From 279fc4e0a3e92bb9ee66b5f6cdcbf54a5af18286 Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 11:21:27 -0400 Subject: [PATCH 1/3] Update babs-init.rst to include examples of --list_sub_file --- docs/source/babs-init.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/source/babs-init.rst b/docs/source/babs-init.rst index 394d52ee..0bce67e8 100644 --- a/docs/source/babs-init.rst +++ b/docs/source/babs-init.rst @@ -20,6 +20,11 @@ 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 `_, + `Multi-session example `_. + --keep_if_failed, --keep-if-failed : @after These words below somehow refuse to appear in the built docs... Please refer to below section From 7297ffe980da0bdcd00e39b85a5adaa50893fbae Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 11:38:36 -0400 Subject: [PATCH 2/3] Update preparation_config_yaml_file.rst to include --list_sub_file example --- docs/source/preparation_config_yaml_file.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/preparation_config_yaml_file.rst b/docs/source/preparation_config_yaml_file.rst index 1cc756fa..6278e73a 100644 --- a/docs/source/preparation_config_yaml_file.rst +++ b/docs/source/preparation_config_yaml_file.rst @@ -147,6 +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``. * :octicon:`alert-fill` :bdg-warning:`warning` Exception for positional arguments: if you have more than one input datasets, you must use ``$INPUT_PATH`` to specify which dataset to use for the positional argument input BIDS dataset. From 00ca7a255f8d5d1dbaada5db2dba0e744ba7379d Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 11:44:32 -0400 Subject: [PATCH 3/3] Update preparation_config_yaml_file.rst --- docs/source/preparation_config_yaml_file.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/preparation_config_yaml_file.rst b/docs/source/preparation_config_yaml_file.rst index 6278e73a..2fcd5cd9 100644 --- a/docs/source/preparation_config_yaml_file.rst +++ b/docs/source/preparation_config_yaml_file.rst @@ -147,7 +147,7 @@ Basics - Manual of writing section ``singularity_run`` * See below :ref:`advanced_manual_singularity_run` --> bullet point regarding ``--bids-filter-file`` for explanations. - * See :ref:`babs-init` for examples of ``--list_sub_file``/``--list-sub-file``. + * See :ref:`babs-init` for examples of ``--list_sub_file``/``--list-sub-file`` to filter subjects and sessions. * :octicon:`alert-fill` :bdg-warning:`warning` Exception for positional arguments: if you have more than one input datasets, you must use ``$INPUT_PATH`` to specify which dataset to use for the positional argument input BIDS dataset.