From 1566bed64b2a1ea548753c57f7362c875b82c6b4 Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Sun, 23 Feb 2025 13:36:36 -0500
Subject: [PATCH 01/14] Update _config_utils.py

allow for config and ctc to be set to None
---
 mne_bids_pipeline/_config_utils.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
index 39837d97a..4f46bf975 100644
--- a/mne_bids_pipeline/_config_utils.py
+++ b/mne_bids_pipeline/_config_utils.py
@@ -463,10 +463,8 @@ def get_mf_cal_fname(
         ).match()[0]
         mf_cal_fpath = bids_path.meg_calibration_fpath
         if mf_cal_fpath is None:
-            raise ValueError(
-                "Could not determine Maxwell Filter Calibration file from BIDS "
-                f"definition for file {bids_path}."
-            )
+            msg = "WARNING: Could not determine Maxwell Filter Calibration file from BIDS. Set to None."
+            logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_cal_fpath = pathlib.Path(config.mf_cal_fname).expanduser().absolute()
         if not mf_cal_fpath.exists():
@@ -491,7 +489,8 @@ def get_mf_ctc_fname(
             root=config.bids_root,
         ).meg_crosstalk_fpath
         if mf_ctc_fpath is None:
-            raise ValueError("Could not find Maxwell Filter cross-talk file.")
+            msg = "WARNING: Could not find Maxwell Filter cross-talk file. Set to None."
+            logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_ctc_fpath = pathlib.Path(config.mf_ctc_fname).expanduser().absolute()
         if not mf_ctc_fpath.exists():

From c6f65075ccae42bf3786227edb0b3b162ff0a1db Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Mon, 24 Feb 2025 12:18:42 -0500
Subject: [PATCH 02/14] include None types for bids paths

---
 mne_bids_pipeline/_config_utils.py | 29 +++++++++++++++++------------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
index 4f46bf975..07f242fe2 100644
--- a/mne_bids_pipeline/_config_utils.py
+++ b/mne_bids_pipeline/_config_utils.py
@@ -452,7 +452,7 @@ def sanitize_cond_name(cond: str) -> str:
 
 def get_mf_cal_fname(
     *, config: SimpleNamespace, subject: str, session: str | None
-) -> pathlib.Path:
+) -> pathlib.Path | None:
     if config.mf_cal_fname is None:
         bids_path = BIDSPath(
             subject=subject,
@@ -460,10 +460,12 @@ def get_mf_cal_fname(
             suffix="meg",
             datatype="meg",
             root=config.bids_root,
-        ).match()[0]
-        mf_cal_fpath = bids_path.meg_calibration_fpath
-        if mf_cal_fpath is None:
-            msg = "WARNING: Could not determine Maxwell Filter Calibration file from BIDS. Set to None."
+        ).match()
+        if len(bids_path) > 0:
+            mf_cal_fpath = bids_path[0].meg_calibration_fpath
+        else: 
+            mf_cal_fpath = None
+            msg = "warning: Could not determine Maxwell Filter Calibration file from BIDS. Set to None."
             logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_cal_fpath = pathlib.Path(config.mf_cal_fname).expanduser().absolute()
@@ -473,23 +475,26 @@ def get_mf_cal_fname(
                 f"file at {str(mf_cal_fpath)}."
             )
 
-    assert isinstance(mf_cal_fpath, pathlib.Path), type(mf_cal_fpath)
+    assert isinstance(mf_cal_fpath, pathlib.Path | None), type(mf_cal_fpath)
     return mf_cal_fpath
 
 
 def get_mf_ctc_fname(
     *, config: SimpleNamespace, subject: str, session: str | None
-) -> pathlib.Path:
+) -> pathlib.Path | None:
     if config.mf_ctc_fname is None:
-        mf_ctc_fpath = BIDSPath(
+        bids_path = BIDSPath(
             subject=subject,
             session=session,
             suffix="meg",
             datatype="meg",
             root=config.bids_root,
-        ).meg_crosstalk_fpath
-        if mf_ctc_fpath is None:
-            msg = "WARNING: Could not find Maxwell Filter cross-talk file. Set to None."
+        ).match()
+        if len(bids_path) > 0:
+            mf_ctc_fpath = bids_path[0].meg_crosstalk_fpath
+        else: 
+            mf_ctc_fpath = None
+            msg = "warning: Could not find Maxwell Filter cross-talk file. Set to None."
             logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_ctc_fpath = pathlib.Path(config.mf_ctc_fname).expanduser().absolute()
@@ -498,7 +503,7 @@ def get_mf_ctc_fname(
                 f"Could not find Maxwell Filter cross-talk file at {str(mf_ctc_fpath)}."
             )
 
-    assert isinstance(mf_ctc_fpath, pathlib.Path), type(mf_ctc_fpath)
+    assert isinstance(mf_ctc_fpath, pathlib.Path | None), type(mf_ctc_fpath)
     return mf_ctc_fpath
 
 

