diff --git a/master/_images/niworkflows-anat-ants-1.png b/master/_images/niworkflows-anat-ants-1.png index 40fe39e2da3..6368abf47a9 100644 Binary files a/master/_images/niworkflows-anat-ants-1.png and b/master/_images/niworkflows-anat-ants-1.png differ diff --git a/master/_images/niworkflows-anat-ants-2.png b/master/_images/niworkflows-anat-ants-2.png index f8019fd8b74..b01932bb059 100644 Binary files a/master/_images/niworkflows-anat-ants-2.png and b/master/_images/niworkflows-anat-ants-2.png differ diff --git a/master/_images/niworkflows-anat-ants-3.png b/master/_images/niworkflows-anat-ants-3.png index 7c24ad19eaa..910623a3c6b 100644 Binary files a/master/_images/niworkflows-anat-ants-3.png and b/master/_images/niworkflows-anat-ants-3.png differ diff --git a/master/_images/niworkflows-anat-coregistration-1.png b/master/_images/niworkflows-anat-coregistration-1.png index 54dba5b4182..9217884f1b9 100644 Binary files a/master/_images/niworkflows-anat-coregistration-1.png and b/master/_images/niworkflows-anat-coregistration-1.png differ diff --git a/master/_images/niworkflows-anat-freesurfer-1.png b/master/_images/niworkflows-anat-freesurfer-1.png index 70e0a569f5d..d815539318f 100644 Binary files a/master/_images/niworkflows-anat-freesurfer-1.png and b/master/_images/niworkflows-anat-freesurfer-1.png differ diff --git a/master/_images/niworkflows-anat-skullstrip-1.png b/master/_images/niworkflows-anat-skullstrip-1.png index 6f513bd034e..2fde4c718f6 100644 Binary files a/master/_images/niworkflows-anat-skullstrip-1.png and b/master/_images/niworkflows-anat-skullstrip-1.png differ diff --git a/master/_images/niworkflows-func-util-1.png b/master/_images/niworkflows-func-util-1.png index 01208ecd9c5..308a7e45243 100644 Binary files a/master/_images/niworkflows-func-util-1.png and b/master/_images/niworkflows-func-util-1.png differ diff --git a/master/_images/niworkflows-func-util-2.png b/master/_images/niworkflows-func-util-2.png index b9abe886da9..ed9d811ba65 100644 Binary files a/master/_images/niworkflows-func-util-2.png and b/master/_images/niworkflows-func-util-2.png differ diff --git a/master/_images/niworkflows-func-util-3.png b/master/_images/niworkflows-func-util-3.png index d3b3b4e8968..664c3b02cbf 100644 Binary files a/master/_images/niworkflows-func-util-3.png and b/master/_images/niworkflows-func-util-3.png differ diff --git a/master/_images/niworkflows-workflows-epi-refmap-1.png b/master/_images/niworkflows-workflows-epi-refmap-1.png index 3d6a5865eec..a9d899c65fa 100644 Binary files a/master/_images/niworkflows-workflows-epi-refmap-1.png and b/master/_images/niworkflows-workflows-epi-refmap-1.png differ diff --git a/master/_modules/niworkflows/interfaces/bids.html b/master/_modules/niworkflows/interfaces/bids.html index e9f40da2150..dc264df63d4 100644 --- a/master/_modules/niworkflows/interfaces/bids.html +++ b/master/_modules/niworkflows/interfaces/bids.html @@ -602,12 +602,13 @@

Source code for niworkflows.interfaces.bids

     _require_funcs = True
 
     def __init__(self, *args, **kwargs):
-        anat_only = kwargs.pop('anat_only')
+        anat_only = kwargs.pop('anat_only', None)
         anat_derivatives = kwargs.pop('anat_derivatives', None)
+        require_t1w = kwargs.pop('require_t1w', True)
         super().__init__(*args, **kwargs)
         if anat_only is not None:
             self._require_funcs = not anat_only
-        self._require_t1w = anat_derivatives is None
+        self._require_t1w = require_t1w and anat_derivatives is None
 
