Set up your environment for diffusion MRI processing

From VrlWiki
Jump to navigation Jump to search

Create a user directory

 mkdir -p /research/graphics/users/$USER/sandbox

Set up your environment

Edit ~/.environment and add the following lines: 

# in the umask section
umask 002

# in the environment variable section
setenvvar       LM_LICENSE_FILE    /cfarm/nag/license.dat
setenvvar       CVSROOT            /research/graphics/cvsroot/
setenvvar       G                  /research/graphics/users/$USER/sandbox
setenvvar       GTO                /research/graphics/users/$USER/sandbox
setenvvar       GARCH              linux
setenvvar       G_COMPILER         gcc3
setenvvar       G_IMPORT           /research/graphics/tools/linux/import

# in the path section
pathappend       PATH       "$G/bin"
pathappend       PATH       "/research/graphics/tools/linux/bin"
setenvifnot      PYTHONPATH "$G/bin"
pathappend       PYTHONPATH "$G/bin"

Then execute: source ~/.environment


Check out, build, and install common code

cd $G && cvs co common/build common/utility common/gg common/mri common/libcurvecollection
cd $G/common/utility/nag && make install
cd $G/common/utility/port && make all && make install
cd $G/common/gg && make all && make install
cd $G/common/mri && make all && make install
cd $G/common/libcurvecollection && make all && make install


Check out, build, and install pipeline code

cd $G && cvs co project/brain/pipeline
cd $G/project/brain/pipeline && make all && make install


Put everything on your $PATH

Retrieved from "http://vrl.cs.brown.edu/wiki/index.php?title=Set_up_your_environment_for_diffusion_MRI_processing&oldid=4689"