diff --git a/sub_sess_id.sh b/sub_sess_id.sh
new file mode 100644
index 0000000..61c8b37
--- /dev/null
+++ b/sub_sess_id.sh
@@ -0,0 +1,202 @@
+proj=$1
+subid=$2
+
+if [[ $proj == "ABCD_NDAR" ]]; then
+    tmp_label=$subid
+    if [[ $tmp_label == "1" ]]; then
+        sub="YCW83AC7"
+        sess="S1"
+    elif [[ $tmp_label == "S1" ]]; then
+        sub="INV6F1LPHLT"
+        sess="S1"
+    elif [[ $tmp_label == "S_1" ]]; then
+        sub="FDM0PRRA"
+        sess="S1"
+    else
+        sub=$subid
+        if [[ $sub == *_S* ]]; then
+          sess=S${sub##*_S}
+          sub=${sub%_S*}
+        elif [[ $sub == *-S* ]]; then
+          sess=S${sub##*-S}
+          sub=${sub%-S*}
+        else
+          sess="S1"
+        fi
+    fi
+    sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Parra_MMMM" ]]; then
+      sub=${subid#$proj-}
+      sess=${sub##*-}
+      sub=${sub%-*}
+      sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Pettit_tDCS" ]]; then
+      sub=${subid#$proj-}
+      sess=${sub##*_}
+      sub=${sub%_*}
+      sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Sibley_Teen" ]]; then
+      if [[ $subid == *Sibley_TEEN* ]]; then
+        sub=${subid#Sibley_TEEN-}
+      else
+        sub=${subid#$proj-}
+      fi
+      sess=${sub##*-}
+      sub=${sub%-*}
+      sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Sutherland_MIP" ]]; then
+      sub=${subid#$proj-}
+      sess=S${sub##*S}
+      if [[ $sub == *-S* ]]; then
+        sub=${sub%-*}
+      else
+        sub=${sub%S*}
+      fi
+      sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Sutherland_ACE" ]]; then
+      sub=${subid#$proj-}
+      sess=${sub##*-}
+      sub=${sub%-*}
+      sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Soto_GRT" ]]; then
+      sub=${subid#$proj-}
+      if [[ $sub == *0003S1-S1 ]]; then
+        sub=${sub%-*}
+        sess="S1"
+      elif [[ $sub == *0003S1-S2 ]]; then
+        sub=${sub%-*}
+        sess="S2"
+      elif [[ $sub == *0003S2-S2 ]]; then
+        sub=${sub%-*}
+        sess="S3"
+      elif [[ $sub == *0003-S1-S1 ]]; then
+        sub=${sub%-*}
+        sub=${sub%-*}
+        sess="S4"
+      elif [[ $sub == *0003-S2-S2 ]]; then
+        sub=${sub%-*}
+        sub=${sub%-*}
+        sess="S5"
+      elif [[ $sub == *0003S3-S3 ]]; then
+        sub=${sub%-*}
+        sess="S6"
+      elif [[ $sub == *0003S4-S4 ]]; then
+        sub=${sub%-*}
+        sess="S7"
+      else
+        sess=${sub##*-}
+        sub=${sub%-*}
+        if [[ $sub == *-S* ]]; then
+          sess=${sub##*-}
+          sub=${sub%-*}
+        elif [[ $sub == *S* ]]; then
+          sub=${sub%S*}
+        fi
+      fi
+      sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Dick_AHEAD" ]]; then
+    sub=${subid##*$proj-}
+    if [[ $sub == *_S1 ]]; then
+      if [[ $sub == *-2_S1 ]]; then
+        sess="S2"
+        sub=${sub%-2_S1*}
+      else
+        sess="S1"
+        sub=${sub%-_*}
+      fi
+    elif [[ $sub == *_1 ]]; then
+      echo $subid >> $data_qc/qc-processed/$proj-processed
+      proj_data=$(cat $data_qc/qc-processed/$proj-processed)
+      continue
+    else
+      sess=${sub##*-}
+      sub=${sub%-*}
+      if [[ $sub == *-S* ]]; then
+        if [[ $sub != *-ST* ]]; then
+          sub=${sub%-*}
+        fi
