nipype.interfaces.nitime.analysis module

Interfaces to functionality from nitime for time-series analysis of fmri data

  • nitime.analysis.CoherenceAnalyzer: Coherence/y

  • nitime.fmri.io:

  • nitime.viz.drawmatrix_channels

CoherenceAnalyzer

Link to code

Bases: NitimeBaseInterface

Wraps nitime.analysis.CoherenceAnalyzer: Coherence/y

Optional Inputs:

  • NFFT (an integer >= 32) – This is the size of the window used for the spectral estimation. Use values between 32 and the number of samples in your time-series.(Defaults to 64.). (Nipype default value: 64)

  • TR (a float) – The TR used to collect the data in your csv file <in_file>.

  • figure_type (‘matrix’ or ‘network’) – The type of plot to generate, where ‘matrix’ denotes a matrix image and’network’ denotes a graph representation. Default: ‘matrix’. (Nipype default value: matrix)

  • frequency_range (a list of from 2 to 2 items which are any value) – The range of frequencies overwhich the analysis will average.[low,high] (Default [0.02,0.15]. (Nipype default value: [0.02, 0.15])

  • in_TS (any value) – A nitime TimeSeries object.

  • in_file (a pathlike object or string representing an existing file) – Csv file with ROIs on the columns and time-points on the rows. ROI names at the top row. Requires inputs: TR.

  • n_overlap (an integer >= 0) – The number of samples which overlapbetween subsequent windows.(Defaults to 0). (Nipype default value: 0)

  • output_csv_file (a pathlike object or string representing a file) – File to write outputs (coherence,time-delay) with file-names: file_name_{coherence,timedelay}.

  • output_figure_file (a pathlike object or string representing a file) – File to write output figures (coherence,time-delay) with file-names: file_name_{coherence,timedelay}. Possible formats: .png,.svg,.pdf,.jpg,…

Outputs:

  • coherence_array (an array) – The pairwise coherence values between the ROIs.

  • coherence_csv (a pathlike object or string representing a file) – A csv file containing the pairwise coherence values.

  • coherence_fig (a pathlike object or string representing a file) – Figure representing