mriqc

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 https://nipoppy.readthedocs.io/.

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

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

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MRIQC

• Use nipoppy/workflow/proc_pipe/mriqc/run_mriqc.py to run MRIQC pipeline directly or wrap the script in an SGE/Slurm script to run on cluster

python nipoppy/workflow/proc_pipe/mriqc/run_mriqc.py \
    --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)