Corrected links after reorganization with src directory

datasets/README.md

@@ -20,19 +20,20 @@ For example, eeg_ds003645s identifies a reduced dataset derived the EEG data
 in OpenNeuro dataset ds003645.
 The suffix modifier indicates what this dataset is designed to test.
 
-| Dataset                           | Description |
-|-----------------------------------|---------------|
-| eeg_ds002893s_hed_attention_shift | Auditory-visual attention shift data.<br>Illustrates remapping of multiple event columns. |
-| eeg_ds003645s_hed                 | Face Perception data using short form tags and definitions.   |
-| eeg_ds003645s_hed_demo            | Face Perception data demonstrating full usage of HED in tsv.  |
-| eeg_ds003645s_hed_library         | Face Perception data using HED libraries.                                |
-| eeg_ds003645s_hed_partnered       | Face Perception data using HED partnered libraries.                      |
-| eeg_ds003645s_hed_remodel | Face Perception data in remodeling. |
-| eeg_ds004105s_hed                 | BCIT Driving with auditory cueing data.<br>Part of a test data corpus for BIDS-MEGA testing. |
-| eeg_ds004106s_hed                 | BCIT Advanced guard duty data.<br> Part of a test data corpus for BIDS-MEGA testing. |
+| Dataset                           | Description                                                                                                   |
+|-----------------------------------|---------------------------------------------------------------------------------------------------------------|
+| eeg_ds002893s_hed_attention_shift | Auditory-visual attention shift data.<br>Illustrates remapping of multiple event columns.                     |
+| eeg_ds003645s_hed                 | Face Perception data using short form tags and definitions.                                                   |
+| eeg_ds003645s_hed_column          | Face Perception data to test annotations in HED column.                                                       |
+| eeg_ds003645s_hed_demo            | Face Perception data demonstrating full usage of HED in tsv.                                                  |
+| eeg_ds003645s_hed_library         | Face Perception data using HED libraries.                                                                     |
+| eeg_ds003645s_hed_partnered       | Face Perception data using HED partnered libraries.                                                           |
+| eeg_ds003645s_hed_remodel         | Face Perception data in remodeling.                                                                           |
+| eeg_ds004105s_hed                 | BCIT Driving with auditory cueing data.<br>Part of a test data corpus for BIDS-MEGA testing.                  |
+| eeg_ds004106s_hed                 | BCIT Advanced guard duty data.<br> Part of a test data corpus for BIDS-MEGA testing.                          |
 | eeg_ds004117s_hed_sternberg       | Sternberg working memory task.<br>Chosen as a replication study for [**EEGManyLabs**](https://osf.io/yb3pq/). |
-| frmi_ds002790s_hed_aomic | AOMIC data example |
-| fmri_soccer21_hed                 | HED tags using a single column.<br>Used for fMRI processing examples.    |
+| frmi_ds002790s_hed_aomic          | AOMIC data example                                                                                            |
+| fmri_soccer21_hed                 | HED tags using a single column.<br>Used for fMRI processing examples.                                         |
 
 
 ### Validating examples using the BIDS validator

datasets/eeg_ds003645s_hed_column/CHANGES

@@ -0,0 +1,6 @@
+1.0.0 2021-05-11
+  - First release
+Revision history for Face Recognition experiment by Wakeman-Henson
+
+version 1.0 - April 2021
+ - Initial release of EEG data in this experiment for HED education purposes

datasets/eeg_ds003645s_hed_column/README

@@ -0,0 +1,24 @@
+**Introduction:**
+This dataset consists of the MEEG (sMRI+MEG+EEG) portion of the multi-subject, multi-modal face processing dataset (ds000117). This dataset was originally acquired and shared by Daniel Wakeman and Richard Henson (https://pubmed.ncbi.nlm.nih.gov/25977808/). The data has been repackaged in EEGLAB format and has undergone minimal preprocessing as well as reorganization and annotation of the dataset events.
+
+**Overview of the experiment:**
+Eighteen participants completed two recording sessions spaced three months apart – one session recorded fMRI  and the other simultaneously recorded MEG and EEG data. During each session, participants performed the same simple perceptual task, responding to presented photographs of famous, unfamiliar, and scrambled faces by pressing one of two keyboard keys to indicate a subjective yes or no decision as to the relative spatial symmetry of the viewed face. Famous faces were feature-matched to unfamiliar faces; half the faces were female. The two sessions (MEEG, fMRI) had different organizations of event timing and presentation because of technological requirements of the respective imaging modalities. Each individual face was presented twice during the session. For half of the presented faces, the second presentation followed immediately after the first. For the other half, the second presentation was delayed by 5-15 face presentations.
+
+**Preprocessing:**
+The preprocessing, which was performed using the `wh_extracteeg_BIDS.m` located in the code directory, includes the following steps:
+* Ignore MRI data except for sMRI.
+* Extract  EEG channels out of the MEG/EEG fif data
+* Add fiducials
+* Rename EOG and EKG channels
+* Extract events from event channel
+* Remove spurious events 5, 6, 7, 13, 14, 15, 17, 18 and 19
+* Remove spurious event 24 for subject 3 run 4
+* Rename events taking into account button assigned to each subject
+* Correct event latencies (events have a shift of 34 ms)
+* Resample data to 250 Hz (this step is performed because this dataset is used in a tutorial for EEGLAB and needs to be lightweight)
+* Remove event fields `urevent` and `duration`
+* Save as EEGLAB .set format
+
+**Data curators:**
+Ramon Martinez, Dung Truong, Scott Makeig, Arnaud Delorme (UCSD, La Jolla, CA, USA), Kay Robbins (UTSA, San Antonio, TX, USA)
+

