Difference between revisions of "User:Haehn"

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! Info ||  
 
! Info ||  
 
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|- 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>
 
|}
 
|}
  
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=== Vessel Segmentation in Slicer3 ===
 
  
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'''Project goal:''' Implementing a vessel/tube segmentation module in Slicer3<br>
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=== VMTK in 3D Slicer ===
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'''Kick-Off:''' 10/15/2008
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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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The official project page:
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http://www.vmtk.org/Main/VmtkIn3DSlicer
  
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=== Task 1: Module for Slicer3 based on old version ===
 
  
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In Slicer2 exists a module called '''vtkExtractAirway'''. This module is based on a centerline approach documented in the following paper: "Aylward, S.: Initialization, Noise, Singularities, and Scale in Height Ridge Traversal for Tubular Object Centerline Extraction (available http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.18.8435)".<br>
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More recent news on this project: <br>
  
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Since the algorithm is not fully implemented yet, the idea is to port the Slicer2 module to Slicer3 and finalize it to be used as a semi-interactive way to segment vessel or other tube shaped ROI.<br>
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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<br>
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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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The semi-interactive way should work like the following that a user clicks into a path of a ROI and then the algorithm computes all the connected tubes and highlights them.<br>
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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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=== Task 2: an interface to VMTK in Slicer3 ===
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==== VMKT in Slicer4 ====
  
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More recent news on this project: http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK
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The VMTK integration in 3D Slicer will be transitioned to Slicer4.
  
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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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Some developer notes:
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<pre>
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# clone the fork
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git clone git@github.com:haehn/vmtk.git
  
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It should be very interesting to offer such techniques in Slicer3. So the plan is to make a python scripted module that connects to VMTK pipes and provides even the possibility of user interaction.<br>
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# check the status
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git status
  
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This task is scheduled for the NAMIC project week 2009. Luca Antiga and me planned to develop it in an "extreme programming"-way. Until then I will focus on the ground work for making an interactive slicer module and on building VMTK pipes.
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# switch to branch superbuild
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git checkout superbuild
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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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