📝 Update default config line numbers

FCP-INDI · Mar 15, 2021 · 2caae5c · 2caae5c
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diff --git a/docs/_sources/user/after_warp.rst b/docs/_sources/user/after_warp.rst
@@ -42,7 +42,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1161-1191
+   :lines: 1184-1214
 
 External Resources
 ^^^^^^^^^^^^^^^^^^

diff --git a/docs/_sources/user/alff.rst b/docs/_sources/user/alff.rst
@@ -44,7 +44,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1270-1280
+   :lines: 1290-1300
 
 References
 ^^^^^^^^^^

diff --git a/docs/_sources/user/anat.rst b/docs/_sources/user/anat.rst
@@ -28,6 +28,15 @@ Configuring CPAC to run initial preprocessing:
 
 #. **N4 Bias Field Correction - [On,Off]:** ANTs N4BiasFieldCorrection - a variant of the popular N3 (nonparametric nonuniform normalization) retrospective bias correction algorithm. Default is Off.
 
+Configuration Without the GUI
+""""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 197-209
+
 Configuring ACPC Alignment options:
 """"""""""""""""""""""""""""""""""""""
 **Note:** These options are pre-set for ACPC Alignment's default values. These do not need to be modified unless you are looking to optimize the results of ACPC alignment for your particular dataset.
@@ -38,6 +47,14 @@ Configuring ACPC Alignment options:
 #. **ACPC Aligned Skull Template - [path]:** Skull template to be used for ACPC alignment. It is not necessary to change this path unless you intend to use a non-standard template.
 #. **ACPC Aligned Brain Template - [path]:** Brain template to be used for ACPC alignment. For human data, it can be 'None'. It is not necessary to change this path unless you intend to use a non-standard template.
 
+Configuration Without the GUI
+""""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 197-198,207-226
 
 Skull-Stripping
 ^^^^^^^^^^^^^^^
@@ -62,6 +79,15 @@ Configuring CPAC to run Skull-Stripping:
 
 #. **Which tool for skull-stripping - [FSL, AFNI, niworkflows-ants]:** Choose if you’d like to use FSL BET, AFNI 3dSkullStrip, or run all options in parallel.
 
+Configuration Without the GUI
+""""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 197-198,228-232
+
 Configuring AFNI 3dSkullStrip options:
 """"""""""""""""""""""""""""""""""""""
 **Note:** These options are pre-set for AFNI 3dSkullStrip's default values. These do not need to be modified unless you are looking to optimize the results of skull-stripping for your particular dataset.
@@ -104,6 +130,15 @@ Configuring AFNI 3dSkullStrip options:
 
 #. **blur_fwhm - [2]:** Blur datasets after spatial normalization. Default value is 2.
 
+Configuration Without the GUI
+""""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 197-198,228-229,234-298
+
 Configuring FSL BET options:
 """"""""""""""""""""""""""""
 **Note:** These options are pre-set for FSL BET's default values. These do not need to be modified unless you are looking to optimize the results of skull-stripping for your particular dataset.
@@ -136,6 +171,15 @@ Configuring FSL BET options:
 
 #. **Robust brain center - [Off, On]:** Robust brain center estimation. Mutually exclusive with functional, reduce_bias, robust, padding, remove_eyes, surfaces.
 
+Configuration Without the GUI
+""""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 197-198,228-229,300-339
+
 Configuring niworkflows-ants options:
 """""""""""""""""""""""""""""""""""""
 **Note:** These templates are used during niworkflows-ants skull stripping. e.g. OASIS template can be downloaded `here <https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/3133832/Oasis.zip>`_.
@@ -148,6 +192,14 @@ Configuring niworkflows-ants options:
 
 #. **niworkflows_ants_regmask_path:** Set the brain extraction registration mask, used for registration to limit the metric computation to a specific region. e.g. OASIStemplate/T_template0_BrainCerebellumRegistrationMask.nii.gz
 
+Configuration Without the GUI
+""""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 197-198,228-229,346-358
 
 Anatomical Registration
 ^^^^^^^^^^^^^^^^^^^^^^^
@@ -194,7 +246,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 192-353
+   :lines: 482-600
 
 Anatomical Tissue Segmentation
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -298,7 +350,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 356-476
+   :lines: 361-479
 