+      fi
+    fi
+    sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Dick_TRAIN" ]]; then
+    sub=${subid#$proj-}
+    sess=${sub##*-}
+    sub=${sub%-*}
+    sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "Mattfeld_RTV" ]]; then
+    sub=${subid#$proj-}
+    sess=${sub##*-}
+    if [[ $sess != S* ]]; then
+      sub=$sub-S1
+      sess=${sub##*-}
+    fi
+    sub=${sub%-*}
+    sub=$(echo ${sub//[-_]/})
+elif [[ $proj == "McMakin_EMU" ]]; then
+    tmp_label=$subid
+    if [[ $tmp_label == "McMakin_EMU_R01_PT-S1-S1" ]]; then
+      sub="R01_PT"
+      sess="S1"
+    elif [[ $tmp_label == "1" ]]; then
+        sub="000-1001"
+        sess="S1"
+    elif [[ $tmp_label == "2" ]]; then
+        sub="000-1005"
+        sess="S2"
+    elif [[ $tmp_label == "S_1" ]]; then
+        sub="000-1004"
+        sess="S1"
+    elif [[ $tmp_label == "S_2" ]]; then
+        sub="000-1004"
+        sess="S2"
+    else
+      if [[ $tmp_label == MCMAKIN_EMU* ]]; then
+        sub=${subid#MCMAKIN_EMU-}
+      else
+        sub=${subid#$proj-}
+      fi
+      if [[ $sub == *_Day2* ]]; then
+        sess="S2"
+        sub=${sub%_*}
+      elif [[ $sub == *_1-S1 ]]; then
+        sess="S1"
+        sub=${sub%_*}
+      elif [[ $sub == *_2-S2 ]]; then
+        sess="S2"
+        sub=${sub%_*}
+      elif [[ $sub == *_1 ]]; then
+        sess="S1"
+        sub=${sub%_*}
+        if [[ $sub == *_* ]]; then
+          sub=${sub%_*}
+        fi
+      elif [[ $sub == *_2 ]]; then
+        sess="S2"
+        sub=${sub%_*}
+        if [[ $sub == *_* ]]; then
+          sub=${sub%_*}
+        fi
+      elif [[ $sub == *_S1 ]]; then
+        sess="S1"
+        sub=${sub%_*}
+      elif [[ $sub == *_S2 ]]; then
+        sess="S2"
+        sub=${sub%_*}
+      else
+        sess=${sub##*-}
+        sub=${sub%-*}
+        if [[ $sub == *-S* ]]; then
+          sub=${sub%-*}
+        elif [[ $sub == *S* ]]; then
+          sub=${sub%S*}
+        fi
+      fi
+    fi
+    sub=$(echo ${sub//[-_]/})
+    if [[ $sub == "000" ]]; then
+      sub="0001002"
+      sess="S3"
+    fi
+fi
+
+echo $sub $sess
diff --git a/xnat_download.sh b/xnat_download.sh
index d8c4a41..2d02ce7 100644
--- a/xnat_download.sh
+++ b/xnat_download.sh
@@ -1,16 +1,16 @@
-if [ ! -e ~/xnatpassfile ]; then
+if [ ! -e ~/xnatpassfile ] & [ ! -e ~/xnatconfigfile ]; then
   read -p 'Username: ' uservar
   read -sp 'Password: ' passvar
-  printf "{\"password\": \"$passvar\", \"user\": \"$uservar\", \"server\": \"http://xnat.fiu.edu\"}" > ~/xnatpassfile
+  printf "{\"password\": \"$passvar\", \"user\": \"$uservar\", \"server\": \"http://xnat.fiu.edu\"}" > ~/xnatconfigfile
+  printf "+$uservar@http://xnat.fiu.edu:8080/xnat=$passvar" > ~/xnatpassfile
 fi
 
-
 while [[ $# -gt 0 ]]; do
     case $1 in
+    -a|--auto) autocheck="$2"; shift;;
     -p|--project) proj="$2" ; shift;;
-    -c|--credentials) passfile="$2" ; shift;;
     -o|--outputdir) outdir="$2" ; shift;;
-    -s|--session) sess="$2" ; shift;;
+    -s|--session) expsess="$2" ; shift;;
     (--) shift; break;;
     (-*) echo "$0: error - unrecognized option $1. Try $0 -h" 1>&2; exit 1;;
     (*) break;;
@@ -18,6 +18,78 @@ while [[ $# -gt 0 ]]; do
     shift
 done
 
-if [ -e ~/xnatpassfile ]; then
-  /xget-public/xget -passfile $passfile -s $sess -o $outdir -proj $proj
