From d63abba06b4f58effcf02b246ff9182bfc8bd48e Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Sun, 17 Mar 2019 22:57:47 +0000
Subject: [PATCH 1/3] fix for dicomexpr

---
 tar2bids | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/tar2bids b/tar2bids
index 05378a2..2d3fe58 100755
--- a/tar2bids
+++ b/tar2bids
@@ -149,14 +149,19 @@ do
 	patient_etc=${date_etc##${date}_}
 	patient=${patient_etc%_[0-9]*.*}
 
+	suffix=${patient_etc##${patient}_}
+
+	
+
 	echo "  PI=$pi Study=$study Date=$date PatientName=$patient"
 	search="${pi}_${study}_${date}_${patientname_search}_[0-9]*.*.t*"
 	subjid=`$execpath/etc/getSubjSessID $patientname_search subject $patient`
 	sessid=`$execpath/etc/getSubjSessID $patientname_search session $patient`
     
     #expression for heudiconv
-    dicom_expr=$folder/${pi}_${study}_????????_${patientname_search}_?.????????.t*
-
+#    dicom_expr=$folder/${pi}_${study}_????????_${patientname_search}_?.????????.t*
+     dicom_expr=$folder/${pi}_${study}_${date}_${patientname_search}_${suffix}
+    echo $dicom_expr >> $dicomexpr_list
 	else
 	#if -s specified, then search in tarfile
     search="${tarfile_search}.t*"
@@ -165,6 +170,7 @@ do
     
     #expression for heudiconv
     dicom_expr=$folder/${tarfile_search}.t*
+    echo $dicom_expr >> $dicomexpr_list
 
 	fi
 	
@@ -185,11 +191,11 @@ do
 	#compile subjid list
 	if [ -n "$sessid" ]
 	then
-		echo "$subjid" >> $heudiconv_subjlist
-		echo "$sessid" >> $heudiconv_sesslist
+		echo "$subjid" >> $heudiconv_subjlist_all
+		echo "$sessid" >> $heudiconv_sesslist_all
 #	echo "-s $subjid -ss $sessid" >> $heudiconv_subjlist
 	else
-		echo "$subjid" >> $heudiconv_subjlist
+		echo "$subjid" >> $heudiconv_subjlist_all
 	fi
 	echo $subjid >> $subjlist
 
@@ -201,8 +207,9 @@ then
  exit 1
 fi
 
-#sort and remove duplicate entries in subjlist
-sort -u $heudiconv_subjlist -o $heudiconv_subjlist
+##sort and remove duplicate entries in subjlist
+sort -u $heudiconv_subjlist_all -o $heudiconv_subjlist
+sort -u $heudiconv_sesslist_all -o $heudiconv_sesslist
 sort -u $subjlist -o $subjlist
 
 
@@ -221,11 +228,11 @@ if [ -n "$sessid" ]
 then
 
 
-parallel -a $heudiconv_subjlist -a $heudiconv_sesslist $popts  "heudiconv ${heudi_opts} -b -d ${dicom_expr} -o $output_dir -f $heuristic_file -s {1} -ss {2} | tee $heudi_log.{1}.{2} "
+parallel --link -a $heudiconv_subjlist_all -a $heudiconv_sesslist_all -a $dicomexpr_list $popts  "heudiconv ${heudi_opts} -b -d {3} -o $output_dir -f $heuristic_file -s {1} -ss {2} | tee $heudi_log.{1}.{2} "
 
 else
 
-parallel -a $heudiconv_subjlist  $popts  "heudiconv ${heudi_opts} -b -d ${dicom_expr} -o $output_dir -f $heuristic_file -s {1}  | tee $heudi_log.{1}"
+parallel --link -a $heudiconv_subjlist_all  -a $dicomexpr_list $popts  "heudiconv ${heudi_opts} -b -d {2} -o $output_dir -f $heuristic_file -s {1}  | tee $heudi_log.{1}"
 
 fi
 

From 730b587b1303b44863e456e30febdccc73f551f6 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Sun, 17 Mar 2019 23:18:13 +0000
Subject: [PATCH 2/3] fix bug

---
 tar2bids | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tar2bids b/tar2bids
index 2d3fe58..d14583e 100755
--- a/tar2bids
+++ b/tar2bids
@@ -113,6 +113,7 @@ heudi_log=$log_dir/logs/heudiconv
 tuneup_log=$log_dir/logs/tuneup
 heudiconv_subjlist=$log_dir/subj_args.txt
 heudiconv_sesslist=$log_dir/sess_args.txt
+dicomexpr_list=$log_dir/dicomexpr.txt
 
 heudi_opts="$heudi_opts --overwrite"
 

From 2ad066d6db4455bb4ca2f5defe585a98da2083f3 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Sun, 17 Mar 2019 23:41:09 +0000
Subject: [PATCH 3/3] another fix

---
 tar2bids | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tar2bids b/tar2bids
index d14583e..6fee36c 100755
--- a/tar2bids
+++ b/tar2bids
@@ -112,7 +112,9 @@ mkdir $log_dir/logs
 heudi_log=$log_dir/logs/heudiconv
 tuneup_log=$log_dir/logs/tuneup
 heudiconv_subjlist=$log_dir/subj_args.txt
+heudiconv_subjlist_all=$log_dir/subj_args.all.txt
 heudiconv_sesslist=$log_dir/sess_args.txt
+heudiconv_sesslist_all=$log_dir/sess_args.all.txt
 dicomexpr_list=$log_dir/dicomexpr.txt
 
 heudi_opts="$heudi_opts --overwrite"
@@ -210,7 +212,10 @@ fi
 
 ##sort and remove duplicate entries in subjlist
 sort -u $heudiconv_subjlist_all -o $heudiconv_subjlist
+if [ -e $heudiconv_sesslist_all ]
+then
 sort -u $heudiconv_sesslist_all -o $heudiconv_sesslist
+fi
 sort -u $subjlist -o $subjlist