BEP030: Add fNIRS examples to master branch

README.md

@@ -118,6 +118,7 @@ bids-examples (in alphabetical order).
 - [qMRI datasets](#qmri-datasets)
 - [PET datasets](#PET-datasets)
 - [Microscopy datasets](#microscopy-datasets)
+- [fNIRS datasets](#fnirs-datasets)
 - [Multimodal datasets](#multimodal-datasets)
 
 ### EEG datasets
@@ -215,6 +216,15 @@ bids-examples (in alphabetical order).
 | micr_SEMzarr  | @TheChymera   | Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions             |
 | micr_SPIM     | @jcohenadad   | Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each |
 
+
+### fNIRS datasets
+
+| name              | maintained by     | description                                                             | link to full data                       |
+| ----------------- | ----------------- | ----------------------------------------------------------------------- | --------------------------------------- |
+| fnirs_tapping     | @rob_luke         | Example fNIRS measurement with three conditions from five subjects      | https://doi.org/10.5281/zenodo.5529797  |
+| fnirs_automaticiy | @robertoostenveld | 24 subjects performing (non-)automatic finger tapping and foot stepping | https://doi.org/10.34973/vesb-mh30      |
+
+
 ### Multimodal datasets
 
 | name                   | maintained by     | description                                                                                                                          | mri                   | meg | eeg | ieeg | genetics | link to full data                                              |

fnirs_automaticity/.bidsignore

@@ -0,0 +1,2 @@
+optode_layout.pdf
+phenotype/practicelogbook.tsv

fnirs_automaticity/CHANGES

@@ -0,0 +1,27 @@
+v1.1.1 2022-02-14
+ - initial release
+
+v1.1.2 2022-02-18
+ - implemented suggestions by R. Oostenveld
+ - fixed task instructions (was the same for each task)
+
+v1.1.2-emptyfiles 2022-06-20
+ - took the original data from the Donders Repository and nulled all snirf files
+ - updated this CHANGES.txt file
+ - updated the README.txt file to reflect that this is only a test version
+ - removed the LICENSE.txt and MANIFEST.txt file
+
+v1.1.3-emptyfiles 2022-06-20
+ - fixed AnatomicalLandmarkCoordinateSy_t_em
+ - fixed NIRSCoordinateUnit_e_s
+ - removed txt from CHANGES
+ - added stimulus MATLAB m-files to bidsignore
+ - added sub-95 with n/a to practicelogbook.tsv
+ - use n/a for empty cells in practicelogbook.tsv
+ - added practicelogbook.tsv to bidsignore - HACK
+ - removed sub-77 json files from sub-75/nirs directory
+ - replaced 0-byte (empty) snirf files with 1-byte (still empty) snirf files - HACK
+ - use forward slashes in scans.tsv
+ - inserted "type" column in all optodes.tsv files
+ - reordered the columns of channels.tsv
+ - renamed /stim into /stimuli

fnirs_automaticity/README.txt

@@ -0,0 +1,19 @@
+Overview
+--------
+This is an example and test version of the dataset that is scheduled to be published on https://doi.org/10.34973/vesb-mh30. As this example is shared prior to completion of the publication, the DOI may or may not yet work.
+
+Cockx, H.M. (Helena), Robert Oostenveld, Tabor, M. (Merel), Savenco, E. (Ecaterina), Setten, A. van (Arne), Cameron, I.G.M. (Ian), Wezel, R.J.A. van (Richard) (2022).
+Automatic and non-automatic finger and leg movements measured with functional near-infrared spectroscopy (fNIRS) [Data set].
+
+Experiment description
+----------------------
+This dataset includes the data of 24 participants performing automatic and non-automatic finger tapping and foot stepping movements in a block design.
+
+For the finger tapping tasks, participants needed to tap their right-hand fingers in the order of a 12-digit sequence on a numeric key pad, with 1, 2, 3, and 4 representing the index, middle, ring, and little finger respectively. For the foot stepping tasks, participants needed to step with their right foot on four floor pads in the order of a 12-digit sequence, with 1, 2, 3, and 4 representing a step in the middle, to the front, to the back, and to the side, respectively. Two different sequences of similar difficulty were learned (A:434141243212 and B:212321324241). One of the two was practiced 7 days before the experiment for 5 minutes a day each limb (considered the automatic sequences). The other sequence was only practiced for 5 minutes on the day of the experiment (considered the non-automatic sequence). Participants were pseudo-randomly assigned to start learning either sequence A or B in advance. Participants performed all four task under two conditions: either with or without a dual-task. The dual-task entailed performing the sequence while simultaneously counting the letter 'G' from a list of randomly appearing letters on the screen.
+
+fNIRS data was sampled with a multichannel fNIRS device (24 long and 12 short separation channels) over the left primary motor cortex, the left premotor cortex, the left and right dorsolateral prefrontal cortex, and the left and right posterior parietal cortex.
+
+Note for events.json
+--------------------
+During the dual-task conditions a random sequence of 8 letters (C, G, Q, or O) is shown (e.g. QGCQOGCG). The exact sequence of displayed letters is coded as 'shown_stimulus' in the events.tsv files.
+However, the number of potential letter combinations was too high to report them all in the events.json file. We therefore only reported one example of a letter string as level for the 'shown_stimulus' column (QGCQOGCG).

