Add XDF to "Reading EEG data" tutorial (#9289)

* Add XDF to "Reading EEG data" tutorial

* Fix flake8 warning

* [circle full] add comment

* Use examples of formats, not exhaustive list

Co-authored-by: Stefan Appelhoff <[email protected]>

* Better motivation for not having an XDF loader

Co-authored-by: Stefan Appelhoff <[email protected]>

* Include .fdt in EEGLAB section

* Provide EDF links earlier

* Forgot > in hyperlink

* Rewording

Co-authored-by: Daniel McCloy <[email protected]>

* ENH: Add separate example

* FIX: Double link

* Apply suggestions from code review

Co-authored-by: Daniel McCloy <[email protected]>

Co-authored-by: Stefan Appelhoff <[email protected]>
Co-authored-by: Daniel McCloy <[email protected]>
Co-authored-by: Eric Larson <[email protected]>

doc/references.bib

@@ -1,4 +1,7 @@
 % Encoding: UTF-8
+%
+% If available, include a DOI (preferred) *or* a URL for a given reference, but
+# not both, as the DOI turns into a link which is redundant with the URL.
 
 % MNE-C reference
 @article{GramfortEtAl2014,
@@ -518,7 +521,6 @@ @article{GramfortEtAl2010
   title = {Graph-Based Variability Estimation in Single-Trial Event-Related Neural Responses},
   journal = {{IEEE} Transactions on Biomedical Engineering},
   doi = {10.1109/tbme.2009.2037139},
-  url = {https://doi.org/10.1109%2Ftbme.2009.2037139},
   year = {2010},
   publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
   volume = {57},
@@ -1306,7 +1308,6 @@ @article{Pascual-Marqui2002
 @article{Pascual-Marqui2011,
   title = {Assessing interactions in the brain with exact low-resolution electromagnetic tomography},
   volume = {369},
-  url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2011.0081},
   doi = {10.1098/rsta.2011.0081},
   number = {1952},
   journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
@@ -1980,7 +1981,6 @@ @article{OReillyEtAl2021
   title = {Structural templates for imaging {EEG} cortical sources in infants},
   volume = {227},
   issn = {1053-8119},
-  url = {http://www.sciencedirect.com/science/article/pii/S1053811920311678},
   doi = {10.1016/j.neuroimage.2020.117682},
   urldate = {2021-01-12},
   journal = {NeuroImage},
@@ -1994,7 +1994,6 @@ @article{RichardsEtAl2016
   title = {A database of age-appropriate average {MRI} templates},
   volume = {124},
   issn = {1053-8119},
-  url = {http://www.sciencedirect.com/science/article/pii/S1053811915003559},
   doi = {10.1016/j.neuroimage.2015.04.055},
   journal = {NeuroImage},
   author = {Richards, John E. and Sanchez, Carmen and Phillips-Meek, Michelle and Xie, Wanze},
@@ -2054,16 +2053,15 @@ @Article{Kappenman2021
 }
 
 @article{GenoveseEtAl2002,
-title = {Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate},
-journal = {NeuroImage},
-volume = {15},
-number = {4},
-pages = {870-878},
-year = {2002},
-issn = {1053-8119},
-doi = {https://doi.org/10.1006/nimg.2001.1037},
-url = {https://www.sciencedirect.com/science/article/pii/S1053811901910377},
-author = {Christopher R. Genovese and Nicole A. Lazar and Thomas Nichols},
+  title = {Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate},
+  journal = {NeuroImage},
+  volume = {15},
+  number = {4},
+  pages = {870-878},
+  year = {2002},
+  issn = {1053-8119},
+  doi = {https://doi.org/10.1006/nimg.2001.1037},
+  author = {Christopher R. Genovese and Nicole A. Lazar and Thomas Nichols},
 }
 
 @article{YaoEtAl2019,
@@ -2077,3 +2075,15 @@ @article{YaoEtAl2019
   doi = {10.1007/s10548-019-00707-x},
   publisher={Springer}
 }
+
+@article{PolonenkoMaddox2019,
+  title = {The {Parallel} {Auditory} {Brainstem} {Response}},
+  volume = {23},
+  issn = {2331-2165},
+  doi = {10.1177/2331216519871395},
+  language = {en},
+  journal = {Trends in Hearing},
+  author = {Polonenko, Melissa J. and Maddox, Ross K.},
+  year = {2019},
+  pages = {2331216519871395}
+}

examples/io/plot_read_xdf.py

@@ -0,0 +1,42 @@
+"""
+.. _ex-read-xdf:
+
+====================
+Reading XDF EEG data
+====================
+
+Here we read some sample XDF data. Although we do not analyze it here, this
+recording is of a short parallel auditory response (pABR) experiment
+:footcite:`PolonenkoMaddox2019` and was provided by the `Maddox Lab
+<https://www.urmc.rochester.edu/labs/maddox.aspx>`__.
+"""
+# Authors: Clemens Brunner <[email protected]>
+#          Eric Larson <[email protected]>
+#
+# License: BSD (3-clause)
+
+import os.path as op
+
+import pyxdf
+
+import mne
+from mne.datasets import misc
+
+fname = op.join(
+    misc.data_path(), 'xdf',
+    'sub-P001_ses-S004_task-Default_run-001_eeg_a2.xdf')
+streams, header = pyxdf.load_xdf(fname)
+data = streams[0]["time_series"].T
+assert data.shape[0] == 5  # four raw EEG plus one stim channel
+data[:4:2] -= data[1:4:2]  # subtract (rereference) to get two bipolar EEG
+data = data[::2]  # subselect
+data[:2] *= (1e-6 / 50 / 2)  # uV -> V and preamp gain
+sfreq = float(streams[0]["info"]["nominal_srate"][0])
+info = mne.create_info(3, sfreq, ["eeg", "eeg", "stim"])
+raw = mne.io.RawArray(data, info)
+raw.plot(scalings=dict(eeg=100e-6), duration=1, start=12)
+
+###############################################################################
+# References
+# ----------
+# .. footbibliography::

mne/datasets/utils.py

@@ -254,7 +254,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
     path = _get_path(path, key, name)
     # To update the testing or misc dataset, push commits, then make a new
     # release on GitHub. Then update the "releases" variable:
-    releases = dict(testing='0.117', misc='0.8')
+    releases = dict(testing='0.117', misc='0.9')
     # And also update the "md5_hashes['testing']" variable below.
     # To update any other dataset, update the data archive itself (upload
     # an updated version) and update the md5 hash.
@@ -345,7 +345,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
             bst_raw='fa2efaaec3f3d462b319bc24898f440c',
             bst_resting='70fc7bf9c3b97c4f2eab6260ee4a0430'),
         fake='3194e9f7b46039bb050a74f3e1ae9908',
-        misc='0f88194266121dd9409be94184231f25',
+        misc='f832ce9c4c27e83396cc977b293b0aa9',
         sample='12b75d1cb7df9dfb4ad73ed82f61094f',
         somato='32fd2f6c8c7eb0784a1de6435273c48b',
         spm='9f43f67150e3b694b523a21eb929ea75',

requirements_doc.txt

@@ -8,3 +8,4 @@ neo
 seaborn
 sphinx_copybutton
 https://github.com/mne-tools/mne-bids/archive/main.zip
+pyxdf