From 0337945703256dcea7e8a4ae77bf68f1322ffa09 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 24 Feb 2025 17:19:09 +0000
Subject: [PATCH 03/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mne_bids_pipeline/_config_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
index 07f242fe2..fe189a7f9 100644
--- a/mne_bids_pipeline/_config_utils.py
+++ b/mne_bids_pipeline/_config_utils.py
@@ -463,7 +463,7 @@ def get_mf_cal_fname(
         ).match()
         if len(bids_path) > 0:
             mf_cal_fpath = bids_path[0].meg_calibration_fpath
-        else: 
+        else:
             mf_cal_fpath = None
             msg = "warning: Could not determine Maxwell Filter Calibration file from BIDS. Set to None."
             logger.info(**gen_log_kwargs(message=msg))
@@ -492,7 +492,7 @@ def get_mf_ctc_fname(
         ).match()
         if len(bids_path) > 0:
             mf_ctc_fpath = bids_path[0].meg_crosstalk_fpath
-        else: 
+        else:
             mf_ctc_fpath = None
             msg = "warning: Could not find Maxwell Filter cross-talk file. Set to None."
             logger.info(**gen_log_kwargs(message=msg))

From fd97f2e09f87ef55ca03ea87b0e8e2d5cf958622 Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Mon, 24 Feb 2025 14:05:37 -0500
Subject: [PATCH 04/14] remove `mf_cal_fname` and `mf_ctc_fname` from
 `in_files`

---
 mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
index 14e255974..4e084521f 100644
--- a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
+++ b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
@@ -281,9 +281,6 @@ def get_input_fnames_maxwell_filter(
         )
         _update_for_splits(in_files, key, single=True)
 
-    # standard files
-    in_files["mf_cal_fname"] = cfg.mf_cal_fname
-    in_files["mf_ctc_fname"] = cfg.mf_ctc_fname
     return in_files
 
 
@@ -380,8 +377,8 @@ def run_maxwell_filter(
     apply_msg += " to"
 
     mf_kws = dict(
-        calibration=in_files.pop("mf_cal_fname"),
-        cross_talk=in_files.pop("mf_ctc_fname"),
+        calibration=cfg.mf_cal_fname,
+        cross_talk=cfg.mf_ctc_fname,
         st_duration=cfg.mf_st_duration,
         st_correlation=cfg.mf_st_correlation,
         origin=cfg.mf_head_origin,

From b39c19688c75e1be1f81e0043af027904a541c9d Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Mon, 24 Feb 2025 14:08:50 -0500
Subject: [PATCH 05/14] wrap text

---
 mne_bids_pipeline/_config_utils.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
index fe189a7f9..b3c523df1 100644
--- a/mne_bids_pipeline/_config_utils.py
+++ b/mne_bids_pipeline/_config_utils.py
@@ -465,7 +465,10 @@ def get_mf_cal_fname(
             mf_cal_fpath = bids_path[0].meg_calibration_fpath
         else:
             mf_cal_fpath = None
-            msg = "warning: Could not determine Maxwell Filter Calibration file from BIDS. Set to None."
+            msg = (
+                "warning: Could not determine Maxwell Filter Calibration file "
+                "from BIDS. Set to None."
+            )
             logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_cal_fpath = pathlib.Path(config.mf_cal_fname).expanduser().absolute()
@@ -494,7 +497,10 @@ def get_mf_ctc_fname(
             mf_ctc_fpath = bids_path[0].meg_crosstalk_fpath
         else:
             mf_ctc_fpath = None
-            msg = "warning: Could not find Maxwell Filter cross-talk file. Set to None."
+            msg = (
+                "warning: Could not find Maxwell Filter cross-talk file "
+                "from BIDS. Set to None."
+            )
             logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_ctc_fpath = pathlib.Path(config.mf_ctc_fname).expanduser().absolute()

From ff827dce7c4cd42c6b0e998456d9d9ff905fb5af Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Mon, 24 Feb 2025 14:20:36 -0500
Subject: [PATCH 06/14] update documentation

---
 docs/source/dev.md.inc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/dev.md.inc b/docs/source/dev.md.inc
index b682b779d..6a1779f0d 100644
--- a/docs/source/dev.md.inc
+++ b/docs/source/dev.md.inc
@@ -28,6 +28,7 @@
 
 - Fix bug where the ``config.proc`` parameter was not used properly during forward model creation (#1014 by @larsoner)
 - Fix bug where emptyroom recordings containing EEG channels would crash the pipeline during maxwell filtering (#1040 by @drammock)
+- `mf_ctc_fname` and `mf_cal_fname` can now be set to `None` (#1057 by @harrisonritz)
 
 ### :books: Documentation
 

From 6c247b3ac3e8f7fe30461cc5bcc3c0592ed3016c Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Mon, 24 Feb 2025 15:53:12 -0500
Subject: [PATCH 07/14] use in_files if paths are provided; update
 01_data_quality to match

---
 .../steps/preprocessing/_01_data_quality.py        | 14 ++++++++++++++
 .../steps/preprocessing/_03_maxfilter.py           | 11 +++++++++--
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py b/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py
index e3030e13c..c93fe1eaf 100644
--- a/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py
+++ b/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py
@@ -60,6 +60,14 @@ def get_input_fnames_data_quality(
                 add_bads=False,
             )
         )
+    
+    # set calibration and crosstalk files (if provided)
+    if _do_mf_autobad(cfg=cfg):
+        if cfg.mf_cal_fname is not None:  
+            in_files["mf_cal_fname"] = cfg.mf_cal_fname
+        if cfg.mf_ctc_fname is not None:
+            in_files["mf_ctc_fname"] = cfg.mf_ctc_fname
+        
     return in_files
 
