BUG: Fix bug with mf_reference_run

mne-tools · Jun 15, 2023 · 67bf6eb · 67bf6eb
1 parent b74f056
commit 67bf6eb
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Showing 6 changed files with 36 additions and 8 deletions.
diff --git a/docs/source/changes.md b/docs/source/changes.md
@@ -1,3 +1,5 @@
+{% include-markdown "./v1.4.md.inc" %}
+
 {% include-markdown "./v1.3.md.inc" %}
 
 {% include-markdown "./v1.2.md.inc" %}

diff --git a/docs/source/v1.3.md.inc b/docs/source/v1.3.md.inc
@@ -1,4 +1,4 @@
-## v1.3.0 (unreleased)
+## v1.3.0 (released 2023/06/01)
 
 ### :new: New features & enhancements
 
@@ -15,7 +15,7 @@
 
 - Avoid using deprecated `openpyxl` API when working with Excel spreadsheets (#735 by @larsoner)
 
-### :bug: Bug fixes)
+### :bug: Bug fixes
 
 - Fix pandas 2.0 compatibility (#732 by @larsoner)
 - Fix bug with `mne.sys_info` insertion in reports (#732 by @larsoner)

diff --git a/docs/source/v1.4.md.inc b/docs/source/v1.4.md.inc
@@ -0,0 +1,17 @@
+## v1.4.0 (unreleased)
+
+[//]: # (### :new: New features & enhancements)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+[//]: # (### :warning: Behavior changes)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+[//]: # (### :medical_symbol: Code health)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+### :bug: Bug fixes
+
+- Fix bug when `mf_reference_run != runs[0]` (#742 by @larsoner)
diff --git a/mne_bids_pipeline/_import_data.py b/mne_bids_pipeline/_import_data.py
@@ -561,9 +561,17 @@ def _get_raw_paths(
                 if task == "rest":
                     raw_fname = bids_path_in.copy().update(run=None, task=task)
                 else:
-                    raw_fname = _read_json(_empty_room_match_path(bids_path_in, cfg))[
-                        "fname"
-                    ]
+                    # This must match the logic of _02_find_empty_room.py
+                    update_kwargs = dict()
+                    if cfg.use_maxwell_filter:
+                        update_kwargs["run"] = cfg.mf_reference_run
+                    raw_fname = _read_json(
+                        _empty_room_match_path(
+                            bids_path_in.copy().update(**update_kwargs),
+                            cfg,
+                        )
+                    )
+                    raw_fname = raw_fname["fname"]
                     if raw_fname is not None:
                         raw_fname = get_bids_path_from_fname(raw_fname)
             if raw_fname is None:

diff --git a/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py b/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py
@@ -294,6 +294,7 @@ def get_config(
         )
         extra_kwargs["mf_reference_run"] = get_mf_reference_run(config=config)
         extra_kwargs["mf_head_origin"] = config.mf_head_origin
+        extra_kwargs["use_maxwell_filter"] = config.use_maxwell_filter
     cfg = SimpleNamespace(
         process_empty_room=config.process_empty_room,
         process_rest=config.process_rest,

diff --git a/mne_bids_pipeline/tests/configs/config_ds000117.py b/mne_bids_pipeline/tests/configs/config_ds000117.py
@@ -17,11 +17,11 @@
 raw_resample_sfreq = 125.0
 crop_runs = (0, 300)  # Reduce memory usage on CI system
 
-find_flat_channels_meg = False
-find_noisy_channels_meg = False
+find_flat_channels_meg = True
+find_noisy_channels_meg = True
 use_maxwell_filter = True
 
-mf_reference_run = "01"
+mf_reference_run = "02"
 mf_cal_fname = bids_root + "/derivatives/meg_derivatives/sss_cal.dat"
 mf_ctc_fname = bids_root + "/derivatives/meg_derivatives/ct_sparse.fif"