Wiki Guides

TI-Toolbox Reports

The TI-Toolbox generates comprehensive HTML reports that provide detailed documentation of preprocessing and simulation workflows. These professional reports ensure reproducibility, facilitate quality control, and provide publication-ready methodology descriptions.

Overview

The toolbox produces two types of reports:

  • Preprocessing Reports: Document anatomical data processing pipeline for each subject
  • Simulation Reports: Detail transcranial stimulation simulation parameters and results
  • Interactive Format: HTML reports with collapsible sections and modern styling
  • Publication Ready: Include boilerplate methodology text for scientific papers

Report Features

Professional Documentation

  • Interactive HTML Interface: Modern, responsive design with collapsible sections
  • Comprehensive Tracking: Complete workflow documentation from input to output
  • Error Management: Detailed error and warning logs with timestamps
  • Software Versioning: Complete tool version tracking for reproducibility

Quality Control

  • Status Indicators: Visual confirmation of processing step completion
  • File Validation: Automatic counting and listing of input/output files
  • Parameter Documentation: Complete record of processing parameters
  • Visual Confirmation: Brain visualizations and NIfTI previews

Example: Simulation Report

Below is an embedded example of a complete simulation report generated by the TI-Toolbox:

Interactive simulation report showing complete workflow documentation, parameters, and results

Preprocessing Reports

Report Structure

Section Content Purpose
Header Subject ID, timestamp, project directory Quick identification
Summary Processing status, file counts, error/warning counts Overview dashboard
Input Data T1/T2 images, DICOM files with counts Data validation
Processing Steps DICOM conversion, m2m creation, atlas segmentation Workflow tracking
Output Data NIfTI files, m2m files, atlas files Result verification
Software Info SimNIBS, dcm2niix, tool versions Reproducibility
Methods Publication-ready methodology text Scientific documentation
Errors/Warnings Timestamped messages Quality control

Key Information Tracked

Subject Information:

  • Subject ID and BIDS compliance
  • Project directory structure
  • Input data inventory (T1, T2, DICOM files)

Processing Pipeline:

  • DICOM to NIfTI conversion status
  • SimNIBS m2m head model creation
  • Atlas segmentation and registration
  • Parameter documentation for each step

Quality Assurance:

  • File count verification
  • Processing step completion status
  • Error and warning documentation
  • Software version tracking

Simulation Reports

Report Structure

Section Content Purpose
Header Session ID, timestamp, project info Session identification
Summary Subject overview, montage info, processing status Executive summary
Parameters Conductivity, simulation mode, EEG configuration Simulation setup
Electrodes Shape, dimensions, thickness, configuration Hardware specification
Subjects Subject IDs, m2m paths, processing status Multi-subject tracking
Montages Electrode pairs, montage types, configurations Stimulation protocols
Results Output files, duration, processing status Outcome documentation
Visualizations Brain renders, NIfTI previews Visual verification
Methods Publication methodology text Scientific documentation

Key Information Tracked

Simulation Configuration:

  • Conductivity settings and tissue properties
  • Simulation mode (unipolar/multipolar)
  • EEG net configuration and electrode positions
  • Current intensities and stimulation parameters

Hardware Specifications:

  • Electrode shape, dimensions, and thickness
  • Montage configurations and electrode pairs
  • Stimulation protocols and current flow patterns

Results Documentation:

  • Processing duration and computational metrics
  • Output file generation and validation
  • Visual confirmation through brain renderings
  • Error tracking and quality assurance

Report Locations

File Organization

derivatives/reports/
├── preprocessing/
│   ├── sub-001_preprocessing_report.html
│   ├── sub-002_preprocessing_report.html
│   └── ...
└── simulation/
    ├── simulation_report_20250610_063527.html
    ├── simulation_report_20250611_142033.html
    └── ...

Naming Convention

  • Preprocessing: sub-{ID}_preprocessing_report.html
  • Simulation: simulation_report_{YYYYMMDD}_{HHMMSS}.html

Viewing and Sharing

Browser Compatibility

  • Modern Browsers: Chrome, Firefox, Safari, Edge
  • Responsive Design: Adapts to different screen sizes
  • No Dependencies: Self-contained HTML files

Sharing Reports

  • Self-Contained: All styling and scripts embedded
  • Portable: Can be shared via email or cloud storage
  • Archive Safe: HTML format ensures long-term accessibility

Publication Integration

Methodology Text

Both report types include publication-ready methodology sections that can be directly incorporated into scientific papers:

  • Complete Parameter Documentation: All processing parameters documented
  • Software Version Tracking: Ensures reproducible methodology descriptions
  • Standard Terminology: Uses established neuroimaging terminology
  • Citation Ready: Includes appropriate tool and method citations

Quality Assurance

  • Peer Review Ready: Comprehensive documentation supports manuscript review
  • Reproducibility: Complete parameter and version tracking
  • Transparency: Open documentation of all processing steps

Last Updated: January 2025
Compatible with: TI-Toolbox v4.0+, Modern Web Browsers