User:Haehn

Daniel Haehn's Page

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Daniel Haehn University of Pennsylvania Department of Radiology Section of Biomedical Image Analysis 3600 Market Street, Suite 380 Philadelphia, PA 19104

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

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