     def _run_interface(self, runtime):
         bids_dict = self.inputs.subject_data
diff --git a/master/_static/pygments.css b/master/_static/pygments.css
index 02b4b128127..c2e07c71e54 100644
--- a/master/_static/pygments.css
+++ b/master/_static/pygments.css
@@ -106,17 +106,17 @@ body[data-theme="dark"] .highlight .cp { color: #ff3a3a; font-weight: bold } /*
 body[data-theme="dark"] .highlight .cpf { color: #ababab; font-style: italic } /* Comment.PreprocFile */
 body[data-theme="dark"] .highlight .c1 { color: #ababab; font-style: italic } /* Comment.Single */
 body[data-theme="dark"] .highlight .cs { color: #e50808; font-weight: bold; background-color: #520000 } /* Comment.Special */
-body[data-theme="dark"] .highlight .gd { color: #ff3a3a } /* Generic.Deleted */
+body[data-theme="dark"] .highlight .gd { color: #d22323 } /* Generic.Deleted */
 body[data-theme="dark"] .highlight .ge { color: #d0d0d0; font-style: italic } /* Generic.Emph */
 body[data-theme="dark"] .highlight .ges { color: #d0d0d0; font-weight: bold; font-style: italic } /* Generic.EmphStrong */
-body[data-theme="dark"] .highlight .gr { color: #ff3a3a } /* Generic.Error */
+body[data-theme="dark"] .highlight .gr { color: #d22323 } /* Generic.Error */
 body[data-theme="dark"] .highlight .gh { color: #ffffff; font-weight: bold } /* Generic.Heading */
 body[data-theme="dark"] .highlight .gi { color: #589819 } /* Generic.Inserted */
 body[data-theme="dark"] .highlight .go { color: #cccccc } /* Generic.Output */
 body[data-theme="dark"] .highlight .gp { color: #aaaaaa } /* Generic.Prompt */
 body[data-theme="dark"] .highlight .gs { color: #d0d0d0; font-weight: bold } /* Generic.Strong */
 body[data-theme="dark"] .highlight .gu { color: #ffffff; text-decoration: underline } /* Generic.Subheading */
-body[data-theme="dark"] .highlight .gt { color: #ff3a3a } /* Generic.Traceback */
+body[data-theme="dark"] .highlight .gt { color: #d22323 } /* Generic.Traceback */
 body[data-theme="dark"] .highlight .kc { color: #6ebf26; font-weight: bold } /* Keyword.Constant */
 body[data-theme="dark"] .highlight .kd { color: #6ebf26; font-weight: bold } /* Keyword.Declaration */
 body[data-theme="dark"] .highlight .kn { color: #6ebf26; font-weight: bold } /* Keyword.Namespace */
@@ -192,17 +192,17 @@ body:not([data-theme="light"]) .highlight .cp { color: #ff3a3a; font-weight: bol
 body:not([data-theme="light"]) .highlight .cpf { color: #ababab; font-style: italic } /* Comment.PreprocFile */
 body:not([data-theme="light"]) .highlight .c1 { color: #ababab; font-style: italic } /* Comment.Single */
 body:not([data-theme="light"]) .highlight .cs { color: #e50808; font-weight: bold; background-color: #520000 } /* Comment.Special */
-body:not([data-theme="light"]) .highlight .gd { color: #ff3a3a } /* Generic.Deleted */
+body:not([data-theme="light"]) .highlight .gd { color: #d22323 } /* Generic.Deleted */
 body:not([data-theme="light"]) .highlight .ge { color: #d0d0d0; font-style: italic } /* Generic.Emph */
 body:not([data-theme="light"]) .highlight .ges { color: #d0d0d0; font-weight: bold; font-style: italic } /* Generic.EmphStrong */
-body:not([data-theme="light"]) .highlight .gr { color: #ff3a3a } /* Generic.Error */
+body:not([data-theme="light"]) .highlight .gr { color: #d22323 } /* Generic.Error */
 body:not([data-theme="light"]) .highlight .gh { color: #ffffff; font-weight: bold } /* Generic.Heading */
 body:not([data-theme="light"]) .highlight .gi { color: #589819 } /* Generic.Inserted */
 body:not([data-theme="light"]) .highlight .go { color: #cccccc } /* Generic.Output */
 body:not([data-theme="light"]) .highlight .gp { color: #aaaaaa } /* Generic.Prompt */
 body:not([data-theme="light"]) .highlight .gs { color: #d0d0d0; font-weight: bold } /* Generic.Strong */
 body:not([data-theme="light"]) .highlight .gu { color: #ffffff; text-decoration: underline } /* Generic.Subheading */
-body:not([data-theme="light"]) .highlight .gt { color: #ff3a3a } /* Generic.Traceback */
+body:not([data-theme="light"]) .highlight .gt { color: #d22323 } /* Generic.Traceback */
 body:not([data-theme="light"]) .highlight .kc { color: #6ebf26; font-weight: bold } /* Keyword.Constant */
 body:not([data-theme="light"]) .highlight .kd { color: #6ebf26; font-weight: bold } /* Keyword.Declaration */
 body:not([data-theme="light"]) .highlight .kn { color: #6ebf26; font-weight: bold } /* Keyword.Namespace */
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diff --git a/master/api/niworkflows-workflows-epi-refmap-1.pdf b/master/api/niworkflows-workflows-epi-refmap-1.pdf
index ceffb18c2b8..ec061537e96 100644
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index 3d6a5865eec..a9d899c65fa 100644
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diff --git a/master/api/niworkflows.data.html b/master/api/niworkflows.data.html
index d595b0cd3d0..46c70368ccb 100644
--- a/master/api/niworkflows.data.html
+++ b/master/api/niworkflows.data.html
@@ -371,7 +371,7 @@
 