datasets/eeg_ds003645s_hed_column/code/task-FacePerception_events_after.json

@@ -0,0 +1,124 @@
+{
+  "onset": {
+    "Description": "Position of event marker in seconds relative to the start.",
+    "Units": "s"
+  },
+  "duration": {
+    "Description": "Duration of the event in seconds.",
+    "Units": "s"
+  },
+  "event_type": {
+    "LongName": "Event category",
+    "Description": "The main category of the event.",
+    "Levels": {
+      "show_face": "Display a face to mark end of pre-stimulus and start of blink-inhibition.",
+      "show_face_initial": "Display a face at the beginning of the recording.",
+      "show_circle": "Display a white circle to mark end of the stimulus and blink inhibition.",
+      "show_cross": "Display only a white cross to mark start of trial and fixation.",
+      "left_press": "Experiment participant presses a key with left index finger.",
+      "right_press": "Experiment participant presses a key with right index finger.",
+      "setup_left_sym": "Setup for experiment with pressing key with left index finger means a face with above average symmetry.",
+      "setup_right_sym": "Setup for experiment with pressing key with right index finger means a face with above average symmetry.",
+      "double_press": "Experiment participant presses both keys ."
+    }
+  },
+  "face_type": {
+    "Description": "Factor indicating type of face image being displayed.",
+    "Levels": {
+      "famous_face": "A face that should be recognized by the participants.",
+      "unfamiliar_face": "A face that should not be recognized by the participants.",
+      "scrambled_face": "A scrambled face image generated by taking face 2D FFT."
+    },
+    "HED": {
+      "famous_face": "Def/Famous-face-cond",
+      "unfamiliar_face": "Def/Unfamiliar-face-cond",
+      "scrambled_face": "Def/Scrambled-face-cond"
+    }
+  },
+  "rep_status": {
+    "Description": "Factor indicating whether this image has been already seen.",
+    "Levels": {
+      "first_show": "Factor level indicating the first display of this face.",
+      "immediate_repeat": "Factor level indicating this face was the same as previous one.",
+      "delayed_repeat": "Factor level indicating face was seen 5 to 15 trials ago."
+    },
+    "HED": {
+      "first_show": "Def/First-show-cond",
+      "immediate_repeat": "Def/Immediate-repeat-cond",
+      "delayed_repeat": "Def/Delayed-repeat-cond"
+    }
+  },
+  "trial": {
+    "Description": "Indicates which trial this event belongs to."
+  },
+  "rep_lag": {
+    "Description": "How face images before this one was the image was previously presented."
+  },
+  "stim_file": {
+    "Description": "Path of the stimulus file in the stimuli directory."
+  },
+  "hed_def_sensory": {
+    "Description": "Metadata dictionary for gathering sensory definitions",
+    "HED": {
+      "cross_only_def": "(Definition/Cross-only, (Visual-presentation, (Foreground-view, (White, Cross), (Center-of, Computer-screen)), (Background-view, Black), Description/A white fixation cross on a black background in the center of the screen.))",
+      "face_image_def": "(Definition/Face-image, (Visual-presentation, (Foreground-view, ((Image, Face, Hair), Color/Grayscale), ((White, Cross), (Center-of, Computer-screen))), (Background-view, Black), Description/A happy or neutral face in frontal or three-quarters frontal pose with long hair cropped presented as an achromatic foreground image on a black background with a white fixation cross superposed.))",
+      "circle_only_def": "(Definition/Circle-only, (Visual-presentation, (Foreground-view, ((White, Circle), (Center-of, Computer-screen))), (Background-view, Black), Description/A white circle on a black background in the center of the screen.))"
+    }
+  },
+  "hed_def_actions": {
+    "Description": "Metadata dictionary for gathering participant action definitions",
+    "HED": {
+      "press_left_finger_def": "(Definition/Press-left-finger, ((Index-finger, (Left-side-of, Experiment-participant)), (Press, Keyboard-key), Description/The participant presses a key with the left index finger to indicate a face symmetry judgment.))",
+      "press_right_finger_def": "(Definition/Press-right-finger, ((Index-finger, (Right-side-of, Experiment-participant)), (Press, Keyboard-key), Description/The participant presses a key with the right index finger to indicate a face symmetry evaluation.))"
