Hauke recommends JIP 2.1 for his pipeline.

For example, on NeuroDebian (http://neuro.debian.net/)

When downloaded from http://www.nitrc.org/projects/jip/, JIP installation comes with define-jip.tcsh config file, but we need .bash file, as listed below (make sure to define JIP_HOME and path to jip correctly):

define-jip.bash

#!/bin/bash
# Include any argument to suppress output.  E.g.,
# source /home/brain/jip/define-jip.bash 1
# from startup file .bashrc
 
# Set the JIP_HOME environment variable to access documentation from programs.
#    e.g., xd -H
export JIP_HOME=/home/brain/jip
 
# These aliases point to scripts that pick the correct executables.
alias jip="$JIP_HOME/bin/jip"
alias jip-display="$JIP_HOME/bin/display"
alias jip-align="$JIP_HOME/bin/align"
alias jip-glm="$JIP_HOME/bin/glm"
alias jip-rem="$JIP_HOME/bin/rem"
 
# Using any argument to this script will suppress output.
if [ $# -eq 0 ]
then
echo " "
echo "Defined JIP_HOME to be $JIP_HOME"
echo "Defined these aliases: jip, xd, align, glm, pet, rem"
echo " "
echo "Get help using:"
echo " "
echo "xd -h        or    xd -H"
echo "align -h     or    align -H"
echo "glm -h       or    glm -H"
echo "rem -h       or    rem -H"
echo "jip [return] help"
echo " "
fi

Add following line to .bashrc:

source /home/brain/jip/define-jip.bash 1