 
@@ -88,6 +96,7 @@ def assess_data_quality(
         bids_path_ref_in = None
     msg, _ = _read_raw_msg(bids_path_in=bids_path_in, run=run, task=task)
     logger.info(**gen_log_kwargs(message=msg))
+
     if run is None and task == "noise":
         raw = import_er_data(
             cfg=cfg,
@@ -111,6 +120,11 @@ def assess_data_quality(
     auto_noisy_chs: list[str] | None = None
     auto_flat_chs: list[str] | None = None
     if _do_mf_autobad(cfg=cfg):
+
+        # use calibration and crosstalk files (if provided)
+        cfg.mf_cal_fname = in_files.pop("mf_cal_fname", None)
+        cfg.mf_ctc_fname = in_files.pop("mf_ctc_fname", None)
+
         (
             auto_noisy_chs,
             auto_flat_chs,
diff --git a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
index 4e084521f..86154a81e 100644
--- a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
+++ b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
@@ -281,6 +281,13 @@ def get_input_fnames_maxwell_filter(
         )
         _update_for_splits(in_files, key, single=True)
 
+        # set calibration and crosstalk files (if provided)
+        if cfg.mf_cal_fname is not None:  
+            in_files["mf_cal_fname"] = cfg.mf_cal_fname
+        if cfg.mf_ctc_fname is not None:
+            in_files["mf_ctc_fname"] = cfg.mf_ctc_fname
+
+
     return in_files
 
 
@@ -377,8 +384,8 @@ def run_maxwell_filter(
     apply_msg += " to"
 
     mf_kws = dict(
-        calibration=cfg.mf_cal_fname,
-        cross_talk=cfg.mf_ctc_fname,
+        calibration=in_files.pop("mf_cal_fname", None),
+        cross_talk=in_files.pop("mf_ctc_fname", None),
         st_duration=cfg.mf_st_duration,
         st_correlation=cfg.mf_st_correlation,
         origin=cfg.mf_head_origin,

From b54ad7d4552208bd2ec3ffc78d148567e7e481f5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 24 Feb 2025 20:53:35 +0000
Subject: [PATCH 08/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mne_bids_pipeline/steps/preprocessing/_01_data_quality.py | 7 +++----
 mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py    | 3 +--
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py b/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py
index c93fe1eaf..1385b3102 100644
--- a/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py
+++ b/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py
@@ -60,14 +60,14 @@ def get_input_fnames_data_quality(
                 add_bads=False,
             )
         )
-    
+
     # set calibration and crosstalk files (if provided)
     if _do_mf_autobad(cfg=cfg):
-        if cfg.mf_cal_fname is not None:  
+        if cfg.mf_cal_fname is not None:
             in_files["mf_cal_fname"] = cfg.mf_cal_fname
         if cfg.mf_ctc_fname is not None:
             in_files["mf_ctc_fname"] = cfg.mf_ctc_fname
-        
+
     return in_files
 
 
@@ -120,7 +120,6 @@ def assess_data_quality(
     auto_noisy_chs: list[str] | None = None
     auto_flat_chs: list[str] | None = None
     if _do_mf_autobad(cfg=cfg):
-
         # use calibration and crosstalk files (if provided)
         cfg.mf_cal_fname = in_files.pop("mf_cal_fname", None)
         cfg.mf_ctc_fname = in_files.pop("mf_ctc_fname", None)
diff --git a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
index 86154a81e..30fd0db4e 100644
--- a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
+++ b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
@@ -282,12 +282,11 @@ def get_input_fnames_maxwell_filter(
         _update_for_splits(in_files, key, single=True)
 
         # set calibration and crosstalk files (if provided)
-        if cfg.mf_cal_fname is not None:  
+        if cfg.mf_cal_fname is not None:
             in_files["mf_cal_fname"] = cfg.mf_cal_fname
         if cfg.mf_ctc_fname is not None:
             in_files["mf_ctc_fname"] = cfg.mf_ctc_fname
 
-
     return in_files
 
 

From b773e65465df77216598c385222ed9e70b7e9acb Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Mon, 24 Feb 2025 16:53:41 -0500
Subject: [PATCH 09/14] fix indenting

---
 mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
index 30fd0db4e..507ecf008 100644
--- a/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
+++ b/mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py
@@ -281,11 +281,11 @@ def get_input_fnames_maxwell_filter(
         )
         _update_for_splits(in_files, key, single=True)
 
