<commit_before>.. include:: links.rst

Usage
-----

Execution and the BIDS format
=============================

The ``fmriprep`` workflow takes as principal input the path of the dataset
that is to be processed.
The only requirement to the input dataset is that it has a valid BIDS_ (Brain
Imaging Data Structure) format.
This can be easily checked online using the
`BIDS Validator <http://incf.github.io/bids-validator/>`_.

The exact command to run ``fmriprep`` depends on the Installation_ method.
The common parts of the command follow the
`BIDS-Apps <https://github.com/BIDS-Apps>`_ definition.
Example: ::

    fmriprep data/bids_root/ out/ participant -w work/

Command-Line Arguments
~~~~~~~~~~~~~~~~~~~~~~

.. include:: args.txt<commit_msg>get rid of inappropriate highlightin in usage<commit_after>.. include:: links.rst

Usage
-----

Execution and the BIDS format
=============================

The ``fmriprep`` workflow takes as principal input the path of the dataset
that is to be processed.
The only requirement to the input dataset is that it has a valid BIDS_ (Brain
Imaging Data Structure) format.
This can be easily checked online using the
`BIDS Validator <http://incf.github.io/bids-validator/>`_.

The exact command to run ``fmriprep`` depends on the Installation_ method.
The common parts of the command follow the
`BIDS-Apps <https://github.com/BIDS-Apps>`_ definition.
Example: ::

    fmriprep data/bids_root/ out/ participant -w work/

Command-Line Arguments
~~~~~~~~~~~~~~~~~~~~~~

.. highlight:: none

.. include:: args.txt
{'fraction_non_alphanumeric': 0.1519639407598197, 'fraction_numerical': 0.0, 'mean_word_length': 4.34020618556701, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3460400', 'n_tokens_mistral': 456, 'n_tokens_neox': 433, 'n_words': 185}