README.md

CLI scripts for BIDS PROV

Compute JSON-LDs in BIDS-PROV format for SPM, FSL and AFNI data

Task which is performed by the Github actions

• Put all your example files in a folder (for example: input_examples)

  • SPM: .m files
  • FSL: report_log.html files
  • AFNI: .sub_001 or .tcsh files

• Execute the following command in your terminal

python launch_parser_on_nidm.py --input_dir input_examples --output_dir output_results

Your output_results directory tree will be generated by itself. A folder is created for each parser and each example contains the input file, the jsonld and the associated png.

Notes

All scripts provide a --help flag, to get an overview of possible parameters and default values Here is an example

>> python -m bids_prov.visualize --help
Usage: visualize.py [OPTIONS] [FILENAMES]...

Options:
  -o, --output_file TEXT
  --omit-details          omit the following low level details : {'Activity':
                          ('startedAtTime', 'endedAtTime'), 'Entity':
                          ('atLocation', 'generatedAt')}

  --help                  Show this message and exit.

>> python -m bids_prov.spm_parser --help
Usage: spm_parser.py [OPTIONS] [FILENAMES]...

Options:
  -o, --output-file TEXT  [required]
  -c, --context-url TEXT
  --help                  Show this message and exit.