diff --git a/ibllib/io/extractors/ephys_fpga.py b/ibllib/io/extractors/ephys_fpga.py
index 2980eb7bf..4da3d6bd8 100644
--- a/ibllib/io/extractors/ephys_fpga.py
+++ b/ibllib/io/extractors/ephys_fpga.py
@@ -69,7 +69,7 @@
 """int: The number of encoder pulses per channel for one complete rotation."""
 
 BPOD_FPGA_DRIFT_THRESHOLD_PPM = 150
-"""int: Throws an error if Bpod to FPGA clock drift is higher than this value."""
+"""int: Logs a warning if Bpod to FPGA clock drift is higher than this value."""
 
 CHMAPS = {'3A':
           {'ap':
@@ -545,17 +545,23 @@ def get_main_probe_sync(session_path, bin_exists=False):
     return sync, sync_chmap
 
 
-def get_protocol_period(session_path, protocol_number, bpod_sync):
+def get_protocol_period(session_path, protocol_number, bpod_sync, exclude_empty_periods=True):
     """
+    Return the start and end time of the protocol number.
+
+    Note that the start time is the start of the spacer pulses and the end time is either None
+    if the protocol is the final one, or the start of the next spacer.
 
     Parameters
     ----------
     session_path : str, pathlib.Path
         The absolute session path, i.e. '/path/to/subject/yyyy-mm-dd/nnn'.
     protocol_number : int
-        The order that the protocol was run in.
+        The order that the protocol was run in, counted from 0.
     bpod_sync : dict
         The sync times and polarities for Bpod BNC1.
+    exclude_empty_periods : bool
+        When true, spacers are ignored if no bpod pulses are detected between periods.
 
     Returns
     -------
@@ -565,7 +571,14 @@ def get_protocol_period(session_path, protocol_number, bpod_sync):
         The time of the next detected spacer or None if this is the last protocol run.
     """
     # The spacers are TTLs generated by Bpod at the start of each protocol
-    spacer_times = Spacer().find_spacers_from_fronts(bpod_sync)
+    sp = Spacer()
+    spacer_times = sp.find_spacers_from_fronts(bpod_sync)
+    if exclude_empty_periods:
+        # Drop dud protocol spacers (those without any bpod pulses after the spacer)
+        spacer_length = len(sp.generate_template(fs=1000)) / 1000
+        periods = np.c_[spacer_times + spacer_length, np.r_[spacer_times[1:], np.inf]]
+        valid = [np.any((bpod_sync['times'] > pp[0]) & (bpod_sync['times'] < pp[1])) for pp in periods]
+        spacer_times = spacer_times[valid]
     # Ensure that the number of detected spacers matched the number of expected tasks
     if acquisition_description := session_params.read_params(session_path):
         n_tasks = len(acquisition_description.get('tasks', []))
diff --git a/ibllib/pipes/behavior_tasks.py b/ibllib/pipes/behavior_tasks.py
index 3f519a10c..be75cf0d6 100644
--- a/ibllib/pipes/behavior_tasks.py
+++ b/ibllib/pipes/behavior_tasks.py
@@ -20,7 +20,7 @@
 from ibllib.pipes import training_status
 from ibllib.plots.figures import BehaviourPlots
 
-_logger = logging.getLogger('ibllib')
+_logger = logging.getLogger(__name__)
 
 
 class HabituationRegisterRaw(base_tasks.RegisterRawDataTask, base_tasks.BehaviourTask):