga (Medical Imaging Unit, Bioengineering Department, Mario Negri Institute, Bergamo, Italy).
 +
 
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==== VMKT in Slicer4 ====
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The VMTK integration in 3D Slicer will be transitioned to Slicer4.
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Some developer notes:
 +
<pre>
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# clone the fork
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git clone git@github.com:haehn/vmtk.git
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# check the status
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git status
  
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VMTK is the Vascular Modeling Toolkit (http://vmtk.org) and offers interesting techniques for segmentation of vessels or tube-shapes.<br>
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# switch to branch superbuild
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git checkout superbuild
  
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This work is done in conjunction with Luca Antiga (Medical Imaging Unit, Bioengineering Department, Mario Negri Institute, Bergamo, Italy).
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# include upstream by editing .git/config
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# 17 [remote "upstream"]
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# 18      url = https://github.com/lantiga/vmtk.git
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# 19      fetch = +refs/heads/*:refs/remotes/upstream/*
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# get the upstream
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git fetch upstream
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# merge the latest changes to local
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git merge upstream/superbuild
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# push the latest changes from upstream to fork
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git push
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</pre>
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Now, somebody forked the repo, made some changes we want in the master:
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<pre>
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# add the remote repo
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git remote add jcfr https://github.com/jcfr/EMSegment4.git
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# fetch it
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git fetch jcfr
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# see diff
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git log -p master jcfr/master
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# now merge the remote with our master
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git merge jcfr/master
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Updating f5d1b39..dd72623
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error: Your local changes to 'CMakeLists.txt' would be overwritten by merge.  Aborting.
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Please, commit your changes or stash them before you can merge.
 +
 
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# let's revert our local changes
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git checkout CMakeLists.txt
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# merge again
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git merge jcfr/master
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# and push it to the master
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git push
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</pre>
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<pre>
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# use cherry-pick to merge a commit from another branch into the current branch
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git cherry-pick COMMITHASH
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# now push
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git push
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</pre>
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=== Images ===
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{|
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|[[File:Becky.png|thumb|400px]]||[[File:Becky2.png|thumb|400px]]||[[File:Beck3.png|thumb|400px]]
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|}

Latest revision as of 14:31, 14 March 2013

Daniel Haehn's Page

Info
Daniel Haehn

http://danielhaehn.com

Haehn.jpg


VMTK in 3D Slicer

The Vascular Modeling Toolkit (VMTK) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. It should be very interesting to offer such techniques in 3D Slicer.

The official project page: http://www.vmtk.org/Main/VmtkIn3DSlicer


More recent news on this project:

http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK
http://www.na-mic.org/Wiki/index.php/Summer2009:The_Vascular_Modeling_Toolkit_in_3D_Slicer
http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week/The_Vascular_Modeling_Toolkit_in_3D_Slicer http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:StenosisDetector

This work is done in conjunction with Luca Antiga (Medical Imaging Unit, Bioengineering Department, Mario Negri Institute, Bergamo, Italy).

VMKT in Slicer4

The VMTK integration in 3D Slicer will be transitioned to Slicer4.

Some developer notes: 

# clone the fork
git clone git@github.com:haehn/vmtk.git

# check the status
git status

# switch to branch superbuild
git checkout superbuild

# include upstream by editing .git/config
# 17 [remote "upstream"]
# 18      url = https://github.com/lantiga/vmtk.git
# 19       fetch = +refs/heads/*:refs/remotes/upstream/*

# get the upstream
git fetch upstream

# merge the latest changes to local
git merge upstream/superbuild

# push the latest changes from upstream to fork
git push

Now, somebody forked the repo, made some changes we want in the master: 

# add the remote repo
git remote add jcfr https://github.com/jcfr/EMSegment4.git

# fetch it
git fetch jcfr

# see diff
git log -p master jcfr/master

# now merge the remote with our master
git merge jcfr/master
Updating f5d1b39..dd72623
error: Your local changes to 'CMakeLists.txt' would be overwritten by merge.  Aborting.
Please, commit your changes or stash them before you can merge.

# let's revert our local changes
git checkout CMakeLists.txt

# merge again
git merge jcfr/master

# and push it to the master
git push

# use cherry-pick to merge a commit from another branch into the current branch
git cherry-pick COMMITHASH

# now push
git push

Images

Becky.png
Becky2.png
Beck3.png
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