Slicer3:Debian

Intro

A Debian package for slicer has been created to make it easier to install "3D Slicer" on Debian machines. This means users can simply do:

sudo apt-get install slicer

and the slicer3 command will be available in their path and system menus. All slicer executables and libraries will be installed along with dependencies.

slicer3

Debian "squeeze"

Debian "squeeze" contains a "3D Slicer 3.4" package.

Debian "wheezy"

The next major Debian release "wheezy" will contain all tools to compile a local "3D Slicer 4.x" version.

sudo aptitude install libxext-dev libxrender-dev make g++
# download the 'supported' Qt version [1]
wget ftp://ftp.qt-project.org/qt/source/qt-everywhere-opensource-src-4.7.4.tar.gz
mkdir qt-everywhere-opensource-build-4.7.4
tar xvfz qt-everywhere-opensource-src-4.7.4.tar.gz
cd qt-everywhere-opensource-src-4.7.4
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -webkit -nomake examples -nomake demos
make -j8
make install

sudo aptitude update
#cmake 2.8.6 required because of libarchive
sudo aptitude install git-svn gitk subversion git gcc g++ make cmake-curses-gui libglu1-mesa-dev #libqt4-dev

git clone https://github.com/Slicer/Slicer.git
cd Slicer
git svn init http://svn.slicer.org/Slicer4/trunk
git update-ref refs/remotes/git-svn refs/remotes/origin/master
git checkout master
git svn rebase

mkdir ../Slicer4-SuperBuild-Debug
cd ../Slicer4-SuperBuild-Debug
#cmake ../Slicer -DSlicer_REQUIRED_QT_VERSION:STRING=4.7.4 # if using system QT
#cmake -DQT_QMAKE_EXECUTABLE:FILEPATH=~/qt-everywhere-opensource-build-4.7.4/bin/qmake -DITK_VERSION_MAJOR:STRING=4 -DSlicer_USE_GIT_PROTOCOL:BOOL=OFF ../Slicer
cmake -DQT_QMAKE_EXECUTABLE:FILEPATH=~/qt-everywhere-opensource-build-4.7.4/bin/qmake ../Slicer
make -j8

# runtime dependency:
sudo aptitude install python-tk

Cloud computing

The EBS AMI ami-6ca05805 contains a ready to use 3D Slicer 3.4 installation. The image can be started as a t1.micro instance (~ $0.02 per hour).

Example session:

AMI=ami-6ca05805
ec2-describe-images $AMI
ec2-run-instances -t t1.micro $AMI -n1 -k mykey
ec2-describe-instances
host=ec2-174-129-170-61.compute-1.amazonaws.com
ssh -i id_rsa-mykey -X ubuntu@${host}

Use Slicer's command line tools

/usr/lib/Slicer3/Plugins/AffineRegistration --help

or start Slicer's GUI

slicer3

Dependencies

Media:slicer_rdep_squeeze.png

Ubuntu

The Ubuntu distribution will also contain a slicer package in their universe repository [2]. This package is probably based on the slicer package taken from Debian "unstable".

"The MOTU team cares for the packages in universe and multiverse (which are comprised mostly of packages from the Debian archive) on a best-effort basis, as there are a large number of packages relative to the resources of the team. Therefore, a vast majority of these packages are used unchanged from Debian, rebuilt in an Ubuntu build environment, and do not receive personal attention from an Ubuntu developer." [3]

Thanks!

These packages were the result of a lot of work by Dominique Belhachemi.