Oddball Session Scripts

This document provides an overview of the scripts specifically used for oddball experimental protocols in this project.

Standard Oddball Protocol

  • Standard_oddball.bonsai - The standard oddball protocol script (generic version)

  • Standard_oddball_slap2.bonsai - Standard oddball protocol optimized for SLAP2 hardware

Standard Oddball with Jitter Random Protocol

  • Standard_oddball_jitter_random.bonsai - Standard oddball protocol with jittered timing and randomized presentation

Sensory-Motor Oddball Protocol

  • Sensory_motor_oddball_slap2.bonsai - Implements the sensory-motor oddball paradigm for SLAP2 hardware

Sequence Mismatch Protocol

  • Sequence Mismatch Protocol - Implements the sequence mismatch paradigm with learned sequences

Generic Oddball Protocol

  • generic_oddball.bonsai - Unified framework for running multiple experimental paradigms using CSV-defined stimulus parameters
    • Located in code/stimulus-control/src/Mindscope/
    • Works with generate_experiment_csv.py to create flexible, reproducible experiments
    • Supports standard oddball, jitter, sequential, and motor paradigms
    • For detailed information, see Generic Oddball Protocol

Bonsai Instructions

For instructions on how to set up and run these Bonsai scripts, please refer to: - Bonsai Instructions

Adding a New Script to Documentation

If you've created a new script that should be added to this documentation, follow these steps:

  1. Place your Bonsai script in code/stimulus-control/src/

  2. Add your script to this list with a brief description

  3. For a new experimental protocol, create a markdown file in docs/stimuli/ explaining:

    • Protocol purpose
    • Key parameters and settings
    • Running instructions
    • Output formats
    • Hardware considerations

  4. Update mkdocs.yml to include your new markdown file

Stimulus Protocols and Analysis

This document provides an overview of the stimulus protocols in this project, now including comprehensive analysis visualizations generated from actual experimental data.

Protocol Analysis Overview

All stimulus protocols have been analyzed using real experimental data to provide clear visualizations of: - Block Structure: Temporal organization of experimental phases - Stimulus Progression: Evolution of stimulus parameters over time
- Oddball Distribution: Timing and frequency of mismatch events

Available Protocols

1. Visual Mismatch (Standard Oddball)

Visual Mismatch Analysis - Description: Classic oddball paradigm with orientation deviants - Documentation: Standard Oddball Protocol - Key Features: 0°/45°/90° orientation violations, RF mapping

2. Sequence Mismatch

Sequence Mismatch Analysis - Description: Sequential learning paradigm with pattern violations - Documentation: Sequence Mismatch Protocol - Key Features: Learned sequences, position-specific violations

3. Sensory-Motor Mismatch

Sensory-Motor Mismatch Analysis - Description: Closed-loop paradigm with motor-visual coupling violations - Documentation: Sensory-Motor Closed-Loop - Key Features: Wheel-coupled stimuli, expectation violations

4. Duration Mismatch

Duration Mismatch Analysis - Description: Temporal predictive coding with duration violations - Documentation: Duration Mismatch Protocol - Key Features: Timing violations, temporal jitter

5. Control Protocols

Control Protocol Analysis - Description: Control conditions without oddball violations - Key Features: Matched stimulation without prediction errors

Analysis Features

Each protocol analysis includes: 1. Block Timeline: Shows duration and sequence of experimental blocks 2. Orientation Progression: Displays stimulus parameters over time 3. Oddball Events: Highlights timing and distribution of mismatch events

These visualizations are generated from actual stimulus tables and provide researchers with clear expectations of experimental structure and timing.

Legacy Documentation

The following sections contain the original protocol listings:

Standard Oddball Protocol

  • Standard_oddball.bonsai - The standard oddball protocol script (generic version)

  • Standard_oddball_slap2.bonsai - Standard oddball protocol optimized for SLAP2 hardware

Standard Oddball with Jitter Random Protocol

  • Standard_oddball_jitter_random.bonsai - Standard oddball protocol with jittered timing and randomized presentation

Sensory-Motor Oddball Protocol

  • Sensory_motor_oddball_slap2.bonsai - Implements the sensory-motor oddball paradigm for SLAP2 hardware

Sequence Mismatch Protocol

  • Sequence Mismatch Protocol - Implements the sequence mismatch paradigm with learned sequences

Generic Oddball Protocol

  • generic_oddball.bonsai - Unified framework for running multiple experimental paradigms using CSV-defined stimulus parameters
    • Located in code/stimulus-control/src/Mindscope/
    • Works with generate_experiment_csv.py to create flexible, reproducible experiments
    • Supports standard oddball, jitter, sequential, and motor paradigms
    • For detailed information, see Generic Oddball Protocol

Bonsai Instructions

For instructions on how to set up and run these Bonsai scripts, please refer to: - Bonsai Instructions

Adding a New Script to Documentation

If you've created a new script that should be added to this documentation, follow these steps:

  1. Place your Bonsai script in code/stimulus-control/src/

  2. Add your script to this list with a brief description

  3. For a new experimental protocol, create a markdown file in docs/stimuli/ explaining:

    • Protocol purpose
    • Key parameters and settings
    • Running instructions
    • Output formats
    • Hardware considerations

  4. Update mkdocs.yml to include your new markdown file

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