diff --git a/master/api/niworkflows-anat-ants-1.pdf b/master/api/niworkflows-anat-ants-1.pdf index 6d3aa0858c5..e4c516ab766 100644 Binary files a/master/api/niworkflows-anat-ants-1.pdf and b/master/api/niworkflows-anat-ants-1.pdf differ diff --git a/master/api/niworkflows-anat-ants-2.pdf b/master/api/niworkflows-anat-ants-2.pdf index bf850843229..d3051616ca0 100644 Binary files a/master/api/niworkflows-anat-ants-2.pdf and b/master/api/niworkflows-anat-ants-2.pdf differ diff --git a/master/api/niworkflows-anat-ants-3.pdf b/master/api/niworkflows-anat-ants-3.pdf index 0b5b02eab21..5af0996a421 100644 Binary files a/master/api/niworkflows-anat-ants-3.pdf and b/master/api/niworkflows-anat-ants-3.pdf differ diff --git a/master/api/niworkflows-anat-coregistration-1.pdf b/master/api/niworkflows-anat-coregistration-1.pdf index c51488029c9..e1d5a1ff375 100644 Binary files a/master/api/niworkflows-anat-coregistration-1.pdf and b/master/api/niworkflows-anat-coregistration-1.pdf differ diff --git a/master/api/niworkflows-anat-freesurfer-1.pdf b/master/api/niworkflows-anat-freesurfer-1.pdf index f9c39f636a9..aac654fa2fd 100644 Binary files a/master/api/niworkflows-anat-freesurfer-1.pdf and b/master/api/niworkflows-anat-freesurfer-1.pdf differ diff --git a/master/api/niworkflows-anat-skullstrip-1.pdf b/master/api/niworkflows-anat-skullstrip-1.pdf index ab4a340fa9f..33a22d38cfe 100644 Binary files a/master/api/niworkflows-anat-skullstrip-1.pdf and b/master/api/niworkflows-anat-skullstrip-1.pdf differ diff --git a/master/api/niworkflows-func-util-1.pdf b/master/api/niworkflows-func-util-1.pdf index 7a823aaa258..02effffd391 100644 Binary files a/master/api/niworkflows-func-util-1.pdf and b/master/api/niworkflows-func-util-1.pdf differ diff --git a/master/api/niworkflows-func-util-2.pdf b/master/api/niworkflows-func-util-2.pdf index 2da9492a365..2f4567d0e3a 100644 Binary files a/master/api/niworkflows-func-util-2.pdf and b/master/api/niworkflows-func-util-2.pdf differ diff --git a/master/api/niworkflows-func-util-3.pdf b/master/api/niworkflows-func-util-3.pdf index 5fd9d2f3af2..7c986fbe01a 100644 Binary files a/master/api/niworkflows-func-util-3.pdf and b/master/api/niworkflows-func-util-3.pdf differ diff --git a/master/api/niworkflows-workflows-epi-refmap-1.pdf b/master/api/niworkflows-workflows-epi-refmap-1.pdf index b1da0147125..58f9847a6e7 100644 Binary files a/master/api/niworkflows-workflows-epi-refmap-1.pdf and b/master/api/niworkflows-workflows-epi-refmap-1.pdf differ diff --git a/master/api/niworkflows.engine.workflows.html b/master/api/niworkflows.engine.workflows.html index 32dab5ff15a..8d0e10ffe91 100644 --- a/master/api/niworkflows.engine.workflows.html +++ b/master/api/niworkflows.engine.workflows.html @@ -343,7 +343,7 @@
class niworkflows.engine.workflows.LiterateWorkflow(name, base_dir=None)[source]
-

Bases: Workflow

+

Bases: Workflow

Controls the setup and execution of a pipeline of processes.

diff --git a/master/api/niworkflows.interfaces.confounds.html b/master/api/niworkflows.interfaces.confounds.html index 5f0342ede20..0fe07b7a1e2 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:

    @@ -474,13 +474,13 @@
    Returns:

    @@ -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 @@

    @@ -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:

    diff --git a/master/api/niworkflows.interfaces.fixes.html b/master/api/niworkflows.interfaces.fixes.html index 66a46dce528..41457e38a19 100644 --- a/master/api/niworkflows.interfaces.fixes.html +++ b/master/api/niworkflows.interfaces.fixes.html @@ -372,9 +372,9 @@ (Nipype default value: False)

  • input_image_type (0 or 1 or 2 or 3) – Option specifying the input image type of scalar (default), vector, tensor, or time series. Maps to a command-line argument: --input-image-type %d.

