From ff24a3a2eb5477787c5c0a4ad58979f1649d0091 Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 16:16:22 -0400 Subject: [PATCH 1/5] Update babs-init.rst Previous edits weren't rendered. --- docs/source/babs-init.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/babs-init.rst b/docs/source/babs-init.rst index 0bce67e..657b55d 100644 --- a/docs/source/babs-init.rst +++ b/docs/source/babs-init.rst @@ -21,6 +21,7 @@ Command-Line Arguments and specific restrictions. --list_sub_file, --list-sub-file : @after + Examples: `Single-session example `_, `Multi-session example `_. From 6b891cb87908206f8f556956e4829bb0403c0f2f Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 16:19:45 -0400 Subject: [PATCH 2/5] 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 2fcd5cd..e04c2de 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`` 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. From c2faf983a120125988042d66646e113054d1b13a Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 16:23:27 -0400 Subject: [PATCH 3/5] Update babs-init.rst --- docs/source/babs-init.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/babs-init.rst b/docs/source/babs-init.rst index 657b55d..ca99b23 100644 --- a/docs/source/babs-init.rst +++ b/docs/source/babs-init.rst @@ -21,7 +21,7 @@ Command-Line Arguments and specific restrictions. --list_sub_file, --list-sub-file : @after - + Add this to test if txt below will be rendered. Examples: `Single-session example `_, `Multi-session example `_. From 844a37d6a8268cc9f7baecf6d81aa6d558fa87ac Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 16:36:24 -0400 Subject: [PATCH 4/5] Update babs-init.rst --- docs/source/babs-init.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/babs-init.rst b/docs/source/babs-init.rst index ca99b23..f307f13 100644 --- a/docs/source/babs-init.rst +++ b/docs/source/babs-init.rst @@ -21,7 +21,8 @@ Command-Line Arguments and specific restrictions. --list_sub_file, --list-sub-file : @after - Add this to test if txt below will be rendered. + Add this to test if txt below will be rendered... + Please render. Examples: `Single-session example `_, `Multi-session example `_. From c4188705a49e101ade1406f8922c6eef2bafccf8 Mon Sep 17 00:00:00 2001 From: Tien Tong <35613222+tientong98@users.noreply.github.com> Date: Fri, 18 Oct 2024 16:56:37 -0400 Subject: [PATCH 5/5] Update babs-init.rst --- docs/source/babs-init.rst | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/docs/source/babs-init.rst b/docs/source/babs-init.rst index f307f13..f5841c1 100644 --- a/docs/source/babs-init.rst +++ b/docs/source/babs-init.rst @@ -20,13 +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 - Add this to test if txt below will be rendered... - Please render. - 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 @@ -88,7 +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 `_, `Multi-session example `_. See :ref:`list_included_subjects` for how this list is determined.