 

 

-load.readable(*segments: str) → Traversable

+load.readable(*segments: str) → Traversable
 
Provide read access to a resource through a Path-like interface.

 
This file may or may not exist on the filesystem, and may be
 efficiently used for read operations, including directory traversal.

diff --git a/master/api/niworkflows.interfaces.confounds.html b/master/api/niworkflows.interfaces.confounds.html
index 84eaad2b5d8..d0d82544145 100644
--- a/master/api/niworkflows.interfaces.confounds.html
+++ b/master/api/niworkflows.interfaces.confounds.html
@@ -450,14 +450,14 @@
 indicates that the first and second exponential terms should be added.
 To retain the original terms, 1 must be included in the list.

 
  • variables (list of str) – List of variables for which exponential terms should be computed.
    • 
-
  • data (DataFrame) – Table of values of all observations of all variables.
    • 
+
  • data (DataFrame) – Table of values of all observations of all variables.
    • 
 
 
    
 
    Returns:
    
 
      
 
    • variables_exp (list) – A list of variables to include in the final data frame after adding
 the specified exponential terms.
      • 
-
    • data_exp (DataFrame) – Table of values of all observations of all variables, including any
+
    • data_exp (DataFrame) – Table of values of all observations of all variables, including any
 specified exponential terms.
      • 
 
    
 
    
@@ -474,13 +474,13 @@
 
      
 
    • expression (str) – Formula expression: either a single variable or a variable group
 paired with an operation (exponentiation or differentiation).
      • 
-
    • parent_data (DataFrame) – The source data for the model expansion.
      • 
+
    • parent_data (DataFrame) – The source data for the model expansion.
      • 
 
    
 
    
 
    Returns:
    
 
      
 
    • variables (list) – A list of variables in the provided formula expression.
      • 
-
    • data (DataFrame) – A tabulation of all terms in the provided formula expression.
      • 
+
    • data (DataFrame) – A tabulation of all terms in the provided formula expression.
      • 
 
    
 
    
 
    
@@ -524,7 +524,7 @@
 
    Temporal derivatives and exponential terms are computed for all terms
 in the grouping symbols that they adjoin.
    
 
-
  • parent_data (DataFrame) – A tabulation of all values usable in the model formula. Each additive
+
  • parent_data (DataFrame) – A tabulation of all values usable in the model formula. Each additive
 term in model_formula should correspond either to a variable in this
 data frame or to instructions for operating on a variable (for
 instance, computing temporal derivatives or exponential terms).
    • 
@@ -534,7 +534,7 @@
 
      
 
    • variables (list of str) – A list of variables included in the model parsed from the provided
 formula.
      • 
-
    • data (DataFrame) – All values in the complete model.
      • 
+
    • data (DataFrame) – All values in the complete model.
      • 
 
    
 
    
 
    
@@ -548,7 +548,7 @@
 
    
 
    Parameters:
    
 
      
-
    • data (DataFrame) – A tabulation of observations from which spike regressors should be
+
    • data (DataFrame) – A tabulation of observations from which spike regressors should be
 estimated.
      • 
 
    • criteria (dict of (str, '>' or '<' or float)) – Criteria for generating a spike regressor. If, for a given frame, the
 value of the variable corresponding to the key exceeds the threshold
@@ -575,7 +575,7 @@
 
      data – The input DataFrame with a column for each spike regressor.
      