    • -

  • interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’) – Maps to a command-line argument: %s. +

  • interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’ or ‘GenericLabel’) – Maps to a command-line argument: %s. (Nipype default value: Linear)

    • -

  • interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float))

    • +

  • interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float) or a tuple of the form: (a string))

  • invert_transform_flags (a list of items which are a boolean)

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

    • diff --git a/master/api/niworkflows.interfaces.freesurfer.html b/master/api/niworkflows.interfaces.freesurfer.html index dbef196b933..c8673fdd8e3 100644 --- a/master/api/niworkflows.interfaces.freesurfer.html +++ b/master/api/niworkflows.interfaces.freesurfer.html @@ -947,7 +947,7 @@ Maps to a command-line argument: --fixtp.

  • in_intensity_scales (a list of items which are a pathlike object or string representing an existing file) – Use initial intensity scales. Maps to a command-line argument: --iscalein %s.

    • -

  • initial_timepoint (an integer) – Use TP# for spacial init (default random), 0: no init. +

  • initial_timepoint (an integer) – Use TP# for special init (default random), 0: no init. Maps to a command-line argument: --inittp %d.

  • initial_transforms (a list of items which are a pathlike object or string representing an existing file) – Use initial transforms (lta) on source. Maps to a command-line argument: --ixforms %s.

    • diff --git a/master/api/niworkflows.interfaces.header.html b/master/api/niworkflows.interfaces.header.html index 97aa1256478..a57c44543a0 100644 --- a/master/api/niworkflows.interfaces.header.html +++ b/master/api/niworkflows.interfaces.header.html @@ -373,7 +373,7 @@
    output_spec
    -

    alias of DynamicTraitedSpec

    +

    alias of DynamicTraitedSpec

    diff --git a/master/api/niworkflows.interfaces.itk.html b/master/api/niworkflows.interfaces.itk.html index d74b009e3ea..e08280207be 100644 --- a/master/api/niworkflows.interfaces.itk.html +++ b/master/api/niworkflows.interfaces.itk.html @@ -393,9 +393,9 @@ (Nipype default value: False)

  • input_image_type (0 or 1 or 2 or 3) – Option specifying the input image type of scalar (default), vector, tensor, or time series. Maps to a command-line argument: --input-image-type %d.

    • -

  • interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’) – Maps to a command-line argument: %s. +

  • interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’ or ‘GenericLabel’) – Maps to a command-line argument: %s. (Nipype default value: Linear)

    • -

  • interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float))

    • +

  • interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float) or a tuple of the form: (a string))

  • invert_transform_flags (a list of items which are a boolean)

  • num_threads (an integer) – Number of parallel processes. (Nipype default value: 1)

    • diff --git a/master/api/niworkflows.interfaces.patches.html b/master/api/niworkflows.interfaces.patches.html index 5bd3f642539..8e4a806db9e 100644 --- a/master/api/niworkflows.interfaces.patches.html +++ b/master/api/niworkflows.interfaces.patches.html @@ -382,7 +382,7 @@

  • norm (a pathlike object or string representing an existing file) – Normalized skull-stripped volume.

  • nu (a pathlike object or string representing an existing file) – Non-uniformity corrected whole-head volume.

  • orig (a pathlike object or string representing an existing file) – Base image conformed to Freesurfer space.

    • -

  • pial (a list of items which are a pathlike object or string representing an existing file) – Gray matter/pia mater surface meshes.

    • +

  • pial (a list of items which are a pathlike object or string representing an existing file) – Gray matter/pia matter surface meshes.

  • rawavg (a pathlike object or string representing an existing file) – Volume formed by averaging input images.

  • ribbon (a list of items which are a pathlike object or string representing an existing file) – Volumetric maps of cortical ribbons.

  • smoothwm (a list of items which are a pathlike object or string representing an existing file) – Smoothed original surface meshes.

    • diff --git a/master/api/niworkflows.interfaces.reportlets.masks.html b/master/api/niworkflows.interfaces.reportlets.masks.html index 799466fdf7e..6b390b5e8c0 100644 --- a/master/api/niworkflows.interfaces.reportlets.masks.html +++ b/master/api/niworkflows.interfaces.reportlets.masks.html @@ -434,7 +434,7 @@ (Nipype default value: report.svg)

  • outline (a boolean) – Create surface outline image. Maps to a command-line argument: -o.

    • -

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

    • +

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • padding (a boolean) – Improve BET if FOV is very small in Z (by temporarily padding end slices). Maps to a command-line argument: -Z. Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.

