don't fail if emptyroom is missing cHPI channels (#977)

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

docs/source/v1.10.md.inc

@@ -12,9 +12,12 @@
 
 [//]: # (- Whatever (#000 by @whoever))
 
-[//]: # (### :bug: Bug fixes)
+### :bug: Bug fixes
 
-[//]: # (- Whatever (#000 by @whoever))
+- When running the pipeline with [`mf_filter_chpi`][mne_bids_pipeline._config.mf_filter_chpi] enabled (#977 by @drammock and @larsoner):
+
+    1. Emptyroom files that lack cHPI channels will now be processed (for line noise only) instead of raising an error.
+    2. cHPI filtering is now performed before movement compensation.
 
 ### :books: Documentation
 

docs/source/v1.9.md.inc

@@ -44,7 +44,7 @@
 
 ### :bug: Bug fixes
 
-- When running the pipeline with [`find_bad_channels_meg`][mne_bids_pipeline._config. find_bad_channels_meg] enabled,
+- When running the pipeline with [`find_noisy_channels_meg`][mne_bids_pipeline._config.find_noisy_channels_meg] enabled,
   then disabling it and running the pipeline again, the pipeline would incorrectly still use automatically detected
   bad channels from the first pipeline run. Now, we ensure that the original bad channels would be used and the
   related section is removed from the report in this case. (#902 by @larsoner)

mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py

@@ -417,6 +417,15 @@ def run_maxwell_filter(
         )
         logger.warning(**gen_log_kwargs(message=msg))
 
+    if filter_chpi:
+        logger.info(**gen_log_kwargs(message="Filtering cHPI"))
+        mne.chpi.filter_chpi(
+            raw,
+            t_window=cfg.mf_mc_t_window,
+            allow_line_only=(task == "noise"),
+        )
+
+    logger.info(**gen_log_kwargs(message="Maxwell filtering"))
     raw_sss = mne.preprocessing.maxwell_filter(raw, **mf_kws)
     del raw
     gc.collect()
@@ -456,13 +465,6 @@ def run_maxwell_filter(
             )
             raise RuntimeError(msg)
 
-    if filter_chpi:
-        logger.info(**gen_log_kwargs(message="Filtering cHPI"))
-        mne.chpi.filter_chpi(
-            raw_sss,
-            t_window=cfg.mf_mc_t_window,
-        )
-
     if cfg.mf_mc and (
         cfg.mf_mc_rotation_velocity_limit is not None
         or cfg.mf_mc_translation_velocity_limit is not None

mne_bids_pipeline/tests/configs/config_ds004229.py

@@ -23,7 +23,7 @@
 mf_int_order = 6  # lower for smaller heads
 mf_mc_t_step_min = 0.5  # just for speed!
 mf_mc_t_window = 0.2  # cleaner cHPI filtering on this dataset
-mf_filter_chpi = False  # for speed, not needed as we low-pass anyway
+mf_filter_chpi = True  # even though we lowpass, set to True for test coverage
 mf_mc_rotation_velocity_limit = 30.0  # deg/s for annotations
 mf_mc_translation_velocity_limit = 20e-3  # m/s
 mf_esss = 8