 
      
 
      Return type:
      
-
      DataFrame
      
+
      DataFrame
      
 
      
 
    
 
    References
    
@@ -601,14 +601,14 @@
 To retain the original terms, 0 must be included in the list.
    
 
  • variables (list of str) – List of variables for which temporal derivative terms should be
 computed.
    • 
-
  • data (DataFrame) – Table of values of all observations of all variables.
    • 
+
  • data (DataFrame) – Table of values of all observations of all variables.
    • 
 
 
 
    Returns:
    
 
      
 
    • variables_deriv (list) – A list of variables to include in the final data frame after adding
 the specified derivative terms.
      • 
-
    • data_deriv (DataFrame) – Table of values of all observations of all variables, including any
+
    • data_deriv (DataFrame) – Table of values of all observations of all variables, including any
 specified derivative terms.
      • 
 
    
 
    
diff --git a/master/api/niworkflows.interfaces.nibabel.html b/master/api/niworkflows.interfaces.nibabel.html
index 61b171c3efc..1f401dae556 100644
--- a/master/api/niworkflows.interfaces.nibabel.html
+++ b/master/api/niworkflows.interfaces.nibabel.html
@@ -634,7 +634,7 @@
 
 
    
 
    
-niworkflows.interfaces.nibabel.reorient_file(in_file: str, *, target_file: str | None = None, target_ornt: str | None = None, newpath: str | None = None) → str[source]
    
+niworkflows.interfaces.nibabel.reorient_file(in_file: str, *, target_file: str = None, target_ornt: str = None, newpath: str = None) → str[source]
 
    Reorient an image.
    
 
    New orientation targets can be either another image, or a string representation of the
 orientation axis.
    
diff --git a/master/api/niworkflows.utils.spaces.html b/master/api/niworkflows.utils.spaces.html
index cc07fe9d67c..f96bee12207 100644
--- a/master/api/niworkflows.utils.spaces.html
+++ b/master/api/niworkflows.utils.spaces.html
@@ -372,7 +372,7 @@
 
 
    
 
    
-class niworkflows.utils.spaces.Reference(space: str | None = None, spec=NOTHING, standard: bool = False, dim: int = 3)[source]
    
+class niworkflows.utils.spaces.Reference(space: str = None, spec=NOTHING, standard: bool = False, dim: int = 3)[source]
 
    Bases: object
    
 
    Represent a (non)standard space specification.
    
 
    Examples
    
diff --git a/master/api/niworkflows.viz.html b/master/api/niworkflows.viz.html
index ab483eeedef..7c4b4152b3d 100644
--- a/master/api/niworkflows.viz.html
+++ b/master/api/niworkflows.viz.html
@@ -363,7 +363,7 @@
 
  • sort_rows (str or False or None) – Apply a clustering algorithm to reorganize the rows of the carpet.
 "", False, and None skip clustering sorting.
 "linkage" uses linkage hierarchical clustering
-scipy.cluster.hierarchy.linkage.
+scipy.cluster.hierarchy.linkage.
 Any other value that Python evaluates to True will use the
 default clustering, which is sklearn.cluster.ward_tree.
    • 
 
diff --git a/master/api/niworkflows.viz.plots.html b/master/api/niworkflows.viz.plots.html
index 2b5567a8be9..25379ec1701 100644
--- a/master/api/niworkflows.viz.plots.html
+++ b/master/api/niworkflows.viz.plots.html
@@ -516,7 +516,7 @@
 
  • sort_rows (str or False or None) – Apply a clustering algorithm to reorganize the rows of the carpet.
 "", False, and None skip clustering sorting.
 "linkage" uses linkage hierarchical clustering
-scipy.cluster.hierarchy.linkage.
+scipy.cluster.hierarchy.linkage.
 Any other value that Python evaluates to True will use the
 default clustering, which is sklearn.cluster.ward_tree.
    •