Index: firmware/App/Controllers/SyringePump.c
===================================================================
diff -u -rbd241ef5231a9869adaf7bb5ed166135beb2c0fb -rc4857379637e79ab8fcc72ecfd791796b9f48e6d
--- firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision bd241ef5231a9869adaf7bb5ed166135beb2c0fb)
+++ firmware/App/Controllers/SyringePump.c	(.../SyringePump.c)	(revision c4857379637e79ab8fcc72ecfd791796b9f48e6d)
@@ -7,8 +7,8 @@
 *
 * @file    SyringePump.c
 *
-* @author  (last)      Sean Nash
-* @date    (last)      15-Nov-2021
+* @author  (last)      Dara Navaei
+* @date    (last)      04-Jan-2022
 *
 * @author  (original)  Sean Nash
 * @date    (original)  04-Mar-2021
@@ -90,8 +90,9 @@
 #define TEN_PCT_OVER_ALLOWANCE                        1.1                                   ///< Allow 10 percent over target before alarming on over travel.
 #define FIVE_PCT_OVER_ALLOWANCE                       1.05                                  ///< Allow 5 percent over target before alarming on over travel.
 
-/// Expected position of empty in relation to home postion.
-#define SYRINGE_PUMP_EMPTY_POS                        ( SYRINGE_ENCODER_COUNTS_PER_ML * 10.84 )
+/// Expected position of empty in relation to home position.
+#define SYRINGE_PUMP_EMPTY_POS                        ( SYRINGE_ENCODER_COUNTS_PER_ML * 10.84 )  ///< get syringe volume from home to empty (11 mL is placeholder)
+
 /// Margin of error for empty position determination.
 #define SYRINGE_PUMP_EMPTY_POS_MARGIN                 ( SYRINGE_ENCODER_COUNTS_PER_ML * 0.5 )
 /// Minimum retract position.
@@ -1033,6 +1034,12 @@
 {
     // Execute syringe pump monitor
     execSyringePumpMonitor();
+
+    // Clear pump running while off alarm persistence if not in off state
+    if ( syringePumpState != SYRINGE_PUMP_OFF_STATE )
+    {
+        isPersistentAlarmTriggered( ALARM_ID_HD_SYRINGE_PUMP_NOT_STOPPED_ERROR, FALSE );
+    }
 
     // Execute syringe pump control state machine
     switch ( syringePumpState )
@@ -1143,6 +1150,9 @@
 {
     SYRINGE_PUMP_STATE_T result = SYRINGE_PUMP_OFF_STATE;
 
+    isPersistentAlarmTriggered( ALARM_ID_HD_SYRINGE_PUMP_ENCODER_DIRECTION_ERROR, FALSE );       // reset direction alarm persistence when pump is off
+    isPersistentAlarmTriggered( ALARM_ID_HD_SYRINGE_PUMP_CONTROLLER_DIRECTION_ERROR, FALSE );    // reset direction alarm persistence when pump is off
+
 #ifndef DISABLE_SYRINGE_PUMP_ALARMS
     // Check position is not changing while stopped
     if ( TRUE == isPersistentAlarmTriggered( ALARM_ID_HD_SYRINGE_PUMP_NOT_STOPPED_ERROR, ( syringePumpLastPosition != getSyringePumpPosition() ) ) )
@@ -1327,7 +1337,6 @@
     if ( TRUE == stopPump )
     {
         stopSyringePump();
-        retractSyringePump();
         result = SYRINGE_PUMP_OFF_STATE;
     }