Installation

Install from github with pip:

pip install -e git+https://github.com/Remi-Gau/bidsgnostic#egg=bidsgnostic

Note: you can re-run this command to re-install with the latest version

Running the app

participant level

Do a dry-run first (-n) and simply print (-p) what would be run:

bidsgnostic /path/to/bids/dir /path/to/output/dir participant -np

Run the app, using all cores:

bidsgnostic /path/to/bids/dir /path/to/output/dir participant --cores all

If any workflow rules require containers, then run with the --use-singularity option.

Generating a report

After your processing is complete, you can use snakemake’s --report feature to generate an HTML report. This report will include a graph of all the jobs run, with clickable nodes to inspect the shell command or python code used in each job, along with the config files and run times for each job. Workflows may also contain append images for quality assurance or to summarize outputs, by using the report(...) function on any snakemake output.

To generate a report, run:

bidsgnostic /path/to/bids/dir /path/to/output/dir participant --report

group level

bidsgnostic_layout /path/to/bids/dir /path/to/output/dir group