Added feature to highlight corresponding ICA trace from topo maps

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "packages/pylossless"]
+	path = packages/pylossless
+	url = https://github.com/lina-usc/pylossless.git

ds002778/CHANGES

@@ -0,0 +1,15 @@
+1.0.5 2022-01-05
+  - Fix missing Beck scores
+  - Update README to be more specific about problematic analyses
+1.0.4 2021-01-17
+  - Update README with example
+1.0.3 2020-07-27
+  - Updated README
+1.0.2 2020-06-26
+  - Updated citations
+1.0.1 2020-05-08
+  - Data entry typo for sub-pd22, the medication was entered incorrectly but is now fixed
+
+1.0.0	2020-05-05
+
+	- Initial snapshot

ds002778/README

@@ -0,0 +1,22 @@
+Welcome to the resting state EEG dataset collected at the University of San Diego and curated by Alex Rockhill at the University of Oregon.
+
+Please email [email protected] before submitting a manuscript to be published in a peer-reviewed journal using this data, we wish to ensure that the data to be analyzed and interpreted with scientific integrity so as not to mislead the public about findings that may have clinical relevance. The purpose of this is to be responsible stewards of the data without an "available upon reasonable request" clause that we feel doesn't fully represent the open-source, reproducible ethos. The data is freely available to download so we cannot stop your publication if we don't support your methods and interpretation of findings, however, in being good data stewards, we would like to offer suggestions in the pre-publication stage so as to reduce conflict in published scientific literature. As far as credit, there is precedent for receiving a mention in the acknowledgements section for reading and providing feedback on the paper or, for more involved consulting, being included as an author may be warranted. The purpose of asking for this is not to inflate our number of authorships; we take ethical considerations of the best way to handle intellectual property in the form of manuscripts very seriously, and, again, sharing is at the discretion of the author although we strongly recommend it. Please be ethical and considerate in your use of this data and all open-source data and be sure to credit authors by citing them.
+
+An example of an analysis that we could consider problematic and would strongly advice to be corrected before submission to a publication would be using machine learning to classify Parkinson's patients from healthy controls using this dataset. This is because there are far too few patients for proper statistics. Parkinson's disease presents heterogeneously across patients, and, with a proper test-training split, there would be fewer than 8 patients in the testing set. Statistics on 8 or fewer patients for such a complicated diease would be inaccurate due to having too small of a sample size. Furthermore, if multiple machine learning algorithms were desired to be tested, a third split would be required to choose the best method, further lowering the number of patients in the testing set. We strongly advise against using any such approach because it would mislead patients and people who are interested in knowing if they have Parkinson's disease.
+
+Note that UPDRS rating scales were collected by laboratory personnel who had completed online training and not a board-certified neurologist. Results should be interpreted accordingly, especially that analyses based largely on these ratings should be taken with the appropriate amount of uncertainty.
+
+In addition to contacting the aforementioned email, please cite the following papers:
+
+Nicko Jackson, Scott R. Cole, Bradley Voytek, Nicole C. Swann. Characteristics of Waveform Shape in Parkinson's Disease Detected with Scalp Electroencephalography. eNeuro 20 May 2019, 6 (3) ENEURO.0151-19.2019; DOI: 10.1523/ENEURO.0151-19.2019.
+
+Swann NC, de Hemptinne C, Aron AR, Ostrem JL, Knight RT, Starr PA. Elevated synchrony in Parkinson disease detected with electroencephalography. Ann Neurol. 2015 Nov;78(5):742-50. doi: 10.1002/ana.24507. Epub 2015 Sep 2. PMID: 26290353; PMCID: PMC4623949.
+
+George JS, Strunk J, Mak-McCully R, Houser M, Poizner H, Aron AR. Dopaminergic therapy in Parkinson's disease decreases cortical beta band coherence in the resting state and increases cortical beta band power during executive control. Neuroimage Clin. 2013 Aug 8;3:261-70. doi: 10.1016/j.nicl.2013.07.013. PMID: 24273711; PMCID: PMC3814961.
+
+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).
+
+Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G.,
+Phillips, C., Delorme, A., Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Scientific Data, 6, 103. https://doi.org/10.1038/s41597-019-0104-8.
+
+Note: see this discussion on the structure of the json files that is sufficient but not optimal and will hopefully be changed in future versions of BIDS: https://neurostars.org/t/behavior-metadata-without-tsv-event-data-related-to-a-neuroimaging-data/6768/25.

ds002778/dataset_description.json

@@ -0,0 +1,13 @@
+{
+    "Name": "UC San Diego Resting State EEG Data from Patients with Parkinson's Disease",
+    "BIDSVersion": "1.2.2",
+    "Authors": [
+        "Alexander P. Rockhill",
+        "Nicko Jackson",
+        "Jobi George",
+        "Adam Aron",
+        "Nicole C. Swann"
+    ],
+    "DatasetDOI": "doi:10.18112/openneuro.ds002778.v1.0.5",
+    "License": "CC0"
+}

ds002778/derivatives/pylossless/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
+
+Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G., Phillips, C., Delorme, A., Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Scientific Data, 6, 103.https://doi.org/10.1038/s41597-019-0104-8
+

ds002778/derivatives/pylossless/dataset_description.json

@@ -0,0 +1,9 @@
+{
+    "Name": "[Unspecified]",
+    "BIDSVersion": "1.7.0",
+    "DatasetType": "raw",
+    "Authors": [
+        "[Unspecified1]",
+        "[Unspecified2]"
+    ]
+}

ds002778/derivatives/pylossless/participants.json

@@ -0,0 +1,32 @@
+{
+    "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"
+        }
+    },
+    "weight": {
+        "Description": "Body weight of the participant",
+        "Units": "kg"
+    },
+    "height": {
+        "Description": "Body height of the participant",
+        "Units": "m"
+    }
+}

ds002778/derivatives/pylossless/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	age	sex	hand	weight	height
+sub-pd6	62	n/a	R	n/a	n/a

ds002778/derivatives/pylossless/sub-pd6/ses-off/eeg/sub-pd6_ses-off_space-CapTrak_coordsystem.json

