Merge branch 'release'

oxford_asl.in

@@ -128,6 +128,10 @@ Usage_extended() {
     echo " --elen      : Length of each epoch in TIs"
     echo " --eol       : Overlap of each epoch in TIs- {deafult: 0}"
     echo ""
+    echo " Miscellaneous "
+    echo " --model-options=<file>  : File containing additional model options to be passed to BASIL/Fabber"
+    echo "                           This is an advanced setting for model-specific options ONLY"
+    echo "                           Do NOT include any standard oxford_asl options here" 
     echo ""
     echo " Notes:"
     echo " Input data - Any combination of label (tag) control images is accepted, see asl_file for more detailed"
@@ -827,6 +831,8 @@ takeargs=0;boolarg="";isbool="";
 	--cblip) cblip=$argument #blip reversed calibration image
 		 takeargs=1;; 
 	# 
+	--model-options) model_options=$argument
+	    takeargs=1;;
 	--verbose) verbose=$argument
 	    takeargs=1;;
 	--debug) debug=1
@@ -1799,6 +1805,11 @@ if [ ! -z $devel ]; then
     basil_options=$basil_options" --devel "
 fi
 
+if [ ! -z $model_options ]; then
+    echo "Appending additional BASIL options to $tempdir/basil_options.txt"
+    cat $model_options >> $tempdir/basil_options.txt
+fi
+
 Log "BASIL options ($tempdir/basil_options.txt):"
 Log "----"
 Log "`cat $tempdir/basil_options.txt`"