init_vars

#!/bin/bash

# For the pipeline. Requires the existence of a SWdir with:
#  - The pipeline
#  - fsl
#  - freesurfer 
export BB_BIN_DIR="$SWdir/bip"
export FSLDIR="$SWdir/fsl"

# For FSL
source $FSLDIR/etc/fslconf/fsl.sh

export FSLOUTPUTTYPE="NIFTI_GZ"
export FSLSUB_CONF="$SWdir/bip/fsl_sub.yml"

# For FreeSurfer
unset FSFAST_HOME
unset MNI_DIR
unset FSL_DIR
export FREESURFER_HOME="$SWdir/freesurfer_7_dev"
export MNI_DIR="${FREESURFER_HOME}/mni"
source $FREESURFER_HOME/SetUpFreeSurfer.sh

# Activate the environment
source $FSLDIR/bin/activate ukb

# Unsetting some problematic variables
unset PYTHONPATH
unset LC_ALL
unset LC_CTYPE

# Creating a useful alias
alias runbip="$BB_BIN_DIR/bip/main.py"
PS1="(ukb) \! "`whoami`@`hostname|cut -d. -f1`@$(basename $(tty))" | \t | \w $ " ; 
export PS1