[MRG] Add motion to BIDSPath

README.md

@@ -58,3 +58,4 @@ Please also cite one of the following papers to credit BIDS, depending on which
 - [EEG-BIDS](https://doi.org/10.1038/s41597-019-0104-8)
 - [iEEG-BIDS](https://doi.org/10.1038/s41597-019-0105-7)
 - [NIRS-BIDS](https://doi.org/10.31219/osf.io/7nmcp)
+- [Motion-BIDS](https://doi.org/10.1038/s41597-024-03559-8)

doc/authors.rst

@@ -57,3 +57,4 @@
 .. _Tom Donoghue: https://github.com/TomDonoghue
 .. _William Turner: https://bootstrapbill.github.io/
 .. _Yorguin Mantilla: https://github.com/yjmantilla
+.. _Julius Welzel: https://github.com/JuliusWelzel

doc/whats_new.rst

@@ -22,8 +22,10 @@ The following authors contributed for the first time. Thank you so much! 🤩
 * `Arne Gottwald`_
 * `Matthias Dold`_
 * `Harrison Ritz`_
+* `Julius Welzel`_
 * `Nathan Azrak`_
 
+
 The following authors had contributed before. Thank you for sticking around! 🤘
 
 * `Stefan Appelhoff`_

mne_bids/config.py

@@ -6,7 +6,7 @@
 from mne import io
 from mne.io.constants import FIFF
 
-BIDS_VERSION = "1.7.0"
+BIDS_VERSION = "1.9.0"
 
 PYBV_VERSION = "0.7.3"
 EEGLABIO_VERSION = "0.0.2"
@@ -15,17 +15,19 @@
 
 EPHY_ALLOWED_DATATYPES = ["meg", "eeg", "ieeg", "nirs"]
 
-ALLOWED_DATATYPES = EPHY_ALLOWED_DATATYPES + ["anat", "beh"]
+ALLOWED_DATATYPES = EPHY_ALLOWED_DATATYPES + ["anat", "beh", "motion"]
 
 MEG_CONVERT_FORMATS = ["FIF", "auto"]
 EEG_CONVERT_FORMATS = ["BrainVision", "auto"]
 IEEG_CONVERT_FORMATS = ["BrainVision", "auto"]
 NIRS_CONVERT_FORMATS = ["auto"]
+MOTION_CONVERT_FORMATS = ["tsv", "auto"]
 CONVERT_FORMATS = {
     "meg": MEG_CONVERT_FORMATS,
     "eeg": EEG_CONVERT_FORMATS,
     "ieeg": IEEG_CONVERT_FORMATS,
     "nirs": NIRS_CONVERT_FORMATS,
+    "motion": MOTION_CONVERT_FORMATS,
 }
 
 # Orientation of the coordinate system dependent on manufacturer
@@ -147,12 +149,17 @@
     ".snirf",  # SNIRF
 ]
 
+allowed_extensions_motion = [
+    ".tsv",  # Tab-separated values
+]
+
 # allowed extensions (data formats) in BIDS spec
 ALLOWED_DATATYPE_EXTENSIONS = {
     "meg": allowed_extensions_meg,
     "eeg": allowed_extensions_eeg,
     "ieeg": allowed_extensions_ieeg,
     "nirs": allowed_extensions_nirs,
+    "motion": allowed_extensions_motion,
 }
 
 # allow additional extensions that are not BIDS
@@ -190,6 +197,7 @@
     "physio",
     "stim",  # behavioral
     "nirs",
+    "motion",  # motion
 ]
 
 # converts suffix to known path modalities
@@ -227,6 +235,7 @@
     "description",
     "suffix",
     "extension",
+    "tracking_system",
 )
 ALLOWED_PATH_ENTITIES_SHORT = {
     "sub": "subject",
@@ -239,6 +248,7 @@
     "recording": "recording",
     "split": "split",
     "desc": "description",
+    "tracksys": "tracking_system",
 }
 
 # Annotations to never remove during reading or writing
@@ -316,6 +326,7 @@
 ALLOWED_SPACES["ieeg"] = BIDS_SHARED_COORDINATE_FRAMES + BIDS_IEEG_COORDINATE_FRAMES
 ALLOWED_SPACES["anat"] = None
 ALLOWED_SPACES["beh"] = None
+ALLOWED_SPACES["motion"] = None
 
 # See: https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html#encephalography-eeg-ieeg-and-meg  # noqa: E501
 ENTITY_VALUE_TYPE = {
@@ -331,6 +342,7 @@
     "description": "label",
     "suffix": "label",
     "extension": "label",
+    "tracking_system": "label",
 }
 
 # mapping from supported BIDs coordinate frames -> MNE

mne_bids/path.py

@@ -385,6 +385,7 @@ def __init__(
         space=None,
         split=None,
         description=None,
+        tracking_system=None,
         root=None,
         suffix=None,
         extension=None,
@@ -881,7 +882,9 @@ def fpath(self):
                 if self.suffix is None or self.suffix in ALLOWED_DATATYPES:
                     # now only use valid datatype extension
                     if self.extension is None:
-                        valid_exts = sum(ALLOWED_DATATYPE_EXTENSIONS.values(), [])
+                        valid_exts = ALLOWED_DATATYPE_EXTENSIONS.get(
+                            self.datatype, sum(ALLOWED_DATATYPE_EXTENSIONS.values(), [])
+                        )
                     else:
                         valid_exts = [self.extension]
                     matching_paths = [

mne_bids/tests/test_path.py

@@ -500,6 +500,7 @@ def test_get_entities_from_fname(fname):
         "recording",
         "split",
         "description",
+        "tracking_system",
     ]
 
 
@@ -537,6 +538,7 @@ def test_get_entities_from_fname_errors(fname):
         "recording",
         "split",
         "description",
+        "tracking_system",
     ]
 
     assert params["subject"] == "01"