//How to install 3d Brain Atlas Reconstructor on Ubuntu?// = 3d Brain Atlas Reconstructor Installation (Ubuntu) = ---- **Note**: This procedure is valid for //Ubuntu 9.04// and //Ubuntu 10.04 LTS// and was tested on 4.08.2011. For guides related to //Ubuntu 8.04// see [[barSoftwareInstallation8.04]]. Installation on other Ubuntu versions or other Linux distributions is similar, however not described yet. ---- [[PageOutline(2-3,, inline)]] == Installing required packages == Installation consists of following steps (just paste code blocks into terminal it should be fine (Ubuntu 9.10). 1. Installing Visualization Toolkit and other graphic libraries: {{{ sudo apt-get install \ libvtk5.2 libvtk5-dev libvtk5.2-qt4 libvtk5-qt4-dev \ tk8.5 tk8.5-dev \ python-vtk libgtkgl2.0-1 libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti }}} 2. Installing python-related packages: {{{ sudo apt-get install \ python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.6 }}} 3. Other packages: {{{ sudo apt-get install \ potrace pstoedit python-setuptools subversion python-epydoc }}} If You are developer, you may also want to install optional packages with documentation: {{{ sudo apt-get install vtkdata vtk-doc vtk-examples }}} If you use Ubuntu 10.04 install following packages: {{{ sudo apt-get install \ libvtk5.2 libvtk5-dev libvtk5.2-qt4 libvtk5-qt4-dev \ tk8.5 tk8.5-dev \ python-vtk libgtkgl2.0-1 libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti }}} {{{ sudo apt-get install \ python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.6 }}} {{{ sudo apt-get install \ potrace pstoedit python-setuptools subversion python-epydoc }}} If you use Ubuntu 10.10 install following packages: {{{ sudo apt-get install \ libvtk5.4 libvtk5-dev libvtk5.4-qt4 libvtk5-qt4-dev \ tk8.5 tk8.5-dev \ python-vtk libgtkgl2.0-1 libgtkgl2.0-dev libgtkglext1 librsvg2-2 python-nifti }}} {{{ sudo apt-get install \ python-gtkglext1 python-rsvg python-opengl python-numpy python-scipy python-wxgtk2.8 }}} {{{ sudo apt-get install \ potrace pstoedit python-setuptools subversion python-epydoc }}} Once all packages are installed, it's time to create directory structure: == Getting code == It is assumed that main directory dedicated for software is `/home/$USERNAME/3dbar`. if You want to install to another directory, please replace `3dbar` with desired path. In order to get latest stable version of 3dBAR fill out [http://service.3dbar.org/downloadForm following form] then download 3dBAR using link provided via email. Unzip the file to your home directory and go to the 3dBAR directory: {{{ unzip -f 3dbar_latest.zip -d ~/3dbar ; cd 3dbar; }}} then create directory where datasets will be stored: {{{ mkdir -p /home/$USERNAME/3dbar/atlases }}} Created directories have following purposes: * **bin**: Holds all executable files, atlas parsers and auxiliary scripts * **lib**: Holds 3dBAR api * **atlases**: Directory, where source data, //CAF datasets// and reconstructed models are stored. Each dataset (denoted as DATASET_NAME) contains following subdirectories: * atlases/DATASET_NAME/src : Here source data is located. It may be put manually by user or ie. downloaded from internet depending on particular parser. * atlases/DATASET_NAME/caf : Is the directory where CAF dataset is generated by particular parsers. * atlases/DATASET_NAME/reconstructions : Directory for reconstructed models. {{{#!comment == Initial build == In order create initial CAF datasets, generate documentation use following command in /home/$USERNAME/3dbar/ directory: {{{ make -B -j N all }}} where N is number of parallel processes You want to use. If everything is installed correctly processing should be performed without any errors. Then 3dBAR GUI should be launched {{{ ./3dbar.sh }}} and used to perform reconstructions. If everything went fine, You may proceed to : == Getting parsers for additional datasets == }}}