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Merge pull request #39 from BioMedicalImaging-Core-NYUAD/kidlang_pipeline
Kidlang pipeline
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‎.github/workflows/box-dataset-info.yml‎

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name: Box Dataset Info
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on:
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workflow_dispatch:
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inputs:
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dataset_name:
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description: "Name of the dataset to inspect (leave empty to list all)"
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required: false
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default: ""
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jobs:
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box-info:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install "boxsdk[jwt]"
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- name: Run Box Info Script
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env:
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BOX_CLIENT_SDK_CONFIG: ${{ secrets.BOX_CLIENT_SDK_CONFIG }}
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BOX_FOLDER_ID: ${{ secrets.BOX_MEG_DATA_PARENT_FOLDER_ID }}
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run: |
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python pipeline/box_info/get_box_dataset_info.py \
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--box-folder-id "$BOX_FOLDER_ID" \
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--dataset-name "${{ github.event.inputs.dataset_name }}"

‎.gitignore‎

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pip-log.txt
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pip-delete-this-directory.txt
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render_log_*.txt
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.quarto
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_output
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# Unit test / coverage reports
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htmlcov/
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.tox/

‎.vscode/launch.json‎

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{
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// Use IntelliSense to learn about possible attributes.
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// Hover to view descriptions of existing attributes.
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// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"name": "KIT Sanity Check Single Channel",
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"type": "debugpy",
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"request": "launch",
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"program": "${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/1-kit_count_sanity_check_single_channel.py",
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"console": "integratedTerminal",
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"args": [
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"-c",
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"${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/pipeline_config_files/config_template.yml"
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],
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"env": {
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"PYTHONPATH": "${workspaceFolder}"
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}
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},
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{
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"name": "CON to FIF",
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"type": "debugpy",
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"request": "launch",
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"program": "${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/2-kit_con_to_fif.py",
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"console": "integratedTerminal",
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"args": [
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"-c",
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"${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/pipeline_config_files/config_template.yml"
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],
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"env": {
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"PYTHONPATH": "${workspaceFolder}"
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}
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},
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{
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"name": "PLOT coreg sensor-laserhead",
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"type": "debugpy",
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"request": "launch",
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"program": "${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/3-kit_fif_plot_headshape_sensor_alignment.py",
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"console": "integratedTerminal",
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"args": [
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"-c",
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"${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/pipeline_config_files/config_template.yml"
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],
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"env": {
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"PYTHONPATH": "${workspaceFolder}"
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}
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},
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{
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"name": "Apply filters",
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"type": "debugpy",
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"request": "launch",
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"program": "${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/4-kit_apply_filters.py",
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"console": "integratedTerminal",
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"args": [
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"-c",
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"${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/pipeline_config_files/config_template.yml"
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],
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"env": {
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"PYTHONPATH": "${workspaceFolder}"
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}
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},
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{
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"name": "Compute events single channel",
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"type": "debugpy",
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"request": "launch",
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"program": "${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/5-kit_compute_events_single_channel.py",
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"console": "integratedTerminal",
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"args": [
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"-c",
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"${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/pipeline_config_files/config_template.yml"
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],
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"env": {
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"PYTHONPATH": "${workspaceFolder}"
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}
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},
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{
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"name": "Compute evoked response",
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"type": "debugpy",
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"request": "launch",
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"program": "${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/6-kit_evoked_response_single_channel.py",
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"console": "integratedTerminal",
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"args": [
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"-c",
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"${workspaceFolder}/pipeline/mne_pipelines/kit_general_pipelines/pipeline_config_files/config_template.yml"
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],
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"env": {
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"PYTHONPATH": "${workspaceFolder}"
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}
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}
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]
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}

‎.vscode/settings.json‎

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{
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"python.envFile": "${workspaceFolder}/.env",
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"git.requireCommitMessage": true
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}

‎docs/source/2-meg-kit-system/6-experiment-design.rst‎

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Saving your event file
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----------------------
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Your experiment should save a tabular event file (.csv or .tsv) with the following columns:
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- `onset`: the onset time of the event in seconds (do not fill this column from your experiment code, it will be filled later when pre-processing your data)
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- `duration`: the duration of the event in seconds (if relevant for the research question, if not leave blank)
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- `trial_type`: the trial type defined as a string symbolising the type of trial (no need to be very detailed: example: cat, dog, afraid, fruit, emotion etc...). This information is used to average trials with the same type together.
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Additionally,
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- if you are using TriggerMode: `single_channel` then add the following column:
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- `channel`: the channel on which the trigger is sent
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- if you are using TriggerMode: `binary_coded` then add the following column:
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- `binary_code`: the binary code associated to the event type
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Files produced by the experiment design
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---------------------------------------
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‎docs/source/4-meg-experiments-gallery/1-meg-experiments.rst‎

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experiments/psychopy/*
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Presentation
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^^^^^^^^^^^^
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.. nbgallery::
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:glob:
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experiments/presentation/*
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‎docs/source/4-meg-experiments-gallery/experiments/presentation/kidlang.rst‎

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Experiment example: Kidlang
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---------------------------
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Author: Sherine Bou Dergham
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Description
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^^^^^^^^^^^
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In this experiment implemented using the `Presentation` framework
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-
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Stimulus Code access
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^^^^^^^^^^^^^^^^^^^^
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Available upon request
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Data access
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^^^^^^^^^^^
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Acquired datasets are stored safely on NYU Box under `kidlang`.
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`MEG Data Directory <https://nyu.box.com/v/meg-datafiles>`_
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Analysis results
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^^^^^^^^^^^^^^^^
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NA
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‎docs/source/4-meg-experiments-gallery/experiments/psychtoolbox/auditory-vs-visual.rst‎

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Code access
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^^^^^^^^^^^
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Stimulus Code access
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^^^^^^^^^^^^^^^^^^^^
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:github-file:`Auditory vs Visual vs Motor Experiment Code <experiments/psychtoolbox/auditory-vs-visual>`
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‎docs/source/4-meg-experiments-gallery/experiments/psychtoolbox/resting-state.rst‎

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- Channel 225 in KIT indexing corresponds to `MISC 002`
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Code access
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^^^^^^^^^^^
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Stimulus Code access
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^^^^^^^^^^^^^^^^^^^^
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:github-file:`Resting State Eyes Closed <experiments/psychtoolbox/restingstate/resting_state_meg_EYES_CLOSED.m>`
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‎docs/source/4-meg-experiments-gallery/experiments/psychtoolbox/visual-crowd-preview.rst‎

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Code access
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Stimulus Code access
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^^^^^^^^^^^^^^^^^^^^
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:github-file:`Visual Crowd Preview <experiments/psychtoolbox/visual_crowding_preview>`
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