diff --git a/docs/_sources/user/after_warp.rst b/docs/_sources/user/after_warp.rst index d73efec13..3f2127bbb 100644 --- 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 index 58847ad26..f72804971 100644 --- 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 index 5cf71f15b..a9d22feb0 100644 --- 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 `: + +.. 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 `: + +.. 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 `: + +.. 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 `: + +.. 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 `: + +.. 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 `_. @@ -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 `: + +.. 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 index 5c418e57f..cdf08785e 100644 --- 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 index 1c3dd4c5d..bbe422065 100644 --- 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 index ddeda45d1..af7192645 100644 --- 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 index 581b3c91b..5c51ac0db 100644 --- 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 `: + +.. 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 \ No newline at end of file diff --git a/docs/_sources/user/longitudinal.rst b/docs/_sources/user/longitudinal.rst index 21acc7b58..8259f7915 100644 --- 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 index 3dc6c1aca..784b55b63 100644 --- 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 index ac9222e51..cfbd4e867 100644 --- 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 index 9b1bebc1e..e0d8be6b2 100644 --- 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 index f30a8bdba..6175071de 100644 --- 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 index 9a4230f1c..f324db9e4 100644 --- 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 index 69500f611..ac567dab2 100644 --- 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 index fb1e0f722..b477bd5bd 100644 --- 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 ^^^^^^^^^^