Add KIT/Yokogawa/Ricoh marker coil extension: ".mrk" to allowed exten…

…sions (#842) * add mrk extension * Update mne_bids/config.py Co-authored-by: Stefan Appelhoff <[email protected]> * changlog * add Jean-Rémi to Authors.rst * fix head_to_mri upstream API change * add KIT test for MRK and CON * update whatsnew Co-authored-by: Stefan Appelhoff <[email protected]>
mne-tools · Jul 13, 2021 · 2d8a721 · 2d8a721
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diff --git a/doc/authors.rst b/doc/authors.rst
@@ -24,3 +24,4 @@
 .. _Tom Donoghue: https://github.com/TomDonoghue
 .. _Richard Köhler: https://github.com/richardkoehler
 .. _Sin Kim: https://github.com/AKSoo
+.. _Jean-Rémi King: https://kingjr.github.io/
diff --git a/doc/whats_new.rst b/doc/whats_new.rst
@@ -27,6 +27,7 @@ Authors
 * `Richard Höchenberger`_
 * `Adam Li`_
 * `Richard Köhler`_ (new contributor)
+* `Jean-Rémi King`_ (new contributor)
 
 Detailed list of changes
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -44,6 +45,7 @@ Enhancements
 - :func:`mne_bids.write_raw_bids` gained a new parameter ``empty_room`` that allows to specify an associated empty-room recording when writing an MEG data file. This information will be stored in the ``AssociatedEmptyRoom`` field of the MEG JSON sidecar file, by `Richard Höchenberger`_ (:gh:`795`)
 - Added support for the new channel type ``'dbs'`` (Deep Brain Stimulation), which was introduced in MNE-Python 0.23, by `Richard Köhler`_ (:gh:`800`)
 - :func:`mne_bids.read_raw_bids` now warns in many situations when it encounters a mismatch between the channels in ``*_channels.tsv`` and the raw data, by `Richard Höchenberger`_ (:gh:`823`)
+- MNE BIDS now accepts ".mrk" head digitization files used in the KIT/Yokogawa/Ricoh MEG system, by `Jean-Rémi King`_ and `Stefan Appelhoff`_ (:gh:`842`)
 
 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/examples/convert_mri_and_trans.py b/examples/convert_mri_and_trans.py
@@ -46,7 +46,7 @@
 
 import mne
 from mne.datasets import sample
-from mne.source_space import head_to_mri
+from mne import head_to_mri
 
 from mne_bids import (write_raw_bids, BIDSPath, write_anat, get_anat_landmarks,
                       get_head_mri_trans, print_dir_tree)

diff --git a/mne_bids/config.py b/mne_bids/config.py
@@ -131,7 +131,8 @@
     ALLOWED_INPUT_EXTENSIONS +
     ['.json', '.tsv', '.tsv.gz', '.nii', '.nii.gz'] +
     ['.pos', '.eeg', '.vmrk'] +  # extra datatype-specific metadata files.
-    ['.dat', '.EEG']  # extra eeg extensions
+    ['.dat', '.EEG'] +  # extra eeg extensions
+    ['.mrk']  # KIT/Yokogawa/Ricoh marker coil
 )
 
 # allowed BIDS path entities

diff --git a/mne_bids/tests/test_write.py b/mne_bids/tests/test_write.py
@@ -886,6 +886,25 @@ def test_kit(_bids_validate, tmpdir):
                        events_data=events_fname, event_id=event_id,
                        overwrite=True)
 
+    # check that everything works with MRK markers, and CON files
+    data_path = op.join(testing.data_path(download=False), 'KIT')
+    raw_fname = op.join(data_path, 'data_berlin.con')
+    hpi_fname = op.join(data_path, 'MQKIT_125.mrk')
+    electrode_fname = op.join(data_path, 'MQKIT_125.elp')
+    headshape_fname = op.join(data_path, 'MQKIT_125.hsp')
+    bids_root = tmpdir.mkdir("bids_kit_mrk")
+    kit_bids_path = _bids_path.copy().update(acquisition=None,
+                                             root=bids_root,
+                                             suffix='meg')
+    raw = _read_raw_kit(
+        raw_fname, mrk=hpi_fname, elp=electrode_fname,
+        hsp=headshape_fname)
+    write_raw_bids(raw, kit_bids_path)
+
+    _bids_validate(bids_root)
+    assert op.exists(bids_root / 'participants.tsv')
+    read_raw_bids(bids_path=kit_bids_path)
+
 
 @pytest.mark.filterwarnings(warning_str['meas_date_set_to_none'])
 def test_ctf(_bids_validate, tmpdir):