fnirs_automaticity/dataset_description.json

@@ -0,0 +1,17 @@
+{
+	"Name": "Automatic and non-automatic finger and leg movements measured with fNIRS",
+	"Authors": [
+		"H. Cockx",
+		"R. Oostenveld",
+		"M. Tabor",
+		"E. Savenco",
+		"A. van Setten",
+		"I. Cameron",
+		"R. van Wezel"
+	],
+	"BIDSVersion": "n/a",
+	"DatasetType": "raw",
+	"EthicsApprovals": ["Research Ethics Committee (REC) of the Faculty of Science of the Radboud University (REC21012)"],
+	"Funding": ["Operational Program European Regional Development Fund (OP ERDF) (PROMPT project, PROJ-00872)"],
+	"Licence": "ODC-BY"
+}

fnirs_automaticity/events.json

@@ -0,0 +1,60 @@
+{
+  "trial_number": {
+    "Description": "Number of trial within the task condition. Each task was repeated 11 times (= 11 trials) in a row within a condition",
+    "Range": "1 to 11"
+  },
+  "event_type": {
+    "Description": "Primary categorization of the event to identify them as a experimental stimulus or a behavioural response by the participant",
+    "Levels": {
+      "stimulus": "experimental stimulus shown to the participant on the presentation screen",
+      "finger press": "behavioural response by the participant: recorded key press",
+      "foot step": "behavioural response by the participant: foot step as assessed by the experimenter, live/on video (value) and an accelerometer on the right foot (onset)"
+    }
+  },
+  "executed_movement": {
+    "Description": "Value of the finger press (recorded key press) or observed foot step (assessed by the researcher, live/on video)",
+    "Levels": {
+      "1": "index finger (finger)/step to the middle floor pad (foot)",
+      "2": "middle finger (finger)/step to the front floor pad (foot)",
+      "3": "ring finger (finger)/step to the back floor pad (foot)",
+      "4": "little finger (finger)/step to the side floor pad (foot)"
+    }
+  },
+  "correct_movement": {
+    "Description": "Value of the finger press or foot step that the participant should have performed according to the given sequences",
+    "Levels": {
+      "1": "index finger (finger)/step to the middle floor pad (foot)",
+      "2": "middle finger (finger)/step to the front floor pad (foot)",
+      "3": "ring finger (finger)/step to the back floor pad (foot)",
+      "4": "little finger (finger)/step to the side floor pad (foot)"
+    }
+  },
+  "shown_stimulus": {
+    "Description": "visual stimulus shown on the presentation screen",
+    "Levels": {
+      "white X": "small white fixation cross on the middle of the screen, indicating that the participant should relax and focus on the cross. At the beginning of a trial, a metronome sound of 1.5 Hz was played during the first 8 seconds of the white fixation cross.",
+      "red X": "small red fixation cross in the middle of the screen, indicating that the participant should start tapping/stepping the sequence (once) during the single-task conditions",
+      "QGCQOGCG": "random sequence of 8 letters (C, G, Q, or O) shown at random intervals (0.5-1.5 s) on the middle of the screen during the dual-task conditions. Participants needed to tap/step the sequence once, while simultaneously counting the letter G."
+    }
+  },
+  "reported_gs": {
+    "Description": "Reported number of G's, as counted by the particpant during the dual-task conditions."
+  },
+  "correct_gs": {
+    "Description": "Correct number of G's, as calculated from the shown 8-letter sequence"
+  },
+  "included_trial": {
+    "Description": "Trial was included in the final analysis",
+    "Levels": {
+      "0": "excluded",
+      "1": "included"
+    }
+  },
+  "reason_for_exclusion": {
+    "Description": "Reason to exclude the trial from the final analysis, if applicable",
+    "Levels": {
+      "test trial": "first trial was always disregarded as a test trial",
+      "erroneous trial": "trial with more than 1 error in the performed sequence"
+    }
+  }
+}