+    }
+  },
+  "hed_def_conds": {
+    "Description": "Metadata dictionary for gathering experimental condition definitions",
+    "HED": {
+      "famous_face_cond_def": "(Definition/Famous-face-cond, (Condition-variable/Face-type, (Image, (Face, Famous)), Description/A face that should be recognized by the participants))",
+      "unfamiliar_face_cond_def": "(Definition/Unfamiliar-face-cond, (Condition-variable/Face-type, (Image, (Face, Unfamiliar)), Description/A face that should not be recognized by the participants.))",
+      "scrambled_face_cond_def": "(Definition/Scrambled-face-cond, (Condition-variable/Face-type, (Image, (Face, Disordered)), Description/A scrambled face image generated by taking face 2D FFT.))",
+      "first_show_cond_def": "(Definition/First-show-cond, ((Condition-variable/Repetition-type, (Item-count/1, Face), Item-interval/0), Description/Factor level indicating the first display of this face.))",
+      "immediate_repeat_cond_def": "(Definition/Immediate-repeat-cond, ((Condition-variable/Repetition-type, (Item-count/2, Face), Item-interval/1), Description/Factor level indicating this face was the same as previous one.))",
+      "delayed_repeat_cond_def": "(Definition/Delayed-repeat-cond, (Condition-variable/Repetition-type, (Item-count/2, Face), (Item-interval, (Greater-than-or-equal-to, Item-interval/5)), Description/Factor level indicating face was seen 5 to 15 trials ago.))",
+      "left_sym_cond_def": "(Definition/Left-sym-cond, (Condition-variable/Key-assignment, ((Index-finger, (Left-side-of, Experiment-participant)), (Behavioral-evidence, Symmetrical)), ((Index-finger, (Right-side-of, Experiment-participant)), (Behavioral-evidence, Asymmetrical)), Description/Left index finger key press indicates a face with above average symmetry.))",
+      "right_sym_cond_def": "(Definition/Right-sym-cond, (Condition-variable/Key-assignment, ((Index-finger, (Right-side-of, Experiment-participant)), (Behavioral-evidence, Symmetrical)), ((Index-finger, (Left-side-of, Experiment-participant)), (Behavioral-evidence, Asymmetrical)), Description/Right index finger key press indicates a face with above average symmetry.))"
+    }
+  },
+  "hed_def_tasks": {
+    "Description": "Metadata dictionary for gathering task definitions",
+    "HED": {
+      "face_symmetry_evaluation_task_def": "(Definition/Face-symmetry-evaluation-task, (Task, Experiment-participant, (See, Face), (Discriminate, (Face, Symmetrical)), (Press, Keyboard-key), Description/Evaluate degree of image symmetry and respond with key press evaluation.))",
+      "blink_inhibition_task_def": "(Definition/Blink-inhibition-task, (Task, Experiment-participant, Inhibit-blinks, Description/Do not blink while the face image is displayed.))",
+      "fixation_task_def": "(Definition/Fixation-task, (Task, Experiment-participant, (Fixate, Cross), Description/Fixate on the cross at the screen center.))"
+    }
+  },
+  "hed_def_setup": {
+     "Description": "Metadata dictionary for gathering setup definitions",
+     "HED": {
+        "setup_def": "(Definition/Initialize-recording, (Recording))"
+      }
+
+  },
+  "value": {
+    "Description": "Numerical event marker",
+    "Levels": {
+      "x0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
+      "x1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
+      "x2": "Initial setup with left finger key press indicating above average symmetry",
+      "x3": "Initial setup with right finger key press indicating above average symmetry",
+      "x5": "Initial presentation of famous face",
+      "x6": "Immediate repeated  presentation of famous face",
+      "x7": "Delayed repeated  presentation of famous face",
+      "x13": "Initial presentation of unfamiliar face",
+      "x14": "Immediate repeated  presentation of unfamiliar face",
+      "x15": "Delayed repeated  presentation of unfamiliar face",
+      "x17": "Initial presentation of scrambled face",
+      "x18": "Immediate repeated  presentation of scrambled face",
+      "x19": "Delayed repeated  presentation of scrambled face",
+      "x256": "Left finger key press",
+      "x4096": "Right finger key press",
+	  "x4352": "Left and right finger key presses"
+    }
+  }
+}