From beb704adbf684eb09ed8d40c5f4b76b2fade89d2 Mon Sep 17 00:00:00 2001 From: NiPreps Bot Date: Fri, 22 Nov 2024 17:33:45 +0000 Subject: [PATCH] docs(master): Update docs of development line --- .../niworkflows/interfaces/utility.html | 11 ++++------ master/_modules/niworkflows/viz/plots.html | 6 +++++- master/api/niworkflows-anat-ants-1.pdf | Bin 20450 -> 20450 bytes master/api/niworkflows-anat-ants-2.pdf | Bin 16179 -> 16179 bytes master/api/niworkflows-anat-ants-3.pdf | Bin 11748 -> 11748 bytes .../api/niworkflows-anat-coregistration-1.pdf | Bin 10523 -> 10523 bytes master/api/niworkflows-anat-freesurfer-1.pdf | Bin 13597 -> 13597 bytes master/api/niworkflows-anat-skullstrip-1.pdf | Bin 12656 -> 12656 bytes master/api/niworkflows-func-util-1.pdf | Bin 10183 -> 10183 bytes master/api/niworkflows-func-util-2.pdf | Bin 15599 -> 15599 bytes master/api/niworkflows-func-util-3.pdf | Bin 12276 -> 12276 bytes .../niworkflows-workflows-epi-refmap-1.pdf | Bin 9669 -> 9669 bytes .../api/niworkflows.interfaces.confounds.html | 20 +++++++++--------- .../api/niworkflows.interfaces.utility.html | 11 ++++------ master/searchindex.js | 2 +- 15 files changed, 24 insertions(+), 26 deletions(-) diff --git a/master/_modules/niworkflows/interfaces/utility.html b/master/_modules/niworkflows/interfaces/utility.html index b9589f98104..890d72faea8 100644 --- a/master/_modules/niworkflows/interfaces/utility.html +++ b/master/_modules/niworkflows/interfaces/utility.html @@ -588,8 +588,7 @@

Source code for niworkflows.interfaces.utility

>>> addheader.inputs.in_file = 'data.tsv' >>> addheader.inputs.columns = ['a', 'b', 'c', 'd', 'e'] >>> res = addheader.run() - >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True, - ... index_col=None) + >>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None) >>> df.columns.ravel().tolist() ['a', 'b', 'c', 'd', 'e'] @@ -651,7 +650,7 @@

Source code for niworkflows.interfaces.utility

>>> join.inputs.in_file = 'data.tsv' >>> join.inputs.join_file = 'add.tsv' >>> res = join.run() - >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True, + >>> df = pd.read_csv(res.outputs.out_file, sep='\s+', ... index_col=None, dtype=float, header=None) >>> df.columns.ravel().tolist() == list(range(5)) True @@ -668,8 +667,7 @@

Source code for niworkflows.interfaces.utility

>>> res = join.run() >>> res.outputs.out_file # doctest: +ELLIPSIS '...data_joined.tsv' - >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True, - ... index_col=None) + >>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None) >>> df.columns.ravel().tolist() ['a', 'b', 'c', 'd', 'e'] @@ -682,8 +680,7 @@

Source code for niworkflows.interfaces.utility

>>> join.inputs.side = 'left' >>> join.inputs.columns = ['a', 'b', 'c', 'd', 'e'] >>> res = join.run() - >>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True, - ... index_col=None) + >>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None) >>> df.columns.ravel().tolist() ['a', 'b', 'c', 'd', 'e'] diff --git a/master/_modules/niworkflows/viz/plots.html b/master/_modules/niworkflows/viz/plots.html index dc42aec1218..03934fabbed 100644 --- a/master/_modules/niworkflows/viz/plots.html +++ b/master/_modules/niworkflows/viz/plots.html @@ -1281,7 +1281,11 @@

Source code for niworkflows.viz.plots

     gs_descending = gs_descending[:max_dim]
     features = [p for p in corr.columns if p in gs_descending]
     corr = corr.loc[features, features]
-    np.fill_diagonal(corr.values, 0)
+
+    # Modifying in-place is no longer supported
+    corr_vals = corr.to_numpy(copy=True)
+    np.fill_diagonal(corr_vals, 0)
+    corr.iloc[:, :] = corr_vals
 
     if figure is None:
         plt.figure(figsize=(15, 5))
diff --git a/master/api/niworkflows-anat-ants-1.pdf b/master/api/niworkflows-anat-ants-1.pdf
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diff --git a/master/api/niworkflows-func-util-1.pdf b/master/api/niworkflows-func-util-1.pdf
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diff --git a/master/api/niworkflows-workflows-epi-refmap-1.pdf b/master/api/niworkflows-workflows-epi-refmap-1.pdf
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diff --git a/master/api/niworkflows.interfaces.confounds.html b/master/api/niworkflows.interfaces.confounds.html
index b2e778f1569..54d959d4e04 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.utility.html b/master/api/niworkflows.interfaces.utility.html
index 8e88f859ef6..3d8682d6214 100644
--- a/master/api/niworkflows.interfaces.utility.html
+++ b/master/api/niworkflows.interfaces.utility.html
@@ -354,8 +354,7 @@
 >>> addheader.inputs.in_file = 'data.tsv'
 >>> addheader.inputs.columns = ['a', 'b', 'c', 'd', 'e']
 >>> res = addheader.run()
->>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True,
-...                  index_col=None)
+>>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None)
 >>> df.columns.ravel().tolist()
 ['a', 'b', 'c', 'd', 'e']
    @@ -409,7 +408,7 @@ >>> join.inputs.in_file = 'data.tsv' >>> join.inputs.join_file = 'add.tsv' >>> res = join.run() ->>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True, +>>> df = pd.read_csv(res.outputs.out_file, sep='\s+', ... index_col=None, dtype=float, header=None) >>> df.columns.ravel().tolist() == list(range(5)) True @@ -427,8 +426,7 @@ >>> res = join.run() >>> res.outputs.out_file '...data_joined.tsv' ->>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True, -... index_col=None) +>>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None) >>> df.columns.ravel().tolist() ['a', 'b', 'c', 'd', 'e']
    @@ -443,8 +441,7 @@ >>> join.inputs.side = 'left' >>> join.inputs.columns = ['a', 'b', 'c', 'd', 'e'] >>> res = join.run() ->>> df = pd.read_csv(res.outputs.out_file, delim_whitespace=True, -... index_col=None) +>>> df = pd.read_csv(res.outputs.out_file, sep='\s+', index_col=None) >>> df.columns.ravel().tolist() ['a', 'b', 'c', 'd', 'e']
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false]], "generatecifti (class in niworkflows.interfaces.cifti)": [[18, "niworkflows.interfaces.cifti.GenerateCifti", false]], "generatesamplingreference (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.GenerateSamplingReference", false]], "get_fs_spaces() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_fs_spaces", false]], "get_gii_meta() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.get_gii_meta", false]], "get_metadata_for_nifti() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.get_metadata_for_nifti", false]], "get_nonstandard() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_nonstandard", false]], "get_parser() (in module niworkflows.cli.boldref)": [[7, "niworkflows.cli.boldref.get_parser", false]], "get_spaces() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_spaces", false]], "get_standard() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_standard", false]], "get_template_specs() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.get_template_specs", false]], "giftinamesource (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.GiftiNameSource", false]], "giftisetanatomicalstructure (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.GiftiSetAnatomicalStructure", false]], "giftitocsv (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.GiftiToCSV", false]], "group_multiecho() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.group_multiecho", false]], "grow_mask() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.grow_mask", false]], "hasspec() (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.hasspec", false]], "ica_aromarpt (class in niworkflows.interfaces.reportlets.segmentation)": [[38, "niworkflows.interfaces.reportlets.segmentation.ICA_AROMARPT", false]], "image_binary_dilation() (in module niworkflows.interfaces.morphology)": [[26, "niworkflows.interfaces.morphology.image_binary_dilation", false]], "index() (niworkflows.reports.core.report method)": [[44, "niworkflows.reports.core.Report.index", false]], "init_atropos_wf() (in module niworkflows.anat.ants)": [[2, "niworkflows.anat.ants.init_atropos_wf", false]], "init_bbreg_wf() (in module niworkflows.anat.coregistration)": [[3, "niworkflows.anat.coregistration.init_bbreg_wf", false]], "init_bold_reference_wf() (in module niworkflows.func.util)": [[14, "niworkflows.func.util.init_bold_reference_wf", false]], "init_brain_extraction_wf() (in module niworkflows.anat.ants)": [[2, "niworkflows.anat.ants.init_brain_extraction_wf", false]], "init_enhance_and_skullstrip_bold_wf() (in module niworkflows.func.util)": [[14, "niworkflows.func.util.init_enhance_and_skullstrip_bold_wf", false]], "init_epi_reference_wf() (in module niworkflows.workflows.epi.refmap)": [[60, "niworkflows.workflows.epi.refmap.init_epi_reference_wf", false]], "init_gifti_surface_wf() (in module niworkflows.anat.freesurfer)": [[4, "niworkflows.anat.freesurfer.init_gifti_surface_wf", false]], "init_layout() (niworkflows.reports.core.report method)": [[44, "niworkflows.reports.core.Report.init_layout", false]], "init_n4_only_wf() (in module niworkflows.anat.ants)": [[2, "niworkflows.anat.ants.init_n4_only_wf", false]], "init_skullstrip_bold_wf() (in module