fnirs_automaticity/participants.json

@@ -0,0 +1,83 @@
+{
+  "sex": {
+    "Description": "sex of the participant as reported by the participant",
+    "Levels": {
+      "M": "male",
+      "F": "female"
+    }
+  },
+  "age": {
+    "Description": "age of the participant on the moment of participation",
+    "Units": "years"
+  },
+  "haircolor": {
+    "Description": "hair color as described by the Fischer-Saller scale",
+    "TermURL": "https://en.wikipedia.org/wiki/Human_hair_color",
+    "Levels": {
+      "bald": "bald",
+      "white": "white",
+      "gray": "gray",
+      "blond": "blond",
+      "light brown": "light brown",
+      "dark brown": "dark brown",
+      "black": "black",
+      "ginger red": "ginger red",
+      "copper red": "copper red"
+    }
+  },
+  "skincolor": {
+    "Description": "skin color as described by the Von Luschan's chromatic scale ",
+    "TermURL": "https://en.wikipedia.org/wiki/Von_Luschan%27s_chromatic_scale",
+    "Levels": {
+      "very light": "very light",
+      "light": "light",
+      "light intermediate": "light intermediate",
+      "dark intermediate": "dark intermediate",
+      "dark": "dark",
+      "very dark": "very dark"
+    }
+  },
+  "handedness": {
+    "Description": "handedness of the participant as a score on the Dutch Handedness Questionnaire",
+    "TermURL": "doi:1765/956",
+    "Range": "-10 (left) to + 10 (right)"
+  },
+  "footedness": {
+    "Description": "footedness of the participant as a score on the Waterloo Footedness Questionnaire",
+    "TermURL": "doi:10.1016/S0028-3932(97)00107-3",
+    "Range": "-20 (left) to + 20 (right)"
+  },
+  "musicality": {
+    "Description": "score on the 'musical training' part of the Goldsmiths Musical Sophistication Index",
+    "TermURL": "https://www.gold.ac.uk/music-mind-brain/gold-msi/",
+    "Range": "7 to 49"
+  },
+  "comfortlevel_begin": {
+    "Description": "Comfort level regarding the fNIRS cap as reported by the participant at the beginning of the measurement",
+    "Range": "1 (very uncomfortable) to 10 (very comfortable)"
+  },
+  "comfortlevel_end": {
+    "Description": "Comfort level regarding the fNIRS cap as reported by the participant at the end of the measurement",
+    "Range": "1 (very uncomfortable) to 10 (very comfortable)"
+  },
+  "included": {
+    "Description": "Participant was included in the final analysis",
+    "Levels": {
+      "0": "excluded",
+      "1": "included"
+    }
+  },
+  "reason_for_exclusion": {
+    "Description": "Reason to exclude the participant from the final analysis if applicable"
+  },
+  "headcircumference": {
+    "Description": "maximal head circumference of the participant",
+    "Units": "cm"
+  },
+  "distance_NzIz": {
+    "Description": "measured distance from nasion to inion"
+  },
+  "distance_LPARPA": {
+    "Description": "measured distance from left preauricular point to right preauricular point"
+  }
+}