@@ -0,0 +1,24 @@
+{
+    "EEGCoordinateSystem": "CapTrak",
+    "EEGCoordinateUnits": "m",
+    "EEGCoordinateSystemDescription": "The X-axis goes from the left preauricular point (LPA) through the right preauricular point (RPA). The Y-axis goes orthogonally to the X-axis through the nasion (NAS). The Z-axis goes orthogonally to the XY-plane through the vertex of the head. This corresponds to a \"RAS\" orientation with the origin of the coordinate system approximately between the ears. See Appendix VIII in the BIDS specification.",
+    "AnatomicalLandmarkCoordinates": {
+        "NAS": [
+            0.0,
+            0.11807366483227957,
+            0.0
+        ],
+        "LPA": [
+            -0.11807366483227957,
+            0.0,
+            0.0
+        ],
+        "RPA": [
+            0.11807366483227957,
+            0.0,
+            0.0
+        ]
+    },
+    "AnatomicalLandmarkCoordinateSystem": "CapTrak",
+    "AnatomicalLandmarkCoordinateUnits": "m"
+}

ds002778/derivatives/pylossless/sub-pd6/ses-off/eeg/sub-pd6_ses-off_space-CapTrak_electrodes.tsv

@@ -0,0 +1,41 @@
+name	x	y	z
+Fp1	-0.03090258833242555	0.114585178792428	0.02786657432908913
+AF3	-0.035186007467538326	0.10912956509481905	0.05643921471178484
+F7	-0.07187662505917264	0.07310352742670875	0.025790455878913307
+F3	-0.05180903841183724	0.08668789888287941	0.07871409302883386
+FC1	-0.03571586037883836	0.06171405984105545	0.11798301537735344
+FC5	-0.07890597635539306	0.05136738419239063	0.062962347939219
+T7	-0.08598207795805729	0.014871638175652204	0.031173373739044698
+C3	-0.0671487229331174	0.023358230537446293	0.10451068106024831
+CP1	-0.03742512541749303	-0.0108242377168398	0.13344371157184132
+CP5	-0.08151351110863697	-0.013345693814222136	0.07313262712367305
+P7	-0.07445796452347851	-0.042123164958505765	0.04127363138738122
+P3	-0.0550382318026169	-0.04421030466234088	0.09990897692200874
+Pz	-0.001709445046746896	-0.045212993324122014	0.12667292418209622
+PO3	-0.03862460152585547	-0.0673615830694722	0.08241555265208235
+O1	-0.03157355787465608	-0.08056835212663661	0.05478964562404762
+Oz	-0.0020602461029908406	-0.0827829905012281	0.06073663060773575
+O2	0.027683100559624117	-0.08048883980936473	0.0547340814777941
+PO4	0.034667793322282536	-0.06766213598039732	0.08164652939132529
+P4	0.05363601546337514	-0.04433452185507687	0.100516027732151
+P8	0.07103247088902218	-0.04225997601209522	0.0411988627819509
+CP6	0.08140110772413488	-0.013462042634867975	0.07336367003861291
+CP2	0.036471959575241124	-0.010903791502932459	0.1328122726312171
+C4	0.06532888071838541	0.0235731049615695	0.10369243420047652
+T8	0.08326136985759491	0.015258189278681372	0.030972968524059938
+FC6	0.0778466192866476	0.052098811200362666	0.06286710628925257
+FC2	0.033130982370817734	0.06182848606183057	0.1167816981344542
+F4	0.050274277731628736	0.08743838910239796	0.07727065434234194
+F8	0.07143526925150917	0.07450512647808137	0.025101027393177114
+AF4	0.0342298581732583	0.10981127208682755	0.05711667432352483
+Fp2	0.028409495337624727	0.11534630990164213	0.027721257722525875
+Fz	-0.001229271161566281	0.09327445200029715	0.1026392934768164
+Cz	-0.0013741334028190722	0.027617093595102737	0.14019949417439556
+EXG1	n/a	n/a	n/a
+EXG2	n/a	n/a	n/a
+EXG3	n/a	n/a	n/a
+EXG4	n/a	n/a	n/a
+EXG5	n/a	n/a	n/a
+EXG6	n/a	n/a	n/a
+EXG7	n/a	n/a	n/a
+EXG8	n/a	n/a	n/a

ds002778/derivatives/pylossless/sub-pd6/ses-off/eeg/sub-pd6_ses-off_task-rest_channels.tsv

@@ -0,0 +1,42 @@
+name	type	units	low_cutoff	high_cutoff	description	sampling_frequency	status	status_description
+Fp1	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+AF3	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+F7	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+F3	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+FC1	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+FC5	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+T7	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+C3	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+CP1	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+CP5	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+P7	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+P3	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+Pz	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+PO3	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+O1	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+Oz	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+O2	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+PO4	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+P4	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+P8	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+CP6	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+CP2	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+C4	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+T8	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+FC6	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+FC2	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+F4	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+F8	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+AF4	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+Fp2	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+Fz	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+Cz	EEG	µV	1.0	100.0	ElectroEncephaloGram	512.0	good	n/a
+EXG1	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+EXG2	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+EXG3	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+EXG4	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+EXG5	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+EXG6	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+EXG7	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+EXG8	EOG	µV	1.0	100.0	ElectroOculoGram	512.0	good	n/a
+Status	TRIG	n/a	1.0	100.0	Trigger	512.0	good	n/a