niworkflows.interfaces.plotting module

Visualization tools.

class niworkflows.interfaces.plotting.CompCorVariancePlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plot the number of components necessary to explain the specified levels of variance.

Mandatory Inputs:

metadata_files (a list of items which are a pathlike object or string representing an existing file) – List of files containing component metadata.

Optional Inputs:

  • metadata_sources (a list of items which are a string) – List of names of decompositions (e.g., aCompCor, tCompCor) yielding the arguments in metadata_files.

  • out_file (a pathlike object or string representing a file or None) – Path to save plot. (Nipype default value: None)

  • variance_thresholds (a tuple of the form: (a float, a float, a float)) – Levels of explained variance to include in plot. (Nipype default value: (0.5, 0.7, 0.9))

Outputs:

out_file (a pathlike object or string representing an existing file) – Path to saved plot.

class niworkflows.interfaces.plotting.ConfoundsCorrelationPlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plot the correlation among confound regressors.

Mandatory Inputs:

confounds_file (a pathlike object or string representing an existing file) – File containing confound regressors.

Optional Inputs:

  • columns (a list of items which are a string) – Filter out all regressors not found in this list.

  • ignore_initial_volumes (an integer) – Number of non-steady-state volumes at the beginning of the scan to ignore. (Nipype default value: 0)

  • max_dim (an integer) – Maximum number of regressors to include in plot. Regressors with highest magnitude of correlation with reference_column will be selected. (Nipype default value: 20)

  • out_file (a pathlike object or string representing a file or None) – Path to save plot. (Nipype default value: None)

  • reference_column (a string) – Column in the confound file for which all correlation magnitudes should be ranked and plotted. (Nipype default value: global_signal)

Outputs:

out_file (a pathlike object or string representing an existing file) – Path to saved plot.

class niworkflows.interfaces.plotting.FMRISummary(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Prepare an fMRI summary plot for the report.

Mandatory Inputs:

in_func (a pathlike object or string representing an existing file)

Optional Inputs:

  • drop_trs (an integer) – Dummy scans. (Nipype default value: 0)

  • dvars (a pathlike object or string representing an existing file)

  • fd (a pathlike object or string representing an existing file)

  • fd_thres (a float) – (Nipype default value: 0.2)

  • in_segm (a pathlike object or string representing an existing file)

  • in_spikes_bg (a pathlike object or string representing an existing file)

  • outliers (a pathlike object or string representing an existing file)

  • tr (a float or None) – The TR. (Nipype default value: None)

Outputs:

out_file (a pathlike object or string representing an existing file) – Written file path.