auto_proc_albs

#!/bin/bash

###############################################################
# Purpose: Automatically detect uploaded scans, copy them to  #
# Big Kahuna, and begin preprocessing.                        #
# Author: Brianne Sutton, PhD                                 #
# Date: July 2018                                             #
#                                                             #
# To add studies, expand the dirrectory and task dictionaries #
#                                                             #
###############################################################

tmp_mnt='/mnt/threetbrain'
sort_files='/home/brianne/tools/general_utilities/sort_files_albs'
cron_test='no'
debug='no'
dt=`date +"%Y%m%d"`
if [[ "$cron_test" == 'yes' ]] ; then
  echo "cron test done"
else
#Create a dictionary of the directories
declare -A dir_dict
dir_dict=(["Dabelea_ECHO"]='echo') # Can add ["Dabelea_HealthyStart"]="hs"
declare -A task_dict
task_dict=( ['echo']="{'rest'}" ) # For example syntax: ['priming']="{'fp_run1' 'fprun2' 'priming'}"

# Convert from dicom to nifti, autodetect ACPC, and start preprocessing
for dk in "${!dir_dict[@]}"; do
  echo ">> Sorting and preprocessing files from: $dk"
  dest=`echo ${dir_dict[$dk]}`
  dest_dir="/data/images/${dest}"
  if [[ -f  ${dest_dir}/subj_to_proc.txt ]] ; then
      readarray -t subjs < ${dest_dir}/subj_to_proc.txt
      subjs=($(printf "%s\n" "${subjs[@]}" | sort -u))
    for s in ${subjs[@]} ; do
      if [[ -e ${dest_dir}/tmp.txt ]] ; then
	  rm ${dest_dir}/tmp.txt
      fi
      echo "Sorting files"
      ${sort_files} ${dest} ${s}  # dicom conversion and AC-PC alignment
      # Took out a section to automatically run through the preprocessing. 
    done
  fi
done
if [[ -e ${dest_dir}/subj_to_proc.txt ]] ; then
    rm ${dest_dir}/subj_to_proc.txt
fi
fi
exit