    • diff --git a/master/api/niworkflows.interfaces.reportlets.registration.html b/master/api/niworkflows.interfaces.reportlets.registration.html index 2a70a43a606..6c9d47c30c7 100644 --- a/master/api/niworkflows.interfaces.reportlets.registration.html +++ b/master/api/niworkflows.interfaces.reportlets.registration.html @@ -372,9 +372,9 @@ (Nipype default value: False)

  • input_image_type (0 or 1 or 2 or 3) – Option specifying the input image type of scalar (default), vector, tensor, or time series. Maps to a command-line argument: --input-image-type %d.

    • -

  • interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’) – Maps to a command-line argument: %s. +

  • interpolation (‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’ or ‘GenericLabel’) – Maps to a command-line argument: %s. (Nipype default value: Linear)

    • -

  • interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float))

    • +

  • interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float) or a tuple of the form: (a string))

  • invert_transform_flags (a list of items which are a boolean)

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

    • @@ -572,7 +572,7 @@ Maps to a command-line argument: --out=%s.

  • out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)

    • -

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

    • +

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • wm_seg (a pathlike object or string representing a file) – Reference white matter segmentation mask. Maps to a command-line argument: -wmseg %s.

    • @@ -670,7 +670,7 @@ Maps to a command-line argument: -omat %s (position: 3).

  • out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)

    • -

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

    • +

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.

  • pedir (an integer) – Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. @@ -874,7 +874,7 @@ Maps to a command-line argument: -omat %s (position: 3).

  • out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)

    • -

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

    • +

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • padding_size (an integer) – For applyxfm: interpolates outside image by size. Maps to a command-line argument: -paddingsize %d.

  • pedir (an integer) – Phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z. @@ -971,7 +971,7 @@ Maps to a command-line argument: --nokspace.

  • out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)

    • -

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

    • +

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • pava (a boolean) – Apply monotonic enforcement via PAVA. Maps to a command-line argument: --pava.

  • phase_conjugate (a boolean) – Apply phase conjugate method of unwarping. diff --git a/master/api/niworkflows.interfaces.reportlets.segmentation.html b/master/api/niworkflows.interfaces.reportlets.segmentation.html index a5e992ab987..40a3bfcaab3 100644 --- a/master/api/niworkflows.interfaces.reportlets.segmentation.html +++ b/master/api/niworkflows.interfaces.reportlets.segmentation.html @@ -391,7 +391,7 @@ Maps to a command-line argument: -B.

  • output_biasfield (a boolean) – Output estimated bias field. Maps to a command-line argument: -b.

    • -

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

    • +

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • probability_maps (a boolean) – Outputs individual probability maps. Maps to a command-line argument: -p.

  • segment_iters (1 <= an integer <= 50) – Number of segmentation-initialisation iterations. @@ -572,7 +572,7 @@ Maps to a command-line argument: --Ounmix.

  • out_white (a boolean) – Output whitening/dewhitening matrices. Maps to a command-line argument: --Owhite.

    • -

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

    • +

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

  • pbsc (a boolean) – Switch off conversion to percent BOLD signal change. Maps to a command-line argument: --pbsc.

  • rem_cmp (a list of items which are an integer) – Component numbers to remove. @@ -625,17 +625,27 @@

    Optional Inputs:
    Return type:
    -

    nipype.interfaces.base.support.InterfaceResult

    +

    nipype.interfaces.base.support.InterfaceResult

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[[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)": [[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, "-", "freesurfer"], [5, 0, 0, "-", "skullstrip"]], "niworkflows.anat.ants": [[2, 1, 1, "", "init_atropos_wf"], [2, 1, 1, "", "init_brain_extraction_wf"], [2, 1, 1, "", "init_n4_only_wf"]], "niworkflows.anat.coregistration": [[3, 1, 1, "", "compare_xforms"], [3, 1, 1, "", "init_bbreg_wf"]], "niworkflows.anat.freesurfer": [[4, 1, 1, "", "init_gifti_surface_wf"]], "niworkflows.anat.skullstrip": [[5, 1, 1, "", "afni_wf"]], "niworkflows.cli": [[7, 0, 0, "-", "boldref"]], "niworkflows.cli.boldref": [[7, 1, 1, "", "get_parser"], [7, 1, 1, "", "main"]], "niworkflows.data": [[8, 1, 1, "", "load"]], "niworkflows.data.load": [[8, 2, 1, "", "as_path"], [8, 2, 1, "", "cached"], [8, 2, 1, "", "readable"]], "niworkflows.engine": [[11, 0, 0, "-", "plugin"], [12, 0, 0, "-", "workflows"]], "niworkflows.engine.plugin": [[11, 3, 1, "", "DistributedPluginBase"], [11, 3, 1, "", "MultiProcPlugin"], [11, 3, 1, "", "PluginBase"], [11, 1, 1, "", "run_node"]], "niworkflows.engine.plugin.DistributedPluginBase": [[11, 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(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 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