-        # set calibration and crosstalk files (if provided)
-        if cfg.mf_cal_fname is not None:
-            in_files["mf_cal_fname"] = cfg.mf_cal_fname
-        if cfg.mf_ctc_fname is not None:
-            in_files["mf_ctc_fname"] = cfg.mf_ctc_fname
+    # set calibration and crosstalk files (if provided)
+    if cfg.mf_cal_fname is not None:
+        in_files["mf_cal_fname"] = cfg.mf_cal_fname
+    if cfg.mf_ctc_fname is not None:
+        in_files["mf_ctc_fname"] = cfg.mf_ctc_fname
 
     return in_files
 

From 12df21c0eaa183eae8feaa36ab095aca6af1b5cd Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Tue, 25 Feb 2025 16:52:58 -0500
Subject: [PATCH 10/14] added: `mf_cal_missing` and `mf_ctc_missing`; new test:
 `ds000248_mf`

---
 docs/source/dev.md.inc                        |  3 +-
 mne_bids_pipeline/_config.py                  | 14 ++++
 mne_bids_pipeline/_config_utils.py            | 72 ++++++++++++++-----
 .../tests/configs/config_ds000248_mf.py       | 60 ++++++++++++++++
 mne_bids_pipeline/tests/test_run.py           |  3 +
 5 files changed, 132 insertions(+), 20 deletions(-)
 create mode 100644 mne_bids_pipeline/tests/configs/config_ds000248_mf.py

diff --git a/docs/source/dev.md.inc b/docs/source/dev.md.inc
index 6a1779f0d..a3b7f6a6f 100644
--- a/docs/source/dev.md.inc
+++ b/docs/source/dev.md.inc
@@ -6,6 +6,7 @@
 - New config option [`allow_missing_sessions`][mne_bids_pipeline._config.allow_missing_sessions] allows to continue when not all sessions are present for all subjects. (#1000 by @drammock)
 - New config option [`mf_extra_kws`][mne_bids_pipeline._config.mf_extra_kws] passes additional keyword arguments to `mne.preprocessing.maxwell_filter`. (#1038 by @drammock)
 - New value `"twa"` for config option [`mf_destination`][mne_bids_pipeline._config.mf_destination], to use the time-weighted average head position across runs as the destination position. (#1043 and #1055 by @drammock)
+- New config option [`mf_cal_missing`][mne_bids_pipeline._config.mf_cal_missing] and [`mf_ctc_missing`][mne_bids_pipeline._config.mf_ctc_missing] for handling missing calibration and cross-talk files ['raise', 'warn', 'ignore'] (#1057 by @harrisonritz)
 
 ### :warning: Behavior changes
 
@@ -28,7 +29,7 @@
 
 - Fix bug where the ``config.proc`` parameter was not used properly during forward model creation (#1014 by @larsoner)
 - Fix bug where emptyroom recordings containing EEG channels would crash the pipeline during maxwell filtering (#1040 by @drammock)
-- `mf_ctc_fname` and `mf_cal_fname` can now be set to `None` (#1057 by @harrisonritz)
+
 
 ### :books: Documentation
 
diff --git a/mne_bids_pipeline/_config.py b/mne_bids_pipeline/_config.py
index 7cf4c3d55..b0b7ecee9 100644
--- a/mne_bids_pipeline/_config.py
+++ b/mne_bids_pipeline/_config.py
@@ -704,6 +704,13 @@
     ```
 """  # noqa : E501
 
+mf_cal_missing: Literal["ignore", "warn", "raise"] = "raise"
+"""
+How to handle the situation where the Maxwell Filter calibration file is
+missing. Possible options are to ignore the missing file, issue a warning,
+or raise an error.
+"""
+
 mf_ctc_fname: str | None = None
 """
 Path to the Maxwell Filter cross-talk file. If `None`, the recommended
@@ -719,6 +726,13 @@
     ```
 """  # noqa : E501
 
+mf_ctc_missing: Literal["ignore", "warn", "raise"] = "raise"
+"""
+How to handle the situation where the Maxwell Filter cross-talk file is
+missing. Possible options are to ignore the missing file, issue a warning,
+or raise an error.
+"""
+
 mf_esss: int = 0
 """
 Number of extended SSS (eSSS) basis projectors to use from empty-room data.
diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
index b3c523df1..66e2ef825 100644
--- a/mne_bids_pipeline/_config_utils.py
+++ b/mne_bids_pipeline/_config_utils.py
@@ -464,19 +464,35 @@ def get_mf_cal_fname(
         if len(bids_path) > 0:
             mf_cal_fpath = bids_path[0].meg_calibration_fpath
         else:
-            mf_cal_fpath = None
-            msg = (
-                "warning: Could not determine Maxwell Filter Calibration file "
-                "from BIDS. Set to None."
-            )
-            logger.info(**gen_log_kwargs(message=msg))
+            if config.mf_cal_missing == 'raise':
+                raise ValueError(
+                    "Could not determine Maxwell Filter cross-talk file from BIDS."
+                )
+            else:
+                mf_cal_fpath = None
+                if  config.mf_cal_missing == 'warn':
+                    msg = (
+                        "WARNING: Could not find Maxwell Filter cross-talk file "
+                        "from BIDS. Set to None."
+                    )
+                    logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_cal_fpath = pathlib.Path(config.mf_cal_fname).expanduser().absolute()
         if not mf_cal_fpath.exists():
-            raise ValueError(
-                f"Could not find Maxwell Filter Calibration "
-                f"file at {str(mf_cal_fpath)}."
-            )
+            if config.mf_cal_missing == 'raise':
+                raise ValueError(
+                    f"Could not find Maxwell Filter Calibration "
+                    f"file at {str(config.mf_cal_fname)}."
+                    )
+            else:
+                mf_cal_fpath = None
+                if config.mf_cal_missing == 'warn':
+                    msg = (
+                        "WARNING: Could not find Maxwell Filter calibration file "
+                        f"at {str(config.mf_cal_fname)}. Set to None."
+                    )
+                    logger.info(**gen_log_kwargs(message=msg))
+            
 