fnirs_automaticity/participants.tsv

@@ -0,0 +1,25 @@
+participant_id	sex	age	haircolor	skincolor	handedness	footedness	musicality	comfortlevel_begin	comfortlevel_end	included	reasonforexclusion	comfortlevel_before	comfortlevel_after	headcircumference	distance_NzIz	distance_LPARPA	reason_for_exclusion
+sub-06	M	29	blond	light	10	10	31	5.5	2.5	1	n/a	5.5	2.5	59	41	39.5	n/a
+sub-10	F	22	dark brown	light intermidiate	10	13	27	n/a	n/a	0	n/a	5	2	57	39	37	more than half of the channels with SCI < 0.7
+sub-19	F	22	light brown	very light	10	6	41	n/a	n/a	1	n/a	7.5	3	56	36	38	n/a
+sub-21	F	21	dark brown	light	10	10	9	n/a	n/a	1	n/a	7	4	55	37	35	n/a
+sub-27	F	25	light brown	light	10	3	7	n/a	n/a	1	n/a	7	2	54	37.5	36	n/a
+sub-31	F	20	blond	light	10	6	10	n/a	n/a	1	n/a	6	3	54	37.5	34	n/a
+sub-33	F	26	dark brown	light	10	9	8	n/a	n/a	1	n/a	7	5	56	37	37	n/a
+sub-34	M	21	dark brown	light	10	10	9	n/a	n/a	1	n/a	9	6	60	40	38	n/a
+sub-38	M	24	light brown	light	10	16	31	n/a	n/a	1	n/a	NA	NA	61	40	41	n/a
+sub-43	F	21	light brown	light	10	15	18	n/a	n/a	1	n/a	7	NA	58	39	38	n/a
+sub-44	M	24	blond	light	9	15	10	n/a	n/a	1	n/a	7.5	6.5	59	40	39	n/a
+sub-52	F	26	dark brown	light	10	16	33	n/a	n/a	1	n/a	7	4	57	39	35	n/a
+sub-53	M	27	completely black	light intermidiate	10	6	10	n/a	n/a	1	n/a	8	2	61	40	39	n/a
+sub-63	M	23	blond	light	10	13	32	n/a	n/a	1	n/a	4	3	57	39	39.5	n/a
+sub-67	F	22	light brown	light	10	5	32	n/a	n/a	1	n/a	8	NA	60	40	37	n/a
+sub-69	F	26	blond	light	9	12	26	n/a	n/a	1	n/a	7.5	4	58	40	39	n/a
+sub-74	M	22	blond	light	9	7	31	n/a	n/a	1	n/a	6.5	5	59	40	38	n/a
+sub-75	F	24	blond	light	10	13	21	n/a	n/a	1	n/a	8	7	55	38	35	n/a
+sub-77	F	23	dark brown	light	9	2	13	n/a	n/a	1	n/a	4	NA	55	37	35	n/a
+sub-84	M	29	light brown	light	10	9	15	n/a	n/a	1	n/a	5	1	57	39	35.5	n/a
+sub-87	M	27	blond	light	10	19	20	n/a	n/a	1	n/a	10	7	57.5	41	39	n/a
+sub-88	F	23	blond	light	9	4	NA	n/a	n/a	1	n/a	9	4	59	40.5	39	n/a
+sub-90	F	23	blond	light	10	9	NA	n/a	n/a	1	n/a	6.5	4	57	38.5	37	n/a
+sub-95	M	26	dark brown	light	10	5	15	n/a	n/a	1	n/a	9	9	59	37	36	n/a

fnirs_automaticity/phenotype/practicelogbook.json

@@ -0,0 +1,31 @@
+{
+  "MeasurementToolMetadata": {
+    "Description": "logbook filled in by the participants after each training session",
+    "Remark": "Exact dates are removed to protect the privacy of the participants and are replaced by relative days in relation to the first practice day. Sometimes the participants forget to fill in the logbook and reported this practice session on another day. In this case, the relative day was reestimated based on their notes and the hour was set to n/a."
+  },
+  "day": {
+    "Description": "practice day, relative to the first practice day (= day 1)"
+  },
+  "hour": {
+    "Description": "hour that the logbook was filled in"
+  },
+  "practiceduration_finger": {
+    "Description": "reported practice time for the finger tapping task",
+    "Units": "minutes"
+  },
+  "practiceduration_foot": {
+    "Description": "reported practice time for the foot stepping task",
+    "Units": "minutes"
+  },
+  "selfassessment_finger": {
+    "Description": "'On a scale from 1 to 10, how would rate your performance today?' for the finger tapping task",
+    "Range": "1 (can't perform the sequence at all) to 10 (automaticity is reached)"
+  },
+  "selfassessment_foot": {
+    "Description": "'On a scale from 1 to 10, how would rate your performance today?' for the foot stepping task",
+    "Range": "1 (can't perform the sequence at all) to 10 (automaticity is reached)"
+  },
+  "notes": {
+    "Description": "additional comments/observations/notes, reported by the participant"
+  }
+}