niworkflows.func.util)": [[14, "niworkflows.func.util.init_skullstrip_bold_wf", false]], "inject_skullstripped() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.inject_skullstripped", false]], "input_spec (niworkflows.interfaces.utility.keyselect attribute)": [[41, "niworkflows.interfaces.utility.KeySelect.input_spec", false]], "insert() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.insert", false]], "intensityclip (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.IntensityClip", false]], "intramodalmerge (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.IntraModalMerge", false]], "is_cached() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.is_cached", false]], "is_empty() (niworkflows.reports.core.reportlet method)": [[44, "niworkflows.reports.core.Reportlet.is_empty", false]], "is_interactive() (in module niworkflows.utils.debug)": [[48, "niworkflows.utils.debug.is_interactive", false]], "jointsvcolumns (class in niworkflows.interfaces.utility)": [[41, "niworkflows.interfaces.utility.JoinTSVColumns", false]], "keyselect (class in niworkflows.interfaces.utility)": [[41, "niworkflows.interfaces.utility.KeySelect", false]], "layout (niworkflows.interfaces.bids.readsidecarjson attribute)": [[16, "niworkflows.interfaces.bids.ReadSidecarJSON.layout", false]], "legacyname (niworkflows.utils.spaces.reference property)": [[51, "niworkflows.utils.spaces.Reference.legacyname", false]], "listify() (in module niworkflows.utils.connections)": [[47, "niworkflows.utils.connections.listify", false]], "literateworkflow (class in niworkflows.engine.workflows)": [[12, "niworkflows.engine.workflows.LiterateWorkflow", false]], "load() (in module niworkflows.data)": [[8, "niworkflows.data.load", false]], "load_transform() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.load_transform", false]], "lta_outputs (niworkflows.interfaces.freesurfer.patchedconcatenatelta attribute)": [[22, "niworkflows.interfaces.freesurfer.PatchedConcatenateLTA.lta_outputs", false]], "lta_outputs (niworkflows.interfaces.freesurfer.patchedltaconvert attribute)": [[22, "niworkflows.interfaces.freesurfer.PatchedLTAConvert.lta_outputs", false]], "lta_outputs (niworkflows.interfaces.freesurfer.patchedrobustregister attribute)": [[22, "niworkflows.interfaces.freesurfer.PatchedRobustRegister.lta_outputs", false]], "lta_outputs (niworkflows.interfaces.freesurfer.truncatelta attribute)": [[22, "niworkflows.interfaces.freesurfer.TruncateLTA.lta_outputs", false]], "main() (in module niworkflows.cli.boldref)": [[7, "niworkflows.cli.boldref.main", false]], "makemidthickness (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.MakeMidthickness", false]], "maplabels (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.MapLabels", false]], "mask() (in module niworkflows.interfaces.norm)": [[30, "niworkflows.interfaces.norm.mask", false]], "maskepi (class in niworkflows.interfaces.nilearn)": [[28, "niworkflows.interfaces.nilearn.MaskEPI", false]], "matchheader (class in niworkflows.interfaces.header)": [[23, "niworkflows.interfaces.header.MatchHeader", false]], "mcflirt2itk (class in niworkflows.interfaces.itk)": [[25, "niworkflows.interfaces.itk.MCFLIRT2ITK", false]], "medial_wall_to_nan() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.medial_wall_to_nan", false]], "medialnans (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.MedialNaNs", false]], "melodicrpt (class in niworkflows.interfaces.reportlets.segmentation)": [[38, "niworkflows.interfaces.reportlets.segmentation.MELODICRPT", false]], "merge (class in niworkflows.interfaces.nilearn)": [[28, "niworkflows.interfaces.nilearn.Merge", false]], "mergerois (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.MergeROIs", false]], "mergeseries (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.MergeSeries", false]], "metricdilate (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricDilate", false]], "metricfillholes (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricFillHoles", false]], "metricmask (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricMask", false]], "metricremoveislands (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricRemoveIslands", false]], "metricresample (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricResample", false]], "module": [[1, "module-niworkflows.anat", false], [2, "module-niworkflows.anat.ants", false], [3, "module-niworkflows.anat.coregistration", false], [4, "module-niworkflows.anat.freesurfer", false], [5, "module-niworkflows.anat.skullstrip", false], [6, "module-niworkflows.cli", false], [7, "module-niworkflows.cli.boldref", false], [8, "module-niworkflows.data", false], [9, "module-niworkflows.dwi", false], [10, "module-niworkflows.engine", false], [11, "module-niworkflows.engine.plugin", false], [12, "module-niworkflows.engine.workflows", false], [13, "module-niworkflows.func", false], [14, "module-niworkflows.func.util", false], [15, "module-niworkflows.interfaces", false], [16, "module-niworkflows.interfaces.bids", false], [17, "module-niworkflows.interfaces.bold", false], [18, "module-niworkflows.interfaces.cifti", false], [19, "module-niworkflows.interfaces.confounds", false], [20, "module-niworkflows.interfaces.conftest", false], [21, "module-niworkflows.interfaces.fixes", false], [22, "module-niworkflows.interfaces.freesurfer", false], [23, "module-niworkflows.interfaces.header", false], [24, "module-niworkflows.interfaces.images", false], [25, "module-niworkflows.interfaces.itk", false], [26, "module-niworkflows.interfaces.morphology", false], [27, "module-niworkflows.interfaces.nibabel", false], [28, "module-niworkflows.interfaces.nilearn", false], [29, "module-niworkflows.interfaces.nitransforms", false], [30, "module-niworkflows.interfaces.norm", false], [31, "module-niworkflows.interfaces.patches", false], [32, "module-niworkflows.interfaces.plotting", false], [33, "module-niworkflows.interfaces.probmaps", false], [34, "module-niworkflows.interfaces.reportlets", false], [35, "module-niworkflows.interfaces.reportlets.base", false], [36, "module-niworkflows.interfaces.reportlets.masks", false], [37, "module-niworkflows.interfaces.reportlets.registration", false], [38, "module-niworkflows.interfaces.reportlets.segmentation", false], [39, "module-niworkflows.interfaces.space", false], [40, "module-niworkflows.interfaces.surf", false], [41, "module-niworkflows.interfaces.utility", false], [42, "module-niworkflows.interfaces.workbench", false], [43, "module-niworkflows.reports", false], [44, "module-niworkflows.reports.core", false], [45, "module-niworkflows.utils", false], [46, "module-niworkflows.utils.bids", false], [47, "module-niworkflows.utils.connections", false], [48, "module-niworkflows.utils.debug", false], [49, "module-niworkflows.utils.images", false], [50, "module-niworkflows.utils.misc", false], [51, "module-niworkflows.utils.spaces", false], [52, "module-niworkflows.utils.testing", false], [53, "module-niworkflows.utils.timeseries", false], [54, "module-niworkflows.viz", false], [55, "module-niworkflows.viz.notebook", false], [56, "module-niworkflows.viz.plots", false], [57, "module-niworkflows.viz.utils", false], [58, "module-niworkflows.workflows", false], [59, "module-niworkflows.workflows.epi", false], [60, "module-niworkflows.workflows.epi.refmap", false]], "mri_info() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.mri_info", false]], "mricoregrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.MRICoregRPT", false]], "multiapplytransforms (class in niworkflows.interfaces.itk)": [[25, "niworkflows.interfaces.itk.MultiApplyTransforms", false]], "multiprocplugin (class in niworkflows.engine.plugin)": [[11, "niworkflows.engine.plugin.MultiProcPlugin", false]], "nii_ones_like() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.nii_ones_like", false]], "niworkflows.anat": [[1, "module-niworkflows.anat", false]], "niworkflows.anat.ants": [[2, "module-niworkflows.anat.ants", false]], "niworkflows.anat.coregistration": [[3, "module-niworkflows.anat.coregistration", false]], "niworkflows.anat.freesurfer": [[4, "module-niworkflows.anat.freesurfer", false]], "niworkflows.anat.skullstrip": [[5, "module-niworkflows.anat.skullstrip", false]], "niworkflows.cli": [[6, "module-niworkflows.cli", false]], "niworkflows.cli.boldref": [[7, "module-niworkflows.cli.boldref", false]], "niworkflows.data": [[8, "module-niworkflows.data", false]], "niworkflows.dwi": [[9, "module-niworkflows.dwi", false]], "niworkflows.engine": [[10, "module-niworkflows.engine", false]], "niworkflows.engine.plugin": [[11, "module-niworkflows.engine.plugin", false]], "niworkflows.engine.workflows": [[12, "module-niworkflows.engine.workflows", false]], "niworkflows.func": [[13, "module-niworkflows.func", false]], "niworkflows.func.util": [[14, "module-niworkflows.func.util", false]], "niworkflows.interfaces": [[15, "module-niworkflows.interfaces", false]], "niworkflows.interfaces.bids": [[16, "module-niworkflows.interfaces.bids", false]], "niworkflows.interfaces.bold": [[17, "module-niworkflows.interfaces.bold", false]], "niworkflows.interfaces.cifti": [[18, "module-niworkflows.interfaces.cifti", false]], "niworkflows.interfaces.confounds": [[19, "module-niworkflows.interfaces