     assert isinstance(mf_cal_fpath, pathlib.Path | None), type(mf_cal_fpath)
     return mf_cal_fpath
@@ -496,18 +512,36 @@ def get_mf_ctc_fname(
         if len(bids_path) > 0:
             mf_ctc_fpath = bids_path[0].meg_crosstalk_fpath
         else:
-            mf_ctc_fpath = None
-            msg = (
-                "warning: Could not find Maxwell Filter cross-talk file "
-                "from BIDS. Set to None."
-            )
-            logger.info(**gen_log_kwargs(message=msg))
+            if config.mf_ctc_missing == 'raise':
+                raise ValueError(
+                    "Could not determine Maxwell Filter cross-talk file from BIDS."
+                )
+            else:
+                mf_ctc_fpath = None
+                if  config.mf_ctc_missing == 'warn':
+                    msg = (
+                        "WARNING: Could not find Maxwell Filter cross-talk file "
+                        "from BIDS. Set to None."
+                    )
+                    logger.info(**gen_log_kwargs(message=msg))
+
     else:
         mf_ctc_fpath = pathlib.Path(config.mf_ctc_fname).expanduser().absolute()
         if not mf_ctc_fpath.exists():
-            raise ValueError(
-                f"Could not find Maxwell Filter cross-talk file at {str(mf_ctc_fpath)}."
-            )
+            if config.mf_ctc_missing == 'raise':
+                raise ValueError(
+                    f"Could not find Maxwell Filter cross-talk file "
+                    f"at {str(config.mf_ctc_fname)}."
+                    )
+            else:
+                mf_ctc_fpath = None
+                if config.mf_ctc_missing == 'warn':
+                    msg = (
+                        "WARNING: Could not find Maxwell Filter cross-talk file "
+                        f"at {str(config.mf_ctc_fname)}. Set to None."
+                    )
+                    logger.info(**gen_log_kwargs(message=msg))
+            
 
     assert isinstance(mf_ctc_fpath, pathlib.Path | None), type(mf_ctc_fpath)
     return mf_ctc_fpath
diff --git a/mne_bids_pipeline/tests/configs/config_ds000248_mf.py b/mne_bids_pipeline/tests/configs/config_ds000248_mf.py
new file mode 100644
index 000000000..fc3cb214f
--- /dev/null
+++ b/mne_bids_pipeline/tests/configs/config_ds000248_mf.py
@@ -0,0 +1,60 @@
+"""MNE Sample Data: M/EEG combined processing."""
+
+import mne
+import mne_bids
+
+bids_root = "~/mne_data/ds000248"
+deriv_root = "~/mne_data/derivatives/mne-bids-pipeline/ds000248_mf"
+subjects_dir = f"{bids_root}/derivatives/freesurfer/subjects"
+
+subjects = ["01"]
+rename_events = {"Smiley": "Emoji", "Button": "Switch"}
+conditions = ["Auditory", "Visual", "Auditory/Left", "Auditory/Right"]
+epochs_metadata_query = "index > 0"  # Just for testing!
+contrasts = [("Visual", "Auditory"), ("Auditory/Right", "Auditory/Left")]
+
+time_frequency_conditions = ["Auditory", "Visual"]
+
+ch_types = ["meg", "eeg"]
+mf_reference_run = "01"
+find_flat_channels_meg = True
+find_noisy_channels_meg = True
+use_maxwell_filter = True
+
+# ADJUST THESE TO TEST ERROR HANDLING ------------------------------------------
+mf_cal_fname = None
+mf_cal_missing = "warn"
+
+mf_ctc_fname =  f"{bids_root}/wrong_ctc.fif"
+mf_ctc_missing = "warn"
+# -----------------------------------------------------------------------------
+
+def noise_cov(bp: mne_bids.BIDSPath) -> mne.Covariance:
+    """Estimate the noise covariance."""
+    # Use pre-stimulus period as noise source
+    bp = bp.copy().update(suffix="epo")
+    if not bp.fpath.exists():
+        bp.update(split="01")
+    epo = mne.read_epochs(bp)
+    cov = mne.compute_covariance(epo, rank="info", tmax=0)
+    return cov
+
+
+spatial_filter = "ssp"
+n_proj_eog = dict(n_mag=1, n_grad=1, n_eeg=1)
+n_proj_ecg = dict(n_mag=1, n_grad=1, n_eeg=0)
+ssp_meg = "combined"
+ecg_proj_from_average = True
+eog_proj_from_average = False
+epochs_decim = 4
+
+bem_mri_images = "FLASH"
+recreate_bem = True
+
+n_jobs = 2
+
+
+def mri_t1_path_generator(bids_path: mne_bids.BIDSPath) -> mne_bids.BIDSPath:
+    """Return the path to a T1 image."""
+    # don't really do any modifications – just for testing!
+    return bids_path
diff --git a/mne_bids_pipeline/tests/test_run.py b/mne_bids_pipeline/tests/test_run.py
index a0f65c2a4..2dcdcdf96 100644
--- a/mne_bids_pipeline/tests/test_run.py
+++ b/mne_bids_pipeline/tests/test_run.py
@@ -88,6 +88,9 @@ class _TestOptionsT(TypedDict, total=False):
     "ds000248_no_mri": {
         "steps": ("preprocessing", "sensor", "source"),
     },
+    "ds000248_mf": {
+        "stage": ("preprocessing"),
+        },
     "ds001810": {
         "steps": ("preprocessing", "preprocessing", "sensor"),
     },