 References
 ^^^^^^^^^^

diff --git a/docs/_sources/user/aroma_ica.rst b/docs/_sources/user/aroma_ica.rst
@@ -40,7 +40,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1024-1035
+   :lines: 1022-1033
 
 EXTERNAL RESOURCES:
 ^^^^^^^^^^^^^^^^^^^

diff --git a/docs/_sources/user/centrality.rst b/docs/_sources/user/centrality.rst
@@ -64,7 +64,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1326-1393
+   :lines: 1346-1413
 
 References
 ^^^^^^^^^^

diff --git a/docs/_sources/user/compute_config.rst b/docs/_sources/user/compute_config.rst
@@ -31,7 +31,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 10-11,76-131
+   :lines: 10-11,81-136
 
 Setting up SGE
 """""""""""""""

diff --git a/docs/_sources/user/func.rst b/docs/_sources/user/func.rst
@@ -38,8 +38,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 602-619,815-847,855-936
-
+   :lines: 602-606,609-610,615-619,815-936
 
 .. _motion_estimate_filter_valid_options:
 
@@ -84,7 +83,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 812-814,844-850
+   :lines: 815-816,848-853
 
 Through the Data Configuration
 """"""""""""""""""""""""""""""
@@ -170,7 +169,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 812-814,916-944
+   :lines: 815-816,938-965
 
 Functional to Anatomical Registration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -188,6 +187,15 @@ Functional to Anatomical Registration
 
 #. **Functional Masking - [AFNI, FSL, FSL_AFNI, Anatomical_Refined]:** Choose which tool to be used in functional masking - AFNI (3dAutoMask), FSL (BET), FSL_AFNI (BET+3dAutoMask) or Anatomical_Refined (generate functional mask by registering anatomical mask to functional space). Default is AFNI.
 
+Configuration Without the GUI
+"""""""""""""""""""""""""""""
+
+The following nested key/value pairs that will be set to these defaults if not defined in your :doc:`pipeline configuration YAML </user/pipelines/pipeline_config>`:
+
+.. literalinclude:: /references/default_pipeline.yml
+   :language: YAML
+   :lines: 482-483,602-614,621-635,815-816,967-971
+
 Configuring FSL BET options:
 """"""""""""""""""""""""""""
 
@@ -231,7 +239,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 479-480,599-631,812-813,946-998
+   :lines: 815-816,973-1014
 
 Functional to Template Registration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -264,4 +272,4 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 479-480,599-600,633-809
+   :lines: 482-483,602-603,636-812
diff --git a/docs/_sources/user/longitudinal.rst b/docs/_sources/user/longitudinal.rst
@@ -29,7 +29,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 157-189
+   :lines: 162-194
 
 References
 ^^^^^^^^^^

diff --git a/docs/_sources/user/nuisance.rst b/docs/_sources/user/nuisance.rst
@@ -136,7 +136,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1001-1158
+   :lines: 1022-1023,1035-1181
 
 An example of nuisance regressors
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/docs/_sources/user/output_config.rst b/docs/_sources/user/output_config.rst
@@ -38,4 +38,4 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 10-75,133-144
+   :lines: 10-80,138-149
diff --git a/docs/_sources/user/pypeer.rst b/docs/_sources/user/pypeer.rst
@@ -31,7 +31,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1398-1431
+   :lines: 1416-1451
 
 References
 ^^^^^^^^^^

diff --git a/docs/_sources/user/reho.rst b/docs/_sources/user/reho.rst
@@ -38,7 +38,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1283-1293
+   :lines: 1303-1313
 
 References
 ^^^^^^^^^^

diff --git a/docs/_sources/user/sca.rst b/docs/_sources/user/sca.rst
@@ -54,7 +54,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1245-1267
+   :lines: 1265-1287
 
 References
 ^^^^^^^^^^

diff --git a/docs/_sources/user/tse.rst b/docs/_sources/user/tse.rst
@@ -34,4 +34,4 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1194-1242
+   :lines: 1217-1262
diff --git a/docs/_sources/user/vmhc.rst b/docs/_sources/user/vmhc.rst
@@ -52,7 +52,7 @@ The following nested key/value pairs that will be set to these defaults if not d
 
 .. literalinclude:: /references/default_pipeline.yml
    :language: YAML
-   :lines: 1296-1323
+   :lines: 1316-1343
 
 References
 ^^^^^^^^^^