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[DOCS] Add examples of --list_sub_file/--list-sub-file - Fixed rendering issues #183

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[DOCS] Add examples of --list_sub_file/--list-sub-file - Fixed rendering issues #183

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Update babs-init.rst
tientong98 Oct 18, 2024
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Update preparation_config_yaml_file.rst
tientong98 Oct 18, 2024
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Update babs-init.rst
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9 changes: 3 additions & 6 deletions docs/source/babs-init.rst
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Expand Up @@ -20,11 +20,6 @@ Command-Line Arguments
:ref:`how-to-define-name-of-input-dataset` below for general guidelines
and specific restrictions.

--list_sub_file, --list-sub-file : @after
Examples:
`Single-session example <https://github.com/PennLINC/babs/blob/ba32e8fd2d6473466d3c33a1b17dfffc4438d541/notebooks/initial_sub_list_single-ses.csv>`_,
`Multi-session example <https://github.com/PennLINC/babs/blob/ba32e8fd2d6473466d3c33a1b17dfffc4438d541/notebooks/initial_sub_list_multi-ses.csv>`_.

--keep_if_failed, --keep-if-failed : @after
These words below somehow refuse to appear in the built docs...
Please refer to below section
Expand Down Expand Up @@ -86,7 +81,9 @@ How is the list of subjects (and sessions) determined?
A list of subjects (and sessions) will be determined when running ``babs-init``,
and will be saved in a CSV file called named ``sub_final_inclu.csv`` (for single-session dataset)
or ``sub_ses_final_inclu.csv`` (for multiple-session dataset),
located at ``/path/to/my_BABS_project/analysis/code``
located at ``/path/to/my_BABS_project/analysis/code``.

**To filter subjects and sessions**, use ``babs-init`` with ``--list-sub-file /path/to/subject/list/csv/file``. Examples: `Single-session example <https://github.com/PennLINC/babs/blob/ba32e8fd2d6473466d3c33a1b17dfffc4438d541/notebooks/initial_sub_list_single-ses.csv>`_, `Multi-session example <https://github.com/PennLINC/babs/blob/ba32e8fd2d6473466d3c33a1b17dfffc4438d541/notebooks/initial_sub_list_multi-ses.csv>`_.

See :ref:`list_included_subjects` for how this list is determined.

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2 changes: 1 addition & 1 deletion docs/source/preparation_config_yaml_file.rst
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Expand Up @@ -147,7 +147,7 @@ Basics - Manual of writing section ``singularity_run``

* See below :ref:`advanced_manual_singularity_run` --> bullet point regarding
``--bids-filter-file`` for explanations.
* See :ref:`babs-init` for examples of ``--list_sub_file``/``--list-sub-file`` to filter subjects and sessions.
* See :doc:`babs-init` for examples of ``--list_sub_file``/``--list-sub-file`` to filter subjects and sessions.

* :octicon:`alert-fill` :bdg-warning:`warning` Exception for positional arguments: if you have more than one input datasets,
you must use ``$INPUT_PATH`` to specify which dataset to use for the positional argument input BIDS dataset.
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