.confounds", false]], "niworkflows.interfaces.conftest": [[20, "module-niworkflows.interfaces.conftest", false]], "niworkflows.interfaces.fixes": [[21, "module-niworkflows.interfaces.fixes", false]], "niworkflows.interfaces.freesurfer": [[22, "module-niworkflows.interfaces.freesurfer", false]], "niworkflows.interfaces.header": [[23, "module-niworkflows.interfaces.header", false]], "niworkflows.interfaces.images": [[24, "module-niworkflows.interfaces.images", false]], "niworkflows.interfaces.itk": [[25, "module-niworkflows.interfaces.itk", false]], "niworkflows.interfaces.morphology": [[26, "module-niworkflows.interfaces.morphology", false]], "niworkflows.interfaces.nibabel": [[27, "module-niworkflows.interfaces.nibabel", false]], "niworkflows.interfaces.nilearn": [[28, "module-niworkflows.interfaces.nilearn", false]], "niworkflows.interfaces.nitransforms": [[29, "module-niworkflows.interfaces.nitransforms", false]], "niworkflows.interfaces.norm": [[30, "module-niworkflows.interfaces.norm", false]], "niworkflows.interfaces.patches": [[31, "module-niworkflows.interfaces.patches", false]], "niworkflows.interfaces.plotting": [[32, "module-niworkflows.interfaces.plotting", false]], "niworkflows.interfaces.probmaps": [[33, "module-niworkflows.interfaces.probmaps", false]], "niworkflows.interfaces.reportlets": [[34, "module-niworkflows.interfaces.reportlets", false]], "niworkflows.interfaces.reportlets.base": [[35, "module-niworkflows.interfaces.reportlets.base", false]], "niworkflows.interfaces.reportlets.masks": [[36, "module-niworkflows.interfaces.reportlets.masks", false]], "niworkflows.interfaces.reportlets.registration": [[37, "module-niworkflows.interfaces.reportlets.registration", false]], "niworkflows.interfaces.reportlets.segmentation": [[38, "module-niworkflows.interfaces.reportlets.segmentation", false]], "niworkflows.interfaces.space": [[39, "module-niworkflows.interfaces.space", false]], "niworkflows.interfaces.surf": [[40, "module-niworkflows.interfaces.surf", false]], "niworkflows.interfaces.utility": [[41, "module-niworkflows.interfaces.utility", false]], "niworkflows.interfaces.workbench": [[42, "module-niworkflows.interfaces.workbench", false]], "niworkflows.reports": [[43, "module-niworkflows.reports", false]], "niworkflows.reports.core": [[44, "module-niworkflows.reports.core", false]], "niworkflows.utils": [[45, "module-niworkflows.utils", false]], "niworkflows.utils.bids": [[46, "module-niworkflows.utils.bids", false]], "niworkflows.utils.connections": [[47, "module-niworkflows.utils.connections", false]], "niworkflows.utils.debug": [[48, "module-niworkflows.utils.debug", false]], "niworkflows.utils.images": [[49, "module-niworkflows.utils.images", false]], "niworkflows.utils.misc": [[50, "module-niworkflows.utils.misc", false]], "niworkflows.utils.spaces": [[51, "module-niworkflows.utils.spaces", false]], "niworkflows.utils.testing": [[52, "module-niworkflows.utils.testing", false]], "niworkflows.utils.timeseries": [[53, "module-niworkflows.utils.timeseries", false]], "niworkflows.viz": [[54, "module-niworkflows.viz", false]], "niworkflows.viz.notebook": [[55, "module-niworkflows.viz.notebook", false]], "niworkflows.viz.plots": [[56, "module-niworkflows.viz.plots", false]], "niworkflows.viz.utils": [[57, "module-niworkflows.viz.utils", false]], "niworkflows.workflows": [[58, "module-niworkflows.workflows", false]], "niworkflows.workflows.epi": [[59, "module-niworkflows.workflows.epi", false]], "niworkflows.workflows.epi.refmap": [[60, "module-niworkflows.workflows.epi.refmap", false]], "nonstandard_2d_references (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.NONSTANDARD_2D_REFERENCES", false]], "nonstandard_references (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.NONSTANDARD_REFERENCES", false]], "nonsteadystatesdetector (class in niworkflows.interfaces.bold)": [[17, "niworkflows.interfaces.bold.NonsteadyStatesDetector", false]], "normalize_surfs() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.normalize_surfs", false]], "normalize_xform() (in module niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.normalize_xform", false]], "normalizemotionparams (class in niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.NormalizeMotionParams", false]], "normalizesurf (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.NormalizeSurf", false]], "nskip (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.nskip", false]], "openmpcommandmixin (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.OpenMPCommandMixin", false]], "out_path_base (niworkflows.interfaces.bids.derivativesdatasink attribute)": [[16, "niworkflows.interfaces.bids.DerivativesDataSink.out_path_base", false]], "output_spec (niworkflows.interfaces.bids.bidsinfo attribute)": [[16, "niworkflows.interfaces.bids.BIDSInfo.output_spec", false]], "output_spec (niworkflows.interfaces.bids.readsidecarjson attribute)": [[16, "niworkflows.interfaces.bids.ReadSidecarJSON.output_spec", false]], "output_spec (niworkflows.interfaces.header.copyxform attribute)": [[23, "niworkflows.interfaces.header.CopyXForm.output_spec", false]], "output_spec (niworkflows.interfaces.surf.path2bids attribute)": [[40, "niworkflows.interfaces.surf.Path2BIDS.output_spec", false]], "output_spec (niworkflows.interfaces.utility.keyselect attribute)": [[41, "niworkflows.interfaces.utility.KeySelect.output_spec", false]], "outputreferencesaction (class in niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.OutputReferencesAction", false]], "overwrite_header() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.overwrite_header", false]], "paired_carpet (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.paired_carpet", false]], "parse_expression() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.parse_expression", false]], "parse_formula() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.parse_formula", false]], "patchedbbregisterrpt (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedBBRegisterRPT", false]], "patchedconcatenatelta (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedConcatenateLTA", false]], "patchedltaconvert (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedLTAConvert", false]], "patchedmricoregrpt (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedMRICoregRPT", false]], "patchedrobustregister (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedRobustRegister", false]], "path2bids (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.Path2BIDS", false]], "plot() (niworkflows.viz.plots.fmriplot method)": [[56, "niworkflows.viz.plots.fMRIPlot.plot", false]], "plot_carpet() (in module niworkflows.viz)": [[54, "niworkflows.viz.plot_carpet", false]], "plot_carpet() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.plot_carpet", false]], "plot_melodic_components() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.plot_melodic_components", false]], "plot_registration() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.plot_registration", false]], "plot_segs() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.plot_segs", false]], "pluginbase (class in niworkflows.engine.plugin)": [[11, "niworkflows.engine.plugin.PluginBase", false]], "ply2gii() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.ply2gii", false]], "plytogifti (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.PLYtoGifti", false]], "pointcloud2ply() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.pointcloud2ply", false]], "poissonrecon (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.PoissonRecon", false]], "pop_file() (in module niworkflows.utils.connections)": [[47, "niworkflows.utils.connections.pop_file", false]], "preparederivative (class in niworkflows.interfaces.bids)": [[16, "niworkflows.interfaces.bids.PrepareDerivative", false]], "read_crashfile() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.read_crashfile", false]], "readable() (niworkflows.data.load method)": [[8, "niworkflows.data.load.readable", false]], "readsidecarjson (class in niworkflows.interfaces.bids)": [[16, "niworkflows.interfaces.bids.ReadSidecarJSON", false]], "reconallrpt (class in niworkflows.interfaces.reportlets.segmentation)": [[38, "niworkflows.interfaces.reportlets.segmentation.ReconAllRPT", false]], "reference (class in niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.Reference", false]], "reference2dict() (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.reference2dict", false]], "references (niworkflows.utils.spaces.spatialreferences property)": [[51, "niworkflows.utils.spaces.SpatialReferences.references", false]], "refine_aseg() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.refine_aseg", false]], "refinebrainmask (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.RefineBrainMask", false]], "registrationrc (class in niworkflows.interfaces.reportlets.base)": [[35, "niworkflows.interfaces.reportlets.base.RegistrationRC", false]], "regridtozooms (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.RegridToZooms", false]], "regridtozooms (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.RegridToZooms", false]], "relative_to_root() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.relative_to_root", false]], "reorient() (in module niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.reorient", false]], "reorient_file() (in module niworkflows.interfaces.nibabel)": 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niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.robust_set_limits", false]], "robustacompcor (class in niworkflows.interfaces.patches)": [[31, "niworkflows.interfaces.patches.RobustACompCor", false]], "robustaverage (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.RobustAverage", false]], "robusttcompcor (class in niworkflows.interfaces.patches)": [[31, "niworkflows.interfaces.patches.RobustTCompCor", false]], "roisplot (class in niworkflows.interfaces.reportlets.masks)": [[36, "niworkflows.interfaces.reportlets.masks.ROIsPlot", false]], "rotate_affine() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.rotate_affine", false]], "rotation2canonical() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.rotation2canonical", false]], "run() (niworkflows.engine.plugin.distributedpluginbase method)": [[11, "niworkflows.engine.plugin.DistributedPluginBase.run", false]], "run() (niworkflows.engine.plugin.pluginbase method)": [[11, "niworkflows.engine.plugin.PluginBase.run", false]], "run() (niworkflows.interfaces.workbench.openmpcommandmixin method)": [[42, "niworkflows.interfaces.workbench.OpenMPCommandMixin.run", false]], "run_node() (in module niworkflows.engine.plugin)": [[11, "niworkflows.engine.plugin.run_node", false]], "run_reports() (in module niworkflows.reports.core)": [[44, "niworkflows.reports.core.run_reports", false]], "sanitizeimage (class in niworkflows.interfaces.header)": [[23, "niworkflows.interfaces.header.SanitizeImage", false]], "savederivative (class in niworkflows.interfaces.bids)": [[16, "niworkflows.interfaces.bids.SaveDerivative", false]], "segmentationrc (class in niworkflows.interfaces.reportlets.base)": [[35, "niworkflows.interfaces.reportlets.base.SegmentationRC", false]], "segments (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.segments", false]], "set_consumables() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.set_consumables", false]], "setup_exceptionhook() (in module niworkflows.utils.debug)": [[48, "niworkflows.utils.debug.setup_exceptionhook", false]], "signalextraction (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.SignalExtraction", false]], "simplebeforeafterrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.SimpleBeforeAfterRPT", false]], "simpleshowmaskrpt (class in niworkflows.interfaces.reportlets.masks)": [[36, "niworkflows.interfaces.reportlets.masks.SimpleShowMaskRPT", false]], "smallest (class in niworkflows.reports.core)": [[44, "niworkflows.reports.core.Smallest", false]], "sort_carpet (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.sort_carpet", false]], "space (niworkflows.utils.spaces.reference attribute)": [[51, "niworkflows.utils.spaces.Reference.space", false]], "spacedatasource (class in niworkflows.interfaces.space)": [[39, "niworkflows.interfaces.space.SpaceDataSource", false]], "spatialnormalization (class in niworkflows.interfaces.norm)": [[30, "niworkflows.interfaces.norm.SpatialNormalization", false]], "spatialnormalizationrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.SpatialNormalizationRPT", false]], "spatialreferences (class in niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.SpatialReferences", false]], "spec (niworkflows.utils.spaces.reference attribute)": [[51, "niworkflows.utils.spaces.Reference.spec", false]], "spike_regressors() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.spike_regressors", false]], "spikeregressors (class in niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.SpikeRegressors", false]], "spikes (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.spikes", false]], "spikesplot() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.spikesplot", false]], "spikesplot_cb() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.spikesplot_cb", false]], "splitext() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.splitext", false]], "splitseries (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.SplitSeries", false]], "standard (niworkflows.utils.spaces.reference attribute)": [[51, "niworkflows.utils.spaces.Reference.standard", false]], "standard_spaces (niworkflows.utils.spaces.spatialreferences attribute)": [[51, "niworkflows.utils.spaces.SpatialReferences.standard_spaces", false]], "structuralreference (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.StructuralReference", false]], "subreport (class in niworkflows.reports.core)": [[44, "niworkflows.reports.core.SubReport", false]], "surfacesegmentationrc (class in niworkflows.interfaces.reportlets.base)": [[35, "niworkflows.interfaces.reportlets.base.SurfaceSegmentationRC", false]], "surfacestopointcloud (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.SurfacesToPointCloud", false]], "svg2str() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.svg2str", false]], "svg_compress() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.svg_compress", false]], "tcompcorrpt (class in niworkflows.interfaces.reportlets.masks)": [[36, "niworkflows.interfaces.reportlets.masks.TCompCorRPT", false]], "templatedimensions (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.TemplateDimensions", false]], "temporal_derivatives() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.temporal_derivatives", false]], "timeseries (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.timeseries", false]], "to_json() (in module niworkflows.utils.testing)": [[52, "niworkflows.utils.testing.to_json", false]], "tpm2roi (class in niworkflows.interfaces.probmaps)": [[33, "niworkflows.interfaces.probmaps.TPM2ROI", false]], "tr (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.tr", false]], "transform_to_2d() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.transform_to_2d", false]], "truncatelta (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.TruncateLTA", false]], "tsv2json (class in niworkflows.interfaces.utility)": [[41, "niworkflows.interfaces.utility.TSV2JSON", false]], "unsafe_write_nifti_header_and_data() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.unsafe_write_nifti_header_and_data", false]], "unzipjoinedsurfaces (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.UnzipJoinedSurfaces", false]], "update_header_fields() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.update_header_fields", false]], "validateimage (class in niworkflows.interfaces.header)": [[23, "niworkflows.interfaces.header.ValidateImage", false]], "vertex_normals() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.vertex_normals", false]], "visit_desc() (niworkflows.engine.workflows.literateworkflow method)": [[12, "niworkflows.engine.workflows.LiterateWorkflow.visit_desc", false]], "volumetosurfacemapping (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.VolumeToSurfaceMapping", false]]}, "objects": {"niworkflows": [[1, 0, 0, "-", "anat"], [6, 0, 0, "-", "cli"], [8, 0, 0, "-", "data"], [9, 0, 0, "-", "dwi"], [10, 0, 0, "-", "engine"], [13, 0, 0, "-", "func"], [15, 0, 0, "-", "interfaces"], [43, 0, 0, "-", "reports"], [45, 0, 0, "-", "utils"], [54, 0, 0, "-", "viz"], [58, 0, 0, "-", "workflows"]], "niworkflows.anat": [[2, 0, 0, "-", "ants"], [3, 0, 0, "-", "coregistration"], [4, 0, 0, "-", 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2, 1, "", "run"]], "niworkflows.engine.plugin.PluginBase": [[11, 2, 1, "", "run"]], "niworkflows.engine.workflows": [[12, 3, 1, "", "LiterateWorkflow"]], "niworkflows.engine.workflows.LiterateWorkflow": [[12, 2, 1, "", "visit_desc"]], "niworkflows.func": [[14, 0, 0, "-", "util"]], "niworkflows.func.util": [[14, 1, 1, "", "init_bold_reference_wf"], [14, 1, 1, "", "init_enhance_and_skullstrip_bold_wf"], [14, 1, 1, "", "init_skullstrip_bold_wf"]], "niworkflows.interfaces": [[16, 0, 0, "-", "bids"], [17, 0, 0, "-", "bold"], [18, 0, 0, "-", "cifti"], [19, 0, 0, "-", "confounds"], [20, 0, 0, "-", "conftest"], [21, 0, 0, "-", "fixes"], [22, 0, 0, "-", "freesurfer"], [23, 0, 0, "-", "header"], [24, 0, 0, "-", "images"], [25, 0, 0, "-", "itk"], [26, 0, 0, "-", "morphology"], [27, 0, 0, "-", "nibabel"], [28, 0, 0, "-", "nilearn"], [29, 0, 0, "-", "nitransforms"], [30, 0, 0, "-", "norm"], [31, 0, 0, "-", "patches"], [32, 0, 0, "-", "plotting"], [33, 0, 0, "-", "probmaps"], [34, 0, 0, "-", 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"IntraModalMerge"], [24, 3, 1, "", "RegridToZooms"], [24, 3, 1, "", "RobustAverage"], [24, 3, 1, "", "SignalExtraction"], [24, 3, 1, "", "TemplateDimensions"], [24, 1, 1, "", "normalize_xform"], [24, 1, 1, "", "reorient"]], "niworkflows.interfaces.itk": [[25, 3, 1, "", "MCFLIRT2ITK"], [25, 3, 1, "", "MultiApplyTransforms"]], "niworkflows.interfaces.morphology": [[26, 3, 1, "", "BinaryDilation"], [26, 3, 1, "", "BinarySubtraction"], [26, 1, 1, "", "image_binary_dilation"]], "niworkflows.interfaces.nibabel": [[27, 3, 1, "", "ApplyMask"], [27, 3, 1, "", "Binarize"], [27, 3, 1, "", "BinaryDilation"], [27, 3, 1, "", "DemeanImage"], [27, 3, 1, "", "FilledImageLike"], [27, 3, 1, "", "GenerateSamplingReference"], [27, 3, 