Wiki Guides

Command Line Interface

The TI-Toolbox CLI supports two complementary workflows:

  • Interactive mode: Guided, prompt-based configuration — ideal for exploration and first-time runs who do not want GUI
  • Direct mode: Fully specified command-line flags — better for scripts and allow advanced control

Interactive vs Direct Mode

Interactive Mode

# Run command with no arguments for guided prompts
simulator

The CLI will guide you through:

  • Subject selection
  • Framework choice (montage/flex)
  • EEG cap selection
  • Montage configuration
  • Parameter setup

Direct Mode

# All parameters specified explicitly
simulator \
  --sub 101 \
  --framework montage \
  --eeg GSN-HydroCel-185.csv \
  --montages my_montage \
  --intensity 2.0

Mode selection is automatic:

  • No arguments → Interactive mode
  • Any arguments present → Direct mode

Available Commands

Command Description Interactive Direct Examples
pre_process Preprocessing pipeline pre_process pre_process --subs 101 --run-recon --create-m2m
flex_search Electrode optimization flex_search flex_search --subject 101 --roi-method spherical
create_leadfield Generate leadfield matrices create_leadfield create_leadfield --sub 101 --eeg cap.csv
ex_search Leadfield-based optimization ex_search ex_search --sub 101 --lf leadfield.hdf5 --pool
simulator Run TI simulations simulator simulator --sub 101 --montages my_montage
analyzer Analyze single subject results analyzer analyzer --sub 101 --sim montage --coordinates 0 0 0
group_analyzer Analyze multiple subjects group_analyzer group_analyzer --subs 101,102 --sim montage
cluster_permutation Statistical analysis cluster_permutation cluster_permutation --csv data.csv --name analysis
blender Create visualizations blender blender --subject 101 --simulation montage

Getting Help

All commands support detailed help via the -h or --help flag:

# Get command-specific help
simulator -h
analyzer --help
blender -h