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Nipoppy docs are moving

Nipoppy is undergoing a major refactor to move from scripts to a command-line interface (CLI) and Python API. The new documentation website (work in progress) can be found at

If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is still the correct place to be. But we encourage you to check out the new website!

MRIQC image processing pipeline

MRIQC processes the participants and produces image quality metrics from T1w, T2w and BOLD data.


python nipoppy/workflow/proc_pipe/mriqc/ \
    --global_config <global_config_file> \
    --participant_id <participant_id> \
    --session_id <session_id> \
    --modalities <modalities> \

The required arguments are: - --global_config: path to the configuration containing the MRIQC container and data directory - --participant_id: participant/subject ID - --session_id: session ID - --modality: modality/modalities to check (valid values: T1w, T2w, bold, dwi)