Mac vistasoft software configuration

Below are some recommendations. You need not follow them exactly. They work well on the Winawer lab machines.

• Tell your bash profile to read your .bashrc file each time the terminal is launched. This way the bashrc will be read irrespective of how you launch your terminal. See [http://www.joshstaiger.org/archives/2005/07/bash_profile_vs.html this page] for explanation of bashrc v bash_profile.

The contents of our .bash_profile file are:

[ -a ~/.bashrc ] && source ~/.bashrc

To check this, type this command from the terminal window

more ~/.bash_profile

• Set Freesurfer paths in your .bashrc file. We do this as a function with the following contents of the .bashrc file:

# Source freesurfer and fsl paths
freesurfer()
{
        export SUBJECTS_DIR=/Volumes/server/Freesurfer_subjects; 
        export FREESURFER_HOME=/Applications/freesurfer; 
        source $FREESURFER_HOME/SetUpFreeSurfer.sh; 
        export FSLDIR=/usr/local/fsl; . ${FSLDIR}/etc/fslconf/fsl.sh;
        PATH=${FSLDIR}/bin:${PATH}; export FSLDIR PATH
}

Check it:

more ~/.bashrc