From f59057b1b53a1c9d2d52496dbdd4d1a13603718e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 25 Feb 2025 21:53:21 +0000
Subject: [PATCH 11/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mne_bids_pipeline/_config_utils.py            | 22 +++++++++----------
 .../tests/configs/config_ds000248_mf.py       |  3 ++-
 mne_bids_pipeline/tests/test_run.py           |  2 +-
 3 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
index 66e2ef825..e702de534 100644
--- a/mne_bids_pipeline/_config_utils.py
+++ b/mne_bids_pipeline/_config_utils.py
@@ -464,13 +464,13 @@ def get_mf_cal_fname(
         if len(bids_path) > 0:
             mf_cal_fpath = bids_path[0].meg_calibration_fpath
         else:
-            if config.mf_cal_missing == 'raise':
+            if config.mf_cal_missing == "raise":
                 raise ValueError(
                     "Could not determine Maxwell Filter cross-talk file from BIDS."
                 )
             else:
                 mf_cal_fpath = None
-                if  config.mf_cal_missing == 'warn':
+                if config.mf_cal_missing == "warn":
                     msg = (
                         "WARNING: Could not find Maxwell Filter cross-talk file "
                         "from BIDS. Set to None."
@@ -479,20 +479,19 @@ def get_mf_cal_fname(
     else:
         mf_cal_fpath = pathlib.Path(config.mf_cal_fname).expanduser().absolute()
         if not mf_cal_fpath.exists():
-            if config.mf_cal_missing == 'raise':
+            if config.mf_cal_missing == "raise":
                 raise ValueError(
                     f"Could not find Maxwell Filter Calibration "
                     f"file at {str(config.mf_cal_fname)}."
-                    )
+                )
             else:
                 mf_cal_fpath = None
-                if config.mf_cal_missing == 'warn':
+                if config.mf_cal_missing == "warn":
                     msg = (
                         "WARNING: Could not find Maxwell Filter calibration file "
                         f"at {str(config.mf_cal_fname)}. Set to None."
                     )
                     logger.info(**gen_log_kwargs(message=msg))
-            
 
     assert isinstance(mf_cal_fpath, pathlib.Path | None), type(mf_cal_fpath)
     return mf_cal_fpath
@@ -512,13 +511,13 @@ def get_mf_ctc_fname(
         if len(bids_path) > 0:
             mf_ctc_fpath = bids_path[0].meg_crosstalk_fpath
         else:
-            if config.mf_ctc_missing == 'raise':
+            if config.mf_ctc_missing == "raise":
                 raise ValueError(
                     "Could not determine Maxwell Filter cross-talk file from BIDS."
                 )
             else:
                 mf_ctc_fpath = None
-                if  config.mf_ctc_missing == 'warn':
+                if config.mf_ctc_missing == "warn":
                     msg = (
                         "WARNING: Could not find Maxwell Filter cross-talk file "
                         "from BIDS. Set to None."
@@ -528,20 +527,19 @@ def get_mf_ctc_fname(
     else:
         mf_ctc_fpath = pathlib.Path(config.mf_ctc_fname).expanduser().absolute()
         if not mf_ctc_fpath.exists():
-            if config.mf_ctc_missing == 'raise':
+            if config.mf_ctc_missing == "raise":
                 raise ValueError(
                     f"Could not find Maxwell Filter cross-talk file "
                     f"at {str(config.mf_ctc_fname)}."
-                    )
+                )
             else:
                 mf_ctc_fpath = None
-                if config.mf_ctc_missing == 'warn':
+                if config.mf_ctc_missing == "warn":
                     msg = (
                         "WARNING: Could not find Maxwell Filter cross-talk file "
                         f"at {str(config.mf_ctc_fname)}. Set to None."
                     )
                     logger.info(**gen_log_kwargs(message=msg))
-            
 
     assert isinstance(mf_ctc_fpath, pathlib.Path | None), type(mf_ctc_fpath)
     return mf_ctc_fpath
diff --git a/mne_bids_pipeline/tests/configs/config_ds000248_mf.py b/mne_bids_pipeline/tests/configs/config_ds000248_mf.py
index fc3cb214f..1e12db34e 100644
--- a/mne_bids_pipeline/tests/configs/config_ds000248_mf.py
+++ b/mne_bids_pipeline/tests/configs/config_ds000248_mf.py
@@ -25,10 +25,11 @@
 mf_cal_fname = None
 mf_cal_missing = "warn"
 
