Table 1.

Categories of command line.

Category of command line	Description	Example usage
run	Run pipelines on BIDS or CAPS datasets. The full list of pipelines is available in section Image Processing Pipelines (clinica run).	clinica run t1-linear bids_directory caps_directory
convert	Convert public neuroimaging datasets into BIDS. The list of the public datasets can be found in section Conversion of Neuroimaging Datasets Into a BIDS Hierarchy (clinica convert).	clinica convert adni-to-bids dataset_directory clinical_data_directory bids_directory
iotools	Set of tools to handle BIDS and CAPS datasets. The list of the I/O tools can be found in section Data Handling Tools (clinica iotools).	clinica iotools merge-tsv bids_directory −−caps_directory caps_directory my_population.tsv
generate	(For developers) Generate the skeleton source code for a new pipeline.	clinica generate template “Modality Feature Extracted” pipeline_folder