neuropipe detect-subjects¶
Scans a directory for subject folders matching the given prefix.
# Print detected subjects to stdout
neuropipe detect-subjects /data/BIDS
# Save to a text file (comma-separated, one line)
neuropipe detect-subjects /data/BIDS --output subjects.txt
# With explicit prefix (default is "sub-")
neuropipe detect-subjects /data/raw --prefix "sub-" -o subjects.txtThe saved file can be passed directly to --subjects in neuropipe run:
neuropipe run --subjects subjects.txt ...Arguments / Options:
| Argument/Option | Description |
|---|---|
input_dir | Directory to scan (positional, required) |
--output / -o | Output file path — prints to stdout if omitted |
--prefix / -p | Subject folder prefix to match (default: sub-) |
neuropipe init¶
Initialises a new project directory with config and script templates copied from the package defaults.
neuropipe init /scratch/my_studyCreates 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 neuropipe commands, or set $NEUROPIPE_CONFIG_DIR once to skip it (see Getting Started).
Arguments / Options:
| Argument/Option | Description |
|---|---|
output_dir | Directory to initialise (positional, required) |
neuropipe list-tasks¶
Lists all task names, scripts, and dependencies from config.yaml.
neuropipe list-tasks --config-dir /data/configOptions:
| Option | Description |
|---|---|
--config-dir | Path to config directory. Optional if $NEUROPIPE_CONFIG_DIR is set. |
neuropipe-gui¶
Launches the web dashboard.
neuropipe-gui # default port 8050
neuropipe-gui --port 8051 # if 8050 is in useOpen http://localhost:8050. The GUI has three tabs:
| Tab | Purpose |
|---|---|
| Analysis Control | Select subjects, configure pipeline, execute/dry-run, generate command preview |
| Project Config | Create/edit project YAML configs and results-check YAMLs |
| Job Monitor | Query job database, read logs, track running jobs |
neuropipe generate-config¶
Generate a blank project config template ({project}_config.yaml). Equivalent to clicking Generate Template in the GUI Project Config tab.
neuropipe generate-config branch --config-dir /data/config
# Write to a custom directory
neuropipe generate-config branch --config-dir /data/config \
--output-dir /scratch/my_project/config/project_configArguments / Options:
| Description | |
|---|---|
PROJECT_NAME | Project name — determines the output filename |
--config-dir | Path to config directory. Optional if $NEUROPIPE_CONFIG_DIR is set. |
--output-dir / -o | Output directory (default: <config-dir>/project_config/) |
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.
neuropipe generate-checks¶
Generate a blank results-check config template ({project}_checks.yaml). Equivalent to clicking New in the GUI Results Check Config tab.
neuropipe generate-checks branch --config-dir /data/config
# Write to a custom directory
neuropipe generate-checks branch --config-dir /data/config \
--output-dir /scratch/my_project/config/results_checkArguments / Options:
| Description | |
|---|---|
PROJECT_NAME | Project name — determines the output filename |
--config-dir | Path to config directory. Optional if $NEUROPIPE_CONFIG_DIR is set. |
--output-dir / -o | Output directory (default: <config-dir>/results_check/) |
The generated file contains commented examples for both required_files and count_check block types. See Output Checks Configuration for the full reference.