-mf_ctc_fname =  f"{bids_root}/wrong_ctc.fif"
+mf_ctc_fname = f"{bids_root}/wrong_ctc.fif"
 mf_ctc_missing = "warn"
 # -----------------------------------------------------------------------------
 
+
 def noise_cov(bp: mne_bids.BIDSPath) -> mne.Covariance:
     """Estimate the noise covariance."""
     # Use pre-stimulus period as noise source
diff --git a/mne_bids_pipeline/tests/test_run.py b/mne_bids_pipeline/tests/test_run.py
index 2dcdcdf96..8354e8f1e 100644
--- a/mne_bids_pipeline/tests/test_run.py
+++ b/mne_bids_pipeline/tests/test_run.py
@@ -90,7 +90,7 @@ class _TestOptionsT(TypedDict, total=False):
     },
     "ds000248_mf": {
         "stage": ("preprocessing"),
-        },
+    },
     "ds001810": {
         "steps": ("preprocessing", "preprocessing", "sensor"),
     },

From 11f2b0ea0382905474f04c8f8f5be1c23eaa33b5 Mon Sep 17 00:00:00 2001
From: Harrison Ritz <harrison.ritz@gmail.com>
Date: Tue, 25 Feb 2025 18:43:34 -0500
Subject: [PATCH 12/14] stage --> steps?

---
 mne_bids_pipeline/tests/test_run.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mne_bids_pipeline/tests/test_run.py b/mne_bids_pipeline/tests/test_run.py
index 8354e8f1e..79a7f9011 100644
--- a/mne_bids_pipeline/tests/test_run.py
+++ b/mne_bids_pipeline/tests/test_run.py
@@ -89,7 +89,7 @@ class _TestOptionsT(TypedDict, total=False):
         "steps": ("preprocessing", "sensor", "source"),
     },
     "ds000248_mf": {
-        "stage": ("preprocessing"),
+        "steps": ("preprocessing"),
     },
     "ds001810": {
         "steps": ("preprocessing", "preprocessing", "sensor"),

From 60571f26b672312f9548f38296fb7ad001fea971 Mon Sep 17 00:00:00 2001
From: Daniel McCloy <dan@mccloy.info>
Date: Wed, 26 Feb 2025 09:51:37 -0600
Subject: [PATCH 13/14] refactor error/warning messages

---
 mne_bids_pipeline/_config_utils.py | 44 ++++++++++--------------------
 1 file changed, 14 insertions(+), 30 deletions(-)

diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
index e702de534..02021de4d 100644
--- a/mne_bids_pipeline/_config_utils.py
+++ b/mne_bids_pipeline/_config_utils.py
@@ -453,6 +453,7 @@ def sanitize_cond_name(cond: str) -> str:
 def get_mf_cal_fname(
     *, config: SimpleNamespace, subject: str, session: str | None
 ) -> pathlib.Path | None:
+    msg = "Could not find Maxwell Filter calibration file {where}."
     if config.mf_cal_fname is None:
         bids_path = BIDSPath(
             subject=subject,
@@ -464,33 +465,24 @@ def get_mf_cal_fname(
         if len(bids_path) > 0:
             mf_cal_fpath = bids_path[0].meg_calibration_fpath
         else:
+            msg = msg.format(where=f"from BIDSPath {bids_path}")
             if config.mf_cal_missing == "raise":
-                raise ValueError(
-                    "Could not determine Maxwell Filter cross-talk file from BIDS."
-                )
+                raise ValueError(msg)
             else:
                 mf_cal_fpath = None
                 if config.mf_cal_missing == "warn":
-                    msg = (
-                        "WARNING: Could not find Maxwell Filter cross-talk file "
-                        "from BIDS. Set to None."
-                    )
+                    msg = f"WARNING: {msg} Set to None."
                     logger.info(**gen_log_kwargs(message=msg))
     else:
         mf_cal_fpath = pathlib.Path(config.mf_cal_fname).expanduser().absolute()
         if not mf_cal_fpath.exists():
+            msg = msg.format(where=f"at {str(config.mf_cal_fname)}")
             if config.mf_cal_missing == "raise":
-                raise ValueError(
-                    f"Could not find Maxwell Filter Calibration "
-                    f"file at {str(config.mf_cal_fname)}."
-                )
+                raise ValueError(msg)
             else:
                 mf_cal_fpath = None
                 if config.mf_cal_missing == "warn":
-                    msg = (
-                        "WARNING: Could not find Maxwell Filter calibration file "
-                        f"at {str(config.mf_cal_fname)}. Set to None."
-                    )
+                    msg = f"WARNING: {msg} Set to None."
                     logger.info(**gen_log_kwargs(message=msg))
 