1, "", "IntensityClip"], [27, 3, 1, "", "MapLabels"], [27, 3, 1, "", "MergeROIs"], [27, 3, 1, "", "MergeSeries"], [27, 3, 1, "", "RegridToZooms"], [27, 3, 1, "", "ReorientImage"], [27, 3, 1, "", "SplitSeries"], [27, 1, 1, "", "reorient_file"], [27, 1, 1, "", 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niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.check_pipeline_version", false]], "check_space() (niworkflows.utils.spaces.spatialreferences static method)": [[51, "niworkflows.utils.spaces.SpatialReferences.check_space", false]], "checkpoint() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.checkpoint", false]], "cifti_surfaces_plot() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.cifti_surfaces_plot", false]], "ciftinamesource (class in niworkflows.interfaces.cifti)": [[18, "niworkflows.interfaces.cifti.CiftiNameSource", false]], "clean_directory() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.clean_directory", false]], "cmdline (niworkflows.interfaces.freesurfer.makemidthickness property)": [[22, "niworkflows.interfaces.freesurfer.MakeMidthickness.cmdline", false]], "cmdline (niworkflows.interfaces.freesurfer.structuralreference property)": [[22, "niworkflows.interfaces.freesurfer.StructuralReference.cmdline", false]], "collect_data() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.collect_data", false]], "collect_participants() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.collect_participants", false]], "combine_entities() (in module niworkflows.utils.testing)": [[52, "niworkflows.utils.testing.combine_entities", false]], "compare_xforms() (in module niworkflows.anat.coregistration)": [[3, "niworkflows.anat.coregistration.compare_xforms", false]], "compcor_variance_plot() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.compcor_variance_plot", false]], "compcorvarianceplot (class in niworkflows.interfaces.plotting)": [[32, "niworkflows.interfaces.plotting.CompCorVariancePlot", false]], "compose_view() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.compose_view", false]], "computeepimask (class in niworkflows.interfaces.nilearn)": [[28, "niworkflows.interfaces.nilearn.ComputeEPIMask", false]], "concatenate_xfms() (in module niworkflows.interfaces.nitransforms)": [[29, "niworkflows.interfaces.nitransforms.concatenate_xfms", false]], "concatenatexfms (class in niworkflows.interfaces.nitransforms)": [[29, "niworkflows.interfaces.nitransforms.ConcatenateXFMs", false]], "conform (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.Conform", false]], "confoundplot() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.confoundplot", false]], "confounds (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.confounds", false]], "confounds_correlation_plot() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.confounds_correlation_plot", false]], "confoundscorrelationplot (class in niworkflows.interfaces.plotting)": [[32, "niworkflows.interfaces.plotting.ConfoundsCorrelationPlot", false]], "copyheader (class in niworkflows.interfaces.header)": [[23, "niworkflows.interfaces.header.CopyHeader", false]], "copyxform (class in niworkflows.interfaces.header)": [[23, "niworkflows.interfaces.header.CopyXForm", false]], "create_cfm() (in module niworkflows.interfaces.norm)": [[30, "niworkflows.interfaces.norm.create_cfm", false]], "createsurfaceroi (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.CreateSurfaceROI", false]], "csvtogifti (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.CSVToGifti", false]], "cuts_from_bbox() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.cuts_from_bbox", false]], "data_dir() (in module niworkflows.interfaces.conftest)": [[20, "niworkflows.interfaces.conftest.data_dir", false]], "demean() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.demean", false]], "demeanimage (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.DemeanImage", false]], "derivativesdatasink (class in niworkflows.interfaces.bids)": [[16, "niworkflows.interfaces.bids.DerivativesDataSink", false]], "detect_inputs() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.detect_inputs", false]], "dictmerge (class in niworkflows.interfaces.utility)": [[41, "niworkflows.interfaces.utility.DictMerge", false]], "dim (niworkflows.utils.spaces.reference attribute)": [[51, "niworkflows.utils.spaces.Reference.dim", false]], "display() (in module niworkflows.viz.notebook)": [[55, "niworkflows.viz.notebook.display", false]], "distributedpluginbase (class in niworkflows.engine.plugin)": [[11, "niworkflows.engine.plugin.DistributedPluginBase", false]], "dseg_label() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.dseg_label", false]], "element (class in niworkflows.reports.core)": [[44, "niworkflows.reports.core.Element", false]], "expandmodel (class in niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.ExpandModel", false]], "exponential_terms() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.exponential_terms", false]], "extract_svg() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.extract_svg", false]], "fastrpt (class in niworkflows.interfaces.reportlets.segmentation)": [[38, "niworkflows.interfaces.reportlets.segmentation.FASTRPT", false]], "filledimagelike (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.FilledImageLike", false]], "fix_lta_length() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.fix_lta_length", false]], "fix_multi_t1w_source_name() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.fix_multi_T1w_source_name", false]], "fixheaderapplytransforms (class in niworkflows.interfaces.fixes)": [[21, "niworkflows.interfaces.fixes.FixHeaderApplyTransforms", false]], "fixheaderregistration (class in niworkflows.interfaces.fixes)": [[21, "niworkflows.interfaces.fixes.FixHeaderRegistration", false]], "fixn4biasfieldcorrection (class in niworkflows.interfaces.fixes)": [[21, "niworkflows.interfaces.fixes.FixN4BiasFieldCorrection", false]], "flirtrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.FLIRTRPT", false]], "fmriplot (class in niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.fMRIPlot", false]], "fmrisummary (class in niworkflows.interfaces.plotting)": [[32, "niworkflows.interfaces.plotting.FMRISummary", false]], "format_reference() (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.format_reference", false]], "freesurfersource (class in niworkflows.interfaces.patches)": [[31, "niworkflows.interfaces.patches.FreeSurferSource", false]], "from_string() (niworkflows.utils.spaces.reference class method)": [[51, "niworkflows.utils.spaces.Reference.from_string", false]], "fsaverage_density (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.FSAVERAGE_DENSITY", false]], "fsaverage_legacy (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.FSAVERAGE_LEGACY", false]], "fsdetectinputs (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.FSDetectInputs", false]], "fsinjectbrainextracted (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.FSInjectBrainExtracted", false]], "fuguerpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.FUGUERPT", false]], "fullname (niworkflows.utils.spaces.reference property)": [[51, "niworkflows.utils.spaces.Reference.fullname", false]], "generate_bids_skeleton() (in module niworkflows.utils.testing)": [[52, "niworkflows.utils.testing.generate_bids_skeleton", false]], "generate_report() (niworkflows.reports.core.report method)": [[44, "niworkflows.reports.core.Report.generate_report", false]], "generate_reports() (in module niworkflows.reports)": [[43, "niworkflows.reports.generate_reports", false]], "generate_reports() (in module niworkflows.reports.core)": [[44, "niworkflows.reports.core.generate_reports", false]], "generatecifti (class in niworkflows.interfaces.cifti)": [[18, "niworkflows.interfaces.cifti.GenerateCifti", false]], "generatesamplingreference (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.GenerateSamplingReference", false]], "get_fs_spaces() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_fs_spaces", false]], "get_gii_meta() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.get_gii_meta", false]], "get_metadata_for_nifti() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.get_metadata_for_nifti", false]], "get_nonstandard() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_nonstandard", false]], "get_parser() (in module niworkflows.cli.boldref)": [[7, "niworkflows.cli.boldref.get_parser", false]], "get_spaces() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_spaces", false]], "get_standard() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.get_standard", false]], "get_template_specs() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.get_template_specs", false]], "giftinamesource (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.GiftiNameSource", false]], "giftisetanatomicalstructure (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.GiftiSetAnatomicalStructure", false]], "giftitocsv (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.GiftiToCSV", false]], "group_multiecho() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.group_multiecho", false]], "grow_mask() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.grow_mask", false]], "hasspec() (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.hasspec", false]], "ica_aromarpt (class in niworkflows.interfaces.reportlets.segmentation)": [[38, "niworkflows.interfaces.reportlets.segmentation.ICA_AROMARPT", false]], "image_binary_dilation() (in module niworkflows.interfaces.morphology)": [[26, "niworkflows.interfaces.morphology.image_binary_dilation", false]], "index() (niworkflows.reports.core.report method)": [[44, "niworkflows.reports.core.Report.index", false]], "init_atropos_wf() (in module niworkflows.anat.ants)": [[2, "niworkflows.anat.ants.init_atropos_wf", false]], "init_bbreg_wf() (in module niworkflows.anat.coregistration)": [[3, "niworkflows.anat.coregistration.init_bbreg_wf", false]], "init_bold_reference_wf() (in module niworkflows.func.util)": [[14, "niworkflows.func.util.init_bold_reference_wf", false]], "init_brain_extraction_wf() (in module niworkflows.anat.ants)": [[2, "niworkflows.anat.ants.init_brain_extraction_wf", false]], "init_enhance_and_skullstrip_bold_wf() (in module niworkflows.func.util)": [[14, "niworkflows.func.util.init_enhance_and_skullstrip_bold_wf", false]], "init_epi_reference_wf() (in module niworkflows.workflows.epi.refmap)": [[60, "niworkflows.workflows.epi.refmap.init_epi_reference_wf", false]], "init_gifti_surface_wf() (in module niworkflows.anat.freesurfer)": [[4, "niworkflows.anat.freesurfer.init_gifti_surface_wf", false]], "init_layout() (niworkflows.reports.core.report method)": [[44, "niworkflows.reports.core.Report.init_layout", false]], "init_n4_only_wf() (in module niworkflows.anat.ants)": [[2, "niworkflows.anat.ants.init_n4_only_wf", false]], "init_skullstrip_bold_wf() (in module niworkflows.func.util)": [[14, "niworkflows.func.util.init_skullstrip_bold_wf", false]], "inject_skullstripped() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.inject_skullstripped", false]], "input_spec (niworkflows.interfaces.utility.keyselect attribute)": [[41, "niworkflows.interfaces.utility.KeySelect.input_spec", false]], "insert() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.insert", false]], "intensityclip (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.IntensityClip", false]], "intramodalmerge (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.IntraModalMerge", false]], "is_cached() (niworkflows.utils.spaces.spatialreferences method)": [[51, "niworkflows.utils.spaces.SpatialReferences.is_cached", false]], "is_empty() (niworkflows.reports.core.reportlet method)": [[44, "niworkflows.reports.core.Reportlet.is_empty", false]], "is_interactive() (in module niworkflows.utils.debug)": [[48, "niworkflows.utils.debug.is_interactive", false]], "jointsvcolumns (class in niworkflows.interfaces.utility)": [[41, "niworkflows.interfaces.utility.JoinTSVColumns", false]], "keyselect (class in niworkflows.interfaces.utility)": [[41, "niworkflows.interfaces.utility.KeySelect", false]], "layout (niworkflows.interfaces.bids.readsidecarjson attribute)": [[16, "niworkflows.interfaces.bids.ReadSidecarJSON.layout", false]], "legacyname (niworkflows.utils.spaces.reference property)": [[51, "niworkflows.utils.spaces.Reference.legacyname", false]], "listify() (in module niworkflows.utils.connections)": [[47, "niworkflows.utils.connections.listify", false]], "literateworkflow (class in niworkflows.engine.workflows)": [[12, "niworkflows.engine.workflows.LiterateWorkflow", false]], "load() (in module niworkflows.data)": [[8, "niworkflows.data.load", false]], "load_transform() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.load_transform", false]], "lta_outputs (niworkflows.interfaces.freesurfer.patchedconcatenatelta attribute)": [[22, "niworkflows.interfaces.freesurfer.PatchedConcatenateLTA.lta_outputs", false]], "lta_outputs (niworkflows.interfaces.freesurfer.patchedltaconvert attribute)": [[22, "niworkflows.interfaces.freesurfer.PatchedLTAConvert.lta_outputs", false]], "lta_outputs (niworkflows.interfaces.freesurfer.patchedrobustregister attribute)": [[22, "niworkflows.interfaces.freesurfer.PatchedRobustRegister.lta_outputs", false]], "lta_outputs (niworkflows.interfaces.freesurfer.truncatelta attribute)": [[22, "niworkflows.interfaces.freesurfer.TruncateLTA.lta_outputs", false]], "main() (in module niworkflows.cli.boldref)": [[7, "niworkflows.cli.boldref.main", false]], "makemidthickness (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.MakeMidthickness", false]], "maplabels (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.MapLabels", false]], "mask() (in module niworkflows.interfaces.norm)": [[30, "niworkflows.interfaces.norm.mask", false]], "maskepi (class in niworkflows.interfaces.nilearn)": [[28, "niworkflows.interfaces.nilearn.MaskEPI", false]], "matchheader (class in niworkflows.interfaces.header)": [[23, "niworkflows.interfaces.header.MatchHeader", false]], "mcflirt2itk (class in niworkflows.interfaces.itk)": [[25, "niworkflows.interfaces.itk.MCFLIRT2ITK", false]], "medial_wall_to_nan() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.medial_wall_to_nan", false]], "medialnans (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.MedialNaNs", false]], "melodicrpt (class in niworkflows.interfaces.reportlets.segmentation)": [[38, "niworkflows.interfaces.reportlets.segmentation.MELODICRPT", false]], "merge (class in niworkflows.interfaces.nilearn)": [[28, "niworkflows.interfaces.nilearn.Merge", false]], "mergerois (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.MergeROIs", false]], "mergeseries (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.MergeSeries", false]], "metricdilate (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricDilate", false]], "metricfillholes (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricFillHoles", false]], "metricmask (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricMask", false]], "metricremoveislands (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricRemoveIslands", false]], "metricresample (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.MetricResample", false]], "module": [[1, "module-niworkflows.anat", false], [2, "module-niworkflows.anat.ants", false], [3, "module-niworkflows.anat.coregistration", false], [4, "module-niworkflows.anat.freesurfer", false], [5, "module-niworkflows.anat.skullstrip", false], [6, "module-niworkflows.cli", false], [7, "module-niworkflows.cli.boldref", false], [8, "module-niworkflows.data", false], [9, "module-niworkflows.dwi", false], [10, "module-niworkflows.engine", false], [11, "module-niworkflows.engine.plugin", false], [12, "module-niworkflows.engine.workflows", false], [13, "module-niworkflows.func", false], [14, "module-niworkflows.func.util", false], [15, "module-niworkflows.interfaces", false], [16, "module-niworkflows.interfaces.bids", false], [17, "module-niworkflows.interfaces.bold", false], [18, "module-niworkflows.interfaces.cifti", false], [19, "module-niworkflows.interfaces.confounds", false], [20, "module-niworkflows.interfaces.conftest", false], [21, "module-niworkflows.interfaces.fixes", false], [22, "module-niworkflows.interfaces.freesurfer", false], [23, "module-niworkflows.interfaces.header", false], [24, "module-niworkflows.interfaces.images", false], [25, "module-niworkflows.interfaces.itk", false], [26, "module-niworkflows.interfaces.morphology", false], [27, "module-niworkflows.interfaces.nibabel", false], [28, "module-niworkflows.interfaces.nilearn", false], [29, "module-niworkflows.interfaces.nitransforms", false], [30, "module-niworkflows.interfaces.norm", false], [31, "module-niworkflows.interfaces.patches", false], [32, "module-niworkflows.interfaces.plotting", false], [33, "module-niworkflows.interfaces.probmaps", false], [34, "module-niworkflows.interfaces.reportlets", false], [35, "module-niworkflows.interfaces.reportlets.base", false], [36, "module-niworkflows.interfaces.reportlets.masks", false], [37, "module-niworkflows.interfaces.reportlets.registration", false], [38, "module-niworkflows.interfaces.reportlets.segmentation", false], [39, "module-niworkflows.interfaces.space", false], [40, "module-niworkflows.interfaces.surf", false], [41, "module-niworkflows.interfaces.utility", false], [42, "module-niworkflows.interfaces.workbench", false], [43, "module-niworkflows.reports", false], [44, "module-niworkflows.reports.core", false], [45, "module-niworkflows.utils", false], [46, "module-niworkflows.utils.bids", false], [47, "module-niworkflows.utils.connections", false], [48, "module-niworkflows.utils.debug", false], [49, "module-niworkflows.utils.images", false], [50, "module-niworkflows.utils.misc", false], [51, "module-niworkflows.utils.spaces", false], [52, "module-niworkflows.utils.testing", false], [53, "module-niworkflows.utils.timeseries", false], [54, "module-niworkflows.viz", false], [55, "module-niworkflows.viz.notebook", false], [56, "module-niworkflows.viz.plots", false], [57, "module-niworkflows.viz.utils", false], [58, "module-niworkflows.workflows", false], [59, "module-niworkflows.workflows.epi", false], [60, "module-niworkflows.workflows.epi.refmap", false]], "mri_info() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.mri_info", false]], "mricoregrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.MRICoregRPT", false]], "multiapplytransforms (class in niworkflows.interfaces.itk)": [[25, "niworkflows.interfaces.itk.MultiApplyTransforms", false]], "multiprocplugin (class in niworkflows.engine.plugin)": [[11, "niworkflows.engine.plugin.MultiProcPlugin", false]], "nii_ones_like() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.nii_ones_like", false]], "niworkflows.anat": [[1, "module-niworkflows.anat", false]], "niworkflows.anat.ants": [[2, "module-niworkflows.anat.ants", false]], "niworkflows.anat.coregistration": [[3, "module-niworkflows.anat.coregistration", false]], "niworkflows.anat.freesurfer": [[4, "module-niworkflows.anat.freesurfer", false]], "niworkflows.anat.skullstrip": [[5, "module-niworkflows.anat.skullstrip", false]], "niworkflows.cli": [[6, "module-niworkflows.cli", false]], "niworkflows.cli.boldref": [[7, "module-niworkflows.cli.boldref", false]], "niworkflows.data": [[8, "module-niworkflows.data", false]], "niworkflows.dwi": [[9, "module-niworkflows.dwi", false]], "niworkflows.engine": [[10, "module-niworkflows.engine", false]], "niworkflows.engine.plugin": [[11, "module-niworkflows.engine.plugin", false]], "niworkflows.engine.workflows": [[12, "module-niworkflows.engine.workflows", false]], "niworkflows.func": [[13, "module-niworkflows.func", false]], "niworkflows.func.util": [[14, "module-niworkflows.func.util", false]], "niworkflows.interfaces": [[15, "module-niworkflows.interfaces", false]], "niworkflows.interfaces.bids": [[16, "module-niworkflows.interfaces.bids", false]], "niworkflows.interfaces.bold": [[17, "module-niworkflows.interfaces.bold", false]], "niworkflows.interfaces.cifti": [[18, "module-niworkflows.interfaces.cifti", false]], "niworkflows.interfaces.confounds": [[19, "module-niworkflows.interfaces.confounds", false]], "niworkflows.interfaces.conftest": [[20, "module-niworkflows.interfaces.conftest", false]], "niworkflows.interfaces.fixes": [[21, "module-niworkflows.interfaces.fixes", false]], "niworkflows.interfaces.freesurfer": [[22, "module-niworkflows.interfaces.freesurfer", false]], "niworkflows.interfaces.header": [[23, "module-niworkflows.interfaces.header", false]], "niworkflows.interfaces.images": [[24, "module-niworkflows.interfaces.images", false]], "niworkflows.interfaces.itk": [[25, "module-niworkflows.interfaces.itk", false]], "niworkflows.interfaces.morphology": [[26, "module-niworkflows.interfaces.morphology", false]], "niworkflows.interfaces.nibabel": [[27, "module-niworkflows.interfaces.nibabel", false]], "niworkflows.interfaces.nilearn": [[28, "module-niworkflows.interfaces.nilearn", false]], "niworkflows.interfaces.nitransforms": [[29, "module-niworkflows.interfaces.nitransforms", false]], "niworkflows.interfaces.norm": [[30, "module-niworkflows.interfaces.norm", false]], "niworkflows.interfaces.patches": [[31, "module-niworkflows.interfaces.patches", false]], "niworkflows.interfaces.plotting": [[32, "module-niworkflows.interfaces.plotting", false]], "niworkflows.interfaces.probmaps": [[33, "module-niworkflows.interfaces.probmaps", false]], "niworkflows.interfaces.reportlets": [[34, "module-niworkflows.interfaces.reportlets", false]], "niworkflows.interfaces.reportlets.base": [[35, "module-niworkflows.interfaces.reportlets.base", false]], "niworkflows.interfaces.reportlets.masks": [[36, "module-niworkflows.interfaces.reportlets.masks", false]], "niworkflows.interfaces.reportlets.registration": [[37, "module-niworkflows.interfaces.reportlets.registration", false]], "niworkflows.interfaces.reportlets.segmentation": [[38, "module-niworkflows.interfaces.reportlets.segmentation", false]], "niworkflows.interfaces.space": [[39, "module-niworkflows.interfaces.space", false]], "niworkflows.interfaces.surf": [[40, "module-niworkflows.interfaces.surf", false]], "niworkflows.interfaces.utility": [[41, "module-niworkflows.interfaces.utility", false]], "niworkflows.interfaces.workbench": [[42, "module-niworkflows.interfaces.workbench", false]], "niworkflows.reports": [[43, "module-niworkflows.reports", false]], "niworkflows.reports.core": [[44, "module-niworkflows.reports.core", false]], "niworkflows.utils": [[45, "module-niworkflows.utils", false]], "niworkflows.utils.bids": [[46, "module-niworkflows.utils.bids", false]], "niworkflows.utils.connections": [[47, "module-niworkflows.utils.connections", false]], "niworkflows.utils.debug": [[48, "module-niworkflows.utils.debug", false]], "niworkflows.utils.images": [[49, "module-niworkflows.utils.images", false]], "niworkflows.utils.misc": [[50, "module-niworkflows.utils.misc", false]], "niworkflows.utils.spaces": [[51, "module-niworkflows.utils.spaces", false]], "niworkflows.utils.testing": [[52, "module-niworkflows.utils.testing", false]], "niworkflows.utils.timeseries": [[53, "module-niworkflows.utils.timeseries", false]], "niworkflows.viz": [[54, "module-niworkflows.viz", false]], "niworkflows.viz.notebook": [[55, "module-niworkflows.viz.notebook", false]], "niworkflows.viz.plots": [[56, "module-niworkflows.viz.plots", false]], "niworkflows.viz.utils": [[57, "module-niworkflows.viz.utils", false]], "niworkflows.workflows": [[58, "module-niworkflows.workflows", false]], "niworkflows.workflows.epi": [[59, "module-niworkflows.workflows.epi", false]], "niworkflows.workflows.epi.refmap": [[60, "module-niworkflows.workflows.epi.refmap", false]], "nonstandard_2d_references (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.NONSTANDARD_2D_REFERENCES", false]], "nonstandard_references (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.NONSTANDARD_REFERENCES", false]], "nonsteadystatesdetector (class in niworkflows.interfaces.bold)": [[17, "niworkflows.interfaces.bold.NonsteadyStatesDetector", false]], "normalize_surfs() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.normalize_surfs", false]], "normalize_xform() (in module niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.normalize_xform", false]], "normalizemotionparams (class in niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.NormalizeMotionParams", false]], "normalizesurf (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.NormalizeSurf", false]], "nskip (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.nskip", false]], "openmpcommandmixin (class in niworkflows.interfaces.workbench)": [[42, "niworkflows.interfaces.workbench.OpenMPCommandMixin", false]], "out_path_base (niworkflows.interfaces.bids.derivativesdatasink attribute)": [[16, "niworkflows.interfaces.bids.DerivativesDataSink.out_path_base", false]], "output_spec (niworkflows.interfaces.bids.bidsinfo attribute)": [[16, "niworkflows.interfaces.bids.BIDSInfo.output_spec", false]], "output_spec (niworkflows.interfaces.bids.readsidecarjson attribute)": [[16, "niworkflows.interfaces.bids.ReadSidecarJSON.output_spec", false]], "output_spec (niworkflows.interfaces.header.copyxform attribute)": [[23, "niworkflows.interfaces.header.CopyXForm.output_spec", false]], "output_spec (niworkflows.interfaces.surf.path2bids attribute)": [[40, "niworkflows.interfaces.surf.Path2BIDS.output_spec", false]], "output_spec (niworkflows.interfaces.utility.keyselect attribute)": [[41, "niworkflows.interfaces.utility.KeySelect.output_spec", false]], "outputreferencesaction (class in niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.OutputReferencesAction", false]], "overwrite_header() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.overwrite_header", false]], "paired_carpet (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.paired_carpet", false]], "parse_expression() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.parse_expression", false]], "parse_formula() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.parse_formula", false]], "patchedbbregisterrpt (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedBBRegisterRPT", false]], "patchedconcatenatelta (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedConcatenateLTA", false]], "patchedltaconvert (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedLTAConvert", false]], "patchedmricoregrpt (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedMRICoregRPT", false]], "patchedrobustregister (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.PatchedRobustRegister", false]], "path2bids (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.Path2BIDS", false]], "plot() (niworkflows.viz.plots.fmriplot method)": [[56, "niworkflows.viz.plots.fMRIPlot.plot", false]], "plot_carpet() (in module niworkflows.viz)": [[54, "niworkflows.viz.plot_carpet", false]], "plot_carpet() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.plot_carpet", false]], "plot_melodic_components() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.plot_melodic_components", false]], "plot_registration() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.plot_registration", false]], "plot_segs() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.plot_segs", false]], "pluginbase (class in niworkflows.engine.plugin)": [[11, "niworkflows.engine.plugin.PluginBase", false]], "ply2gii() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.ply2gii", false]], "plytogifti (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.PLYtoGifti", false]], "pointcloud2ply() (in module niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.pointcloud2ply", false]], "poissonrecon (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.PoissonRecon", false]], "pop_file() (in module niworkflows.utils.connections)": [[47, "niworkflows.utils.connections.pop_file", false]], "preparederivative (class in niworkflows.interfaces.bids)": [[16, "niworkflows.interfaces.bids.PrepareDerivative", false]], "read_crashfile() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.read_crashfile", false]], "readable() (niworkflows.data.load method)": [[8, "niworkflows.data.load.readable", false]], "readsidecarjson (class in niworkflows.interfaces.bids)": [[16, "niworkflows.interfaces.bids.ReadSidecarJSON", false]], "reconallrpt (class in niworkflows.interfaces.reportlets.segmentation)": [[38, "niworkflows.interfaces.reportlets.segmentation.ReconAllRPT", false]], "reference (class in niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.Reference", false]], "reference2dict() (in module niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.reference2dict", false]], "references (niworkflows.utils.spaces.spatialreferences property)": [[51, "niworkflows.utils.spaces.SpatialReferences.references", false]], "refine_aseg() (in module niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.refine_aseg", false]], "refinebrainmask (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.RefineBrainMask", false]], "registrationrc (class in niworkflows.interfaces.reportlets.base)": [[35, "niworkflows.interfaces.reportlets.base.RegistrationRC", false]], "regridtozooms (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.RegridToZooms", false]], "regridtozooms (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.RegridToZooms", false]], "relative_to_root() (in module niworkflows.utils.bids)": [[46, "niworkflows.utils.bids.relative_to_root", false]], "reorient() (in module niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.reorient", false]], "reorient_file() (in module niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.reorient_file", false]], "reorient_image() (in module niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.reorient_image", false]], "reorientimage (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.ReorientImage", false]], "report (class in niworkflows.reports.core)": [[44, "niworkflows.reports.core.Report", false]], "reportinginterface (class in niworkflows.interfaces.reportlets.base)": [[35, "niworkflows.interfaces.reportlets.base.ReportingInterface", false]], "reportlet (class in niworkflows.reports.core)": [[44, "niworkflows.reports.core.Reportlet", false]], "resample_by_spacing() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.resample_by_spacing", false]], "resamplebeforeafterrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.ResampleBeforeAfterRPT", false]], "robust_set_limits() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.robust_set_limits", false]], "robustacompcor (class in niworkflows.interfaces.patches)": [[31, "niworkflows.interfaces.patches.RobustACompCor", false]], "robustaverage (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.RobustAverage", false]], "robusttcompcor (class in niworkflows.interfaces.patches)": [[31, "niworkflows.interfaces.patches.RobustTCompCor", false]], "roisplot (class in niworkflows.interfaces.reportlets.masks)": [[36, "niworkflows.interfaces.reportlets.masks.ROIsPlot", false]], "rotate_affine() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.rotate_affine", false]], "rotation2canonical() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.rotation2canonical", false]], "run() (niworkflows.engine.plugin.distributedpluginbase method)": [[11, "niworkflows.engine.plugin.DistributedPluginBase.run", false]], "run() (niworkflows.engine.plugin.pluginbase method)": [[11, "niworkflows.engine.plugin.PluginBase.run", false]], "run() (niworkflows.interfaces.workbench.openmpcommandmixin method)": [[42, "niworkflows.interfaces.workbench.OpenMPCommandMixin.run", false]], "run_node() (in module niworkflows.engine.plugin)": [[11, "niworkflows.engine.plugin.run_node", false]], "run_reports() (in module niworkflows.reports.core)": [[44, "niworkflows.reports.core.run_reports", false]], "sanitizeimage (class in niworkflows.interfaces.header)": [[23, "niworkflows.interfaces.header.SanitizeImage", false]], "savederivative (class in niworkflows.interfaces.bids)": [[16, "niworkflows.interfaces.bids.SaveDerivative", false]], "segmentationrc (class in niworkflows.interfaces.reportlets.base)": [[35, "niworkflows.interfaces.reportlets.base.SegmentationRC", false]], "segments (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.segments", false]], "set_consumables() (in module niworkflows.utils.images)": [[49, "niworkflows.utils.images.set_consumables", false]], "setup_exceptionhook() (in module niworkflows.utils.debug)": [[48, "niworkflows.utils.debug.setup_exceptionhook", false]], "signalextraction (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.SignalExtraction", false]], "simplebeforeafterrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.SimpleBeforeAfterRPT", false]], "simpleshowmaskrpt (class in niworkflows.interfaces.reportlets.masks)": [[36, "niworkflows.interfaces.reportlets.masks.SimpleShowMaskRPT", false]], "smallest (class in niworkflows.reports.core)": [[44, "niworkflows.reports.core.Smallest", false]], "sort_carpet (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.sort_carpet", false]], "space (niworkflows.utils.spaces.reference attribute)": [[51, "niworkflows.utils.spaces.Reference.space", false]], "spacedatasource (class in niworkflows.interfaces.space)": [[39, "niworkflows.interfaces.space.SpaceDataSource", false]], "spatialnormalization (class in niworkflows.interfaces.norm)": [[30, "niworkflows.interfaces.norm.SpatialNormalization", false]], "spatialnormalizationrpt (class in niworkflows.interfaces.reportlets.registration)": [[37, "niworkflows.interfaces.reportlets.registration.SpatialNormalizationRPT", false]], "spatialreferences (class in niworkflows.utils.spaces)": [[51, "niworkflows.utils.spaces.SpatialReferences", false]], "spec (niworkflows.utils.spaces.reference attribute)": [[51, "niworkflows.utils.spaces.Reference.spec", false]], "spike_regressors() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.spike_regressors", false]], "spikeregressors (class in niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.SpikeRegressors", false]], "spikes (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.spikes", false]], "spikesplot() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.spikesplot", false]], "spikesplot_cb() (in module niworkflows.viz.plots)": [[56, "niworkflows.viz.plots.spikesplot_cb", false]], "splitext() (in module niworkflows.utils.misc)": [[50, "niworkflows.utils.misc.splitext", false]], "splitseries (class in niworkflows.interfaces.nibabel)": [[27, "niworkflows.interfaces.nibabel.SplitSeries", false]], "standard (niworkflows.utils.spaces.reference attribute)": [[51, "niworkflows.utils.spaces.Reference.standard", false]], "standard_spaces (niworkflows.utils.spaces.spatialreferences attribute)": [[51, "niworkflows.utils.spaces.SpatialReferences.standard_spaces", false]], "structuralreference (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.StructuralReference", false]], "subreport (class in niworkflows.reports.core)": [[44, "niworkflows.reports.core.SubReport", false]], "surfacesegmentationrc (class in niworkflows.interfaces.reportlets.base)": [[35, "niworkflows.interfaces.reportlets.base.SurfaceSegmentationRC", false]], "surfacestopointcloud (class in niworkflows.interfaces.surf)": [[40, "niworkflows.interfaces.surf.SurfacesToPointCloud", false]], "svg2str() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.svg2str", false]], "svg_compress() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.svg_compress", false]], "tcompcorrpt (class in niworkflows.interfaces.reportlets.masks)": [[36, "niworkflows.interfaces.reportlets.masks.TCompCorRPT", false]], "templatedimensions (class in niworkflows.interfaces.images)": [[24, "niworkflows.interfaces.images.TemplateDimensions", false]], "temporal_derivatives() (in module niworkflows.interfaces.confounds)": [[19, "niworkflows.interfaces.confounds.temporal_derivatives", false]], "timeseries (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.timeseries", false]], "to_json() (in module niworkflows.utils.testing)": [[52, "niworkflows.utils.testing.to_json", false]], "tpm2roi (class in niworkflows.interfaces.probmaps)": [[33, "niworkflows.interfaces.probmaps.TPM2ROI", false]], "tr (niworkflows.viz.plots.fmriplot attribute)": [[56, "niworkflows.viz.plots.fMRIPlot.tr", false]], "transform_to_2d() (in module niworkflows.viz.utils)": [[57, "niworkflows.viz.utils.transform_to_2d", false]], "truncatelta (class in niworkflows.interfaces.freesurfer)": [[22, "niworkflows.interfaces.freesurfer.TruncateLTA", false]], "tsv2json (class in niworkflows.interfaces.utility)": [[41, "niworkflows.interfaces.utility.TSV2JSON", false]], "unsafe_write_nifti_header_and_data() (in module niworkflows.utils.images)": 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