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Getting the Nipoppy pipeline specification files for a new pipeline

To run pipeline containers within Nipoppy, you need to download the required pipeline configuration files from Zenodo. Together, these files allow Nipoppy to recognize, configure, run, and monitor the custom container image as part of its structured processing framework. You will need the following:

  • descriptor.json
  • invocation.json
  • config.json
  • tracker_config.json

A quick way to download these four files is by running: nipoppy pipeline install --dataset <DATASET_ROOT> <ZENODO_ID>

Please read more instructions about adding a pipeline to a dataset on the nipoppy documentation page.

Note: Every time a new pipeline is installed, you will need to change some paths in the global config file, depending on the pipeline.

Examples

fmriprep

Latest pipeline version: fmriprep-24.1.1

Zenodo id: 15427833

freesurfer_subseg

Latest pipeline version: freesurfer_subseg-1.0

Zenodo id: 15877956

fsqc

Latest pipeline version: fsqc-2.1.1

Zenodo id: 16810923