     assert isinstance(mf_cal_fpath, pathlib.Path | None), type(mf_cal_fpath)
@@ -500,6 +492,7 @@ def get_mf_cal_fname(
 def get_mf_ctc_fname(
     *, config: SimpleNamespace, subject: str, session: str | None
 ) -> pathlib.Path | None:
+    msg = "Could not find Maxwell Filter cross-talk file {where}."
     if config.mf_ctc_fname is None:
         bids_path = BIDSPath(
             subject=subject,
@@ -511,34 +504,25 @@ def get_mf_ctc_fname(
         if len(bids_path) > 0:
             mf_ctc_fpath = bids_path[0].meg_crosstalk_fpath
         else:
+            msg = msg.format(where=f"from BIDSPath {bids_path}")
             if config.mf_ctc_missing == "raise":
-                raise ValueError(
-                    "Could not determine Maxwell Filter cross-talk file from BIDS."
-                )
+                raise ValueError(msg)
             else:
                 mf_ctc_fpath = None
                 if config.mf_ctc_missing == "warn":
-                    msg = (
-                        "WARNING: Could not find Maxwell Filter cross-talk file "
-                        "from BIDS. Set to None."
-                    )
+                    msg = f"WARNING: {msg} Set to None."
                     logger.info(**gen_log_kwargs(message=msg))
 
     else:
         mf_ctc_fpath = pathlib.Path(config.mf_ctc_fname).expanduser().absolute()
         if not mf_ctc_fpath.exists():
+            msg = msg.format(where=f"at {str(config.mf_ctc_fname)}")
             if config.mf_ctc_missing == "raise":
-                raise ValueError(
-                    f"Could not find Maxwell Filter cross-talk file "
-                    f"at {str(config.mf_ctc_fname)}."
-                )
+                raise ValueError(msg)
             else:
                 mf_ctc_fpath = None
                 if config.mf_ctc_missing == "warn":
-                    msg = (
-                        "WARNING: Could not find Maxwell Filter cross-talk file "
-                        f"at {str(config.mf_ctc_fname)}. Set to None."
-                    )
+                    msg = f"WARNING: {msg} Set to None."
                     logger.info(**gen_log_kwargs(message=msg))
 
     assert isinstance(mf_ctc_fpath, pathlib.Path | None), type(mf_ctc_fpath)

From d2676527a0ec26d0d3ee24c1e0523f56f1bd2416 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2025 11:55:51 -0500
Subject: [PATCH 14/14] Apply suggestions from code review

Co-authored-by: Daniel McCloy <dan@mccloy.info>
---
 docs/source/dev.md.inc       |  2 +-
 mne_bids_pipeline/_config.py | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/docs/source/dev.md.inc b/docs/source/dev.md.inc
index a3b7f6a6f..b30400b0c 100644
--- a/docs/source/dev.md.inc
+++ b/docs/source/dev.md.inc
@@ -6,7 +6,7 @@
 - New config option [`allow_missing_sessions`][mne_bids_pipeline._config.allow_missing_sessions] allows to continue when not all sessions are present for all subjects. (#1000 by @drammock)
 - New config option [`mf_extra_kws`][mne_bids_pipeline._config.mf_extra_kws] passes additional keyword arguments to `mne.preprocessing.maxwell_filter`. (#1038 by @drammock)
 - New value `"twa"` for config option [`mf_destination`][mne_bids_pipeline._config.mf_destination], to use the time-weighted average head position across runs as the destination position. (#1043 and #1055 by @drammock)
-- New config option [`mf_cal_missing`][mne_bids_pipeline._config.mf_cal_missing] and [`mf_ctc_missing`][mne_bids_pipeline._config.mf_ctc_missing] for handling missing calibration and cross-talk files ['raise', 'warn', 'ignore'] (#1057 by @harrisonritz)
+- New config options [`mf_cal_missing`][mne_bids_pipeline._config.mf_cal_missing] and [`mf_ctc_missing`][mne_bids_pipeline._config.mf_ctc_missing] for handling missing calibration and cross-talk files (#1057 by @harrisonritz)
 
 ### :warning: Behavior changes
 
diff --git a/mne_bids_pipeline/_config.py b/mne_bids_pipeline/_config.py
index b0b7ecee9..ad7f7bc26 100644
--- a/mne_bids_pipeline/_config.py
+++ b/mne_bids_pipeline/_config.py
@@ -706,9 +706,9 @@
 
 mf_cal_missing: Literal["ignore", "warn", "raise"] = "raise"
 """
-How to handle the situation where the Maxwell Filter calibration file is
-missing. Possible options are to ignore the missing file, issue a warning,
-or raise an error.
+How to handle the situation where the MEG device's fine calibration file is missing.
+Possible options are to ignore the missing file (as may be appropriate for OPM data),
+issue a warning, or raise an error.
 """
 
 mf_ctc_fname: str | None = None
@@ -728,9 +728,9 @@
 
 mf_ctc_missing: Literal["ignore", "warn", "raise"] = "raise"
 """
-How to handle the situation where the Maxwell Filter cross-talk file is
-missing. Possible options are to ignore the missing file, issue a warning,
-or raise an error.
+How to handle the situation where the MEG device's cross-talk file is missing. Possible
+options are to ignore the missing file (as may be appropriate for OPM data), issue a
+warning, or raise an error (appropriate for data from Electa/Neuromag/MEGIN systems).
 """
 
 mf_esss: int = 0