+function download_experiment {
+
+  # create a temporary directory with the subject filters
+  # if the temporary directory exists (it should not), create it
+  if [ ! -d $outdir/$proj ]; then
+    mkdir -p $outdir/$proj
+  fi
+
+  # download the subject file into the temporary directory
+  /xget-public/xget -passfile ~/xnatpassfile -s ${exps[i]} -o $outdir/$proj -proj $proj
+  unzip $outdir/$proj/${exps[i]}_acq.zip -d $outdir/$proj/
+  rm $outdir/$proj/${exps[i]}_acq.zip
+  tar -C $outdir/$proj/${labels[i]} -cf $outdir/$proj/sub-"$sub"_ses-${sess}.tar scans/
+  rm -r $outdir/$proj/${labels[i]}
+  printf "sub-%s_ses-%s.tar\n" $sub $sess >> ~/XNAT-data-transfer/$proj-processed
+
+  # get date and time
+  date_time=
+  date_time=$(date)
+  # append the email message
+  echo "Data transferred from XNAT to FIU-HPC for Project: $proj Subject: $sub Session: $sess on $date_time" >> ~/XNAT-data-transfer/$proj-processed-message
+
+}
+
+# call a python script to get a list of experiments in the XNAT project
+exps=($(python /scripts/xnat_list.py ~/xnatconfigfile $proj 'experiments'))
+labels=($(python /scripts/xnat_list.py ~/xnatconfigfile $proj 'labels'))
+
+#for each subject identified
+for ((i=0;i<${#exps[@]};i++)); do
+  labelinfo=($(bash /scripts/sub_sess_id.sh $proj ${labels[i]}))
+  sub=${labelinfo[0]}
+  sess=${labelinfo[1]}
+  if [[ $autocheck == "y" ]] | [[ $autocheck == "yes" ]]; then
+
+    if [ -e ~/XNAT-data-transfer/$proj-processed ]; then
+      proj_data=`cat ~/XNAT-data-transfer/$proj-processed`
+      # if the subject has not previously been processed
+      if [[ $proj_data != *sub-"$sub"_ses-"$sess".tar* ]]; then
+        download_experiment
+      fi
+    else
+      mkdir ~/XNAT-data-transfer
+      download_experiment
+    fi
+
+  else
+    if [[ $expsess == XNAT_* ]]; then
+      if [[ ${exps[i]} == $expsess ]]; then
+        if [ ! -e ~/XNAT-data-transfer/$proj-processed ]; then
+          mkdir ~/XNAT-data-transfer
+        else
+          proj_data=`cat ~/XNAT-data-transfer/$proj-processed`
+          if [[ $proj_data != *sub-"$sub"_ses-"$sess".tar* ]]; then
+            download_experiment
+          else
+            echo "Experiment session has already been downloaded!"
+            exit
+          fi
+        fi
+      else
+        echo "Experiment session '$expsess' is not in project '$proj'!"
+        exit
+      fi
+    else
+      echo "Experiment session should start with 'XNAT_*'!"
+      exit
+    fi
+  fi
+done
+
+if [ -e ~/XNAT-data-transfer/$proj-processed-message ]; then
+  mail -s 'FIU XNAT-HPC Data Transfer Update Project $proj' $USER@fiu.edu < ~/XNAT-data-transfer/$proj-processed-message
+  rm ~/XNAT-data-transfer/$proj-processed-message
 fi
diff --git a/xnat_list.py b/xnat_list.py
new file mode 100644
index 0000000..58a8a34
--- /dev/null
+++ b/xnat_list.py
@@ -0,0 +1,15 @@
+#!/usr/bin/env python
+from pyxnat import Interface
+import sys
+
+config_file = sys.argv[1]
+project = sys.argv[2]
+ref = sys.argv[3]
+
+central = Interface(config=config_file)
+select_exp = '/projects/' + project +'/experiments'
+exps = central.select(select_exp).get()
+if ref == 'experiments':
+    print " ".join([str(x) for x in exps])
+elif ref == 'labels':
+    print " ".join([central.select(select_exp + '/' + x).label() for x in exps])