Bug/ieeg/coords

mne_bids/tests/data/ieeg_bids/README

@@ -0,0 +1,6 @@
+References
+----------
+Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
+
+Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S., David, O., … Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Scientific Data, 6, 102. https://doi.org/10.1038/s41597-019-0105-7
+

mne_bids/tests/data/ieeg_bids/dataset_description.json

@@ -0,0 +1,8 @@
+{
+    "Name": " ",
+    "BIDSVersion": "1.6.0",
+    "DatasetType": "raw",
+    "Authors": [
+        "[Unspecified]"
+    ]
+}

mne_bids/tests/data/ieeg_bids/participants.json

@@ -0,0 +1,24 @@
+{
+    "participant_id": {
+        "Description": "Unique participant identifier"
+    },
+    "age": {
+        "Description": "Age of the participant at time of testing",
+        "Units": "years"
+    },
+    "sex": {
+        "Description": "Biological sex of the participant",
+        "Levels": {
+            "F": "female",
+            "M": "male"
+        }
+    },
+    "hand": {
+        "Description": "Handedness of the participant",
+        "Levels": {
+            "R": "right",
+            "L": "left",
+            "A": "ambidextrous"
+        }
+    }
+}

mne_bids/tests/data/ieeg_bids/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	age	sex	hand
+sub-01	n/a	n/a	n/a

mne_bids/tests/data/ieeg_bids/sub-01/ses-01/ieeg/sub-01_ses-01_space-MNI152NLin2009bAsym_coordsystem.json

@@ -0,0 +1,5 @@
+{
+    "iEEGCoordinateSystem": "MNI152NLin2009bAsym",
+    "iEEGCoordinateSystemDescription": "mni",
+    "iEEGCoordinateUnits": "mm"
+}

mne_bids/tests/data/ieeg_bids/sub-01/ses-01/ieeg/sub-01_ses-01_space-MNI152NLin2009bAsym_electrodes.tsv

@@ -0,0 +1,11 @@
+name	x	y	z	type
+ECOG_0	22.5	-38.5	83.0	ECOG
+ECOG_1	28.0	-29.0	81.5	ECOG
+ECOG_2	32.0	-19.5	78.0	ECOG
+ECOG_3	37.0	-10.5	73.5	ECOG
+ECOG_4	40.5	-2.0	69.5	ECOG
+ECOG_5	42.5	6.5	63.0	ECOG
+ECOG_6	45.5	13.5	55.5	ECOG
+ECOG_7	48.0	22.5	48.5	ECOG
+ECOG_8	45.5	13.5	55.5	ECOG
+ECOG_9	48.0	22.5	48.5	ECOG

mne_bids/tests/data/ieeg_bids/sub-01/ses-01/ieeg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv

@@ -0,0 +1,11 @@
+name	type	units	low_cutoff	high_cutoff	description	sampling_frequency	status	status_description
+ECOG_0	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_1	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_2	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_3	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_4	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_5	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_6	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_7	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_8	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_9	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a

mne_bids/tests/data/ieeg_bids/sub-01/ses-01/ieeg/sub-01_ses-01_task-audiovisual_run-01_ieeg.json

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+{
+    "TaskName": "audiovisual",
+    "Manufacturer": "BrainProducts",
+    "PowerLineFrequency": "n/a",
+    "SamplingFrequency": 1000.0,
+    "SoftwareFilters": "n/a",
+    "RecordingDuration": 0.999,
+    "RecordingType": "continuous",
+    "iEEGReference": "n/a",
+    "ECOGChannelCount": 10,
+    "SEEGChannelCount": 0,
+    "EEGChannelCount": 0,
+    "EOGChannelCount": 0,
+    "ECGChannelCount": 0,
+    "EMGChannelCount": 0,
+    "MiscChannelCount": 0,
+    "TriggerChannelCount": 0
+}

mne_bids/tests/data/ieeg_bids/sub-01/ses-01/ieeg/sub-01_ses-01_task-audiovisual_run-01_ieeg.vhdr

@@ -0,0 +1,35 @@
+Brain Vision Data Exchange Header File Version 1.0
+; Written using pybv 0.6.0
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=sub-01_ses-01_task-audiovisual_run-01_ieeg.eeg
+MarkerFile=sub-01_ses-01_task-audiovisual_run-01_ieeg.vmrk
+DataFormat=BINARY
+; Data orientation: MULTIPLEXED=ch1,pt1, ch2,pt1 ...
+DataOrientation=MULTIPLEXED
+NumberOfChannels=10
+; Sampling interval in microseconds
+SamplingInterval=1000.0
+
+[Binary Infos]
+BinaryFormat=IEEE_FLOAT_32
+
+[Channel Infos]
+; Each entry: Ch<Channel number>=<Name>,<Reference channel name>,
+; <Resolution in "Unit">,<Unit>, Future extensions..
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in channel names are coded as "\1".
+Ch1=ECOG_0,,0.1,µV
+Ch2=ECOG_1,,0.1,µV
+Ch3=ECOG_2,,0.1,µV
+Ch4=ECOG_3,,0.1,µV
+Ch5=ECOG_4,,0.1,µV
+Ch6=ECOG_5,,0.1,µV
+Ch7=ECOG_6,,0.1,µV
+Ch8=ECOG_7,,0.1,µV
+Ch9=ECOG_8,,0.1,µV
+Ch10=ECOG_9,,0.1,µV
+
+[Comment]
+

mne_bids/tests/data/ieeg_bids/sub-01/ses-01/ieeg/sub-01_ses-01_task-audiovisual_run-01_ieeg.vmrk

@@ -0,0 +1,13 @@
+Brain Vision Data Exchange Marker File, Version 1.0
+;Exported using pybv 0.6.0
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=sub-01_ses-01_task-audiovisual_run-01_ieeg.eeg
+
+[Marker Infos]
+; Each entry: Mk<Marker number>=<Type>,<Description>,<Position in data points>,
+;             <Size in data points>, <Channel number (0 = marker is related to all channels)>
+;             <Date (YYYYMMDDhhmmssuuuuuu)>
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in type or description text are coded as "\1".

mne_bids/tests/data/ieeg_bids/sub-01/ses-01/sub-01_ses-01_scans.tsv

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+filename	acq_time
+ieeg/sub-01_ses-01_task-audiovisual_run-01_ieeg.vhdr	n/a

mne_bids/tests/test_read.py

@@ -1335,3 +1335,18 @@ def test_gsr_and_temp_reading():
     raw = read_raw_bids(bids_path)
     assert raw.get_channel_types(['GSR']) == ['gsr']
     assert raw.get_channel_types(['Temperature']) == ['temperature']
+
+
+def test_read_ieeg_coord_frame():
+    """Ensure that the iEEG coordinate frame is read correctly."""
+    bids_path = BIDSPath(
+        subject="01",
+        session="01",
+        task="audiovisual",
+        run="01",
+        root=Path(__file__).parent / "data" / "ieeg_bids",
+    )
+    raw_read = read_raw_bids(bids_path)
+
+    coord_frame = raw_read.get_montage().get_positions()["coord_frame"]
+    assert coord_frame == "MNI152NLin2009bAsym"