Utility Commands

neuromaestro detect-subjects¶

Scans a directory for subject folders matching the given prefix.

# Print detected subjects to stdout
neuromaestro detect-subjects /data/BIDS

# Save to a text file (comma-separated, one line)
neuromaestro detect-subjects /data/BIDS --output subjects.txt

# With explicit prefix (default is "sub-")
neuromaestro detect-subjects /data/raw --prefix "sub-" -o subjects.txt

The saved file can be passed directly to --subjects in neuromaestro run:

neuromaestro run --subjects subjects.txt ...

Arguments / Options:

neuromaestro init¶

Initialises a new project directory with config and script templates copied from the package defaults.

neuromaestro init /scratch/my_study

Creates the following layout under the given directory:

/scratch/my_study/
├── config/
│   ├── config.yaml
│   ├── hpc_config.yaml
│   └── project_config/
└── scripts/
    └── (template .sh scripts)

Pass --config-dir /scratch/my_study/config in all subsequent neuromaestro commands, or set $NEUROMAESTRO_CONFIG_DIR once to skip it (see Getting Started).

Arguments / Options:

neuromaestro list-tasks¶

Lists all task names, scripts, and dependencies from config.yaml.

neuromaestro list-tasks --config-dir /data/config

Options:

neuromaestro-gui¶

Launches the web dashboard.

neuromaestro-gui                 # default port 8050
neuromaestro-gui --port 8051     # if 8050 is in use

Open http://localhost:8050. The GUI has three tabs:

neuromaestro generate-config¶

Generate a blank project config template ({project}_config.yaml). Equivalent to clicking Generate Template in the GUI Project Config tab.

neuromaestro generate-config branch --config-dir /data/config

# Write to a custom directory
neuromaestro generate-config branch --config-dir /data/config \
  --output-dir /scratch/my_project/config/project_config

Arguments / Options:

The command refuses to overwrite an existing {project}_config.yaml and exits with code 1, so regenerating a template cannot silently discard settings you have already filled in. Pass --force when you really do want to start over.

The generated file is a fully-commented YAML template. Open it in the GUI editor or any text editor and fill in paths, modules, and task parameters.

neuromaestro generate-checks¶

Generate a blank results-check config template ({project}_checks.yaml). Equivalent to clicking New in the GUI Results Check Config tab.

neuromaestro generate-checks branch --config-dir /data/config

# Write to a custom directory
neuromaestro generate-checks branch --config-dir /data/config \
  --output-dir /scratch/my_project/config/results_check

Arguments / Options:

As with generate-config, an existing {project}_checks.yaml is never overwritten unless --force is given.

The generated file contains commented examples for both required_files and count_check block types. See Output Checks Configuration for the full reference.