setup_env.sh

#!/bin/bash

# We should have lots of paths from the BIDS environment. If we are
# run from the command line, setup the one(s) we actually need.
case $( hostname ) in
    rushmore)
        GROUP=fnl
        if [ -z "${CARET7DIR}" ] ; then
            export CARET7DIR="/mnt/max/software/workbench/bin_linux64"
        fi
        export FSLDIR=/mnt/max/software/fsl-5.0.10
        export FSL_DIR=/mnt/max/software/fsl-5.0.10
        source ${FSLDIR}/etc/fslconf/fsl.sh > /dev/null 2>&1
        ;;
    *)
        GROUP=fnl_lab
        if [ -z "${CARET7DIR}" ] ; then
            export CARET7DIR="/home/exacloud/lustre1/fnl_lab/code/external/utilities/workbench-1.3.2/bin_rh_linux64"
        fi
        ;;
esac
export wb_command=${CARET7DIR}/wb_command
export AtlasSpaceFolder="MNINonLinear"

# Not sure any of this is used anymore. Need to check this someday....
motion_filename="motion_numbers.txt"
skip_seconds=5
brain_radius_in_mm=50
expected_contiguous_frame_count=5

# frame displacement th to calculate beta coefficients for regression
fd_th=0.2

# Define filter parameters
bp_order=2 #band pass filter order
lp_Hz=0.009 # low pass frequency, Hz
hp_Hz=0.080 # high pass frequency, Hz

# Define constants
vent_lt_L=4 # white matter lower threshold Left
vent_ut_L=4 # white matter upper threshold Left
vent_lt_R=43 # white matter lower threshold Right
vent_ut_R=43 # white matter upper threshold Right

wm_lt_R=2950 # ventricles lower threshold Right
wm_ut_R=3050 # ventricles upper threshold Right
wm_lt_L=3950 # ventricles lower threshold Left
wm_ut_L=4050 # ventricles upper threshold Left