mkdocs.yml

site_name: "Standard Operating Procedures of the HCPh project"
site_description: Step-by-step instructions (standard operating procedures; SOPs) to replicate our Human Connectome PHantom project (HCPh)
site_author: The AxonLab

# Copyright
copyright: Copyright © 2023

nav:
    - Home: index.md
    - Change History: changes.md
    - Recruitment, Scheduling, and Screening:
      - Recruitment and screening: recruitment-scheduling-screening/recruitment.md
      - Scheduling: recruitment-scheduling-screening/scheduling.md
    - Data collection:
      - Overall experimental settings: data-collection/intro.md
      - Before data collection starts: data-collection/setup.md
      - Before session day: data-collection/pre-session.md
      - Session preparation: data-collection/tear-up.md
      - Preparing the participant: data-collection/participant-prep.md
      - Running the scanning session: data-collection/scanning.md
      - Session tear-down: data-collection/tear-down.md
      - Emergency procedures: data-collection/emergency-procedures.md
    - Data management:
      - Overall post-scanner steps: data-management/intro.md
      - Before data acquisition (storage preparation): data-management/preliminary.md
      - Post-session retrieval and BIDS: data-management/post-session.md
      - QA/QC protocol overview: data-management/qaqc-general.md
      - QC of unprocessed data: data-management/mriqc.md
    - Processing: 
      - Preparing environments for execution: processing/environment.md
      - Preprocessing: processing/preprocessing.md
      - Extracting functional connectivity: processing/functional-connectivity.md
    - Analysis:
      - Quality control task activation analysis: analysis/qct-activation.ipynb
      - Calibrating regressor to flag HCPh T1w images for exclusion: analysis/qc-regressor-hcph.ipynb
    - Release of data: release.md
    - Appendices:
      - Notes on the scanner's console: data-collection/notes-scanning.md
      - ET extended guidelines: data-collection/notes-et.md
      - Additional miscellaneous protocols: data-collection/notes-misc.md
      - Notes on software installation and tips: data-collection/notes-software.md
      - Converting physio into BIDS (notebook): data-management/physio-to-bids.ipynb
      - Converting eye-tracking into BIDS: data-management/edf-to-bids.md
    - QA/QC Appendices:
      - QA/QC criteria for unprocessed data: data-management/qaqc-criteria-unprocessed.md
      - QA/QC criteria for preprocessed data: processing/qaqc-criteria-preprocessed.md
      - QA/QC criteria for functional connectivity: processing/qaqc-criteria-FC.md
      - Eyetracking data screening (notebook): data-management/eyetrack-qc.ipynb
    - Deprecated procedures:
      - Legacy procedure for the ET mirror: data-collection/legacy-et.md

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  #     author: The Axon Lab
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