x.PreProc_RUN_Template

#!/bin/sh

# A starting template of how to RUN these functions together and across subjects
# Copy this RUN file into your project directory. Then just change this file, not the specific functions.

#####################################
# Chose analysis options below (1=run)
#####################################
DO_PreProc_BET_3D=0
DO_PreProc_SEG_anat=0
DO_PreProc_VolReg_4D=0
DO_PreProc_DistortCorrect=0
DO_PreProc_BET_4D=0
DO_PreProc_Mask_4D=0
DO_PreProc_TissueReg=0
DO_PreProc_Transform_MASK=0
DO_PreProc_MEANTS=0

code_dir='/Users/XXXX/Documents/GitHub/PreProc_BRAIN' #change this to where the PreProc_BRAIN repo is on your computer

################################
################################
################################

for subject in sub-01 sub-02
do

echo "*********************"
echo "Processing ${subject}"
echo "*********************"

##################################
###### x.PreProc_BET_3D ########
##################################

if [ "${DO_PreProc_BET_3D}" -eq 1 ]

then
  echo "*****************************************"
  echo "Running x.PreProc_BET_3D for ${subject}"
  echo "*****************************************"

  ${code_dir}/x.PreProc_BET-3D /path_to_T1_input_file /path_to_output_dir

else
  echo "*********************************************"
  echo "Not running x.PreProc_BET_anat for ${subject}"
  echo "*********************************************"
fi

##################################
###### x.PreProc_SEG_anat ########
##################################

if [ "${DO_PreProc_SEG_anat}" -eq 1 ]

then
  echo "*****************************************"
  echo "Running x.PreProc_SEG_anat for ${subject}"
  echo "*****************************************"

  ${code_dir}/x.PreProc_SEG-anat /path_to_T1_input_file /path_to_output_dir partial_volume_threshold

else
  echo "*********************************************"
  echo "Not running x.PreProc_SEG_anat for ${subject}"
  echo "*********************************************"
fi

###################################
########## NEXT FUNCTION ##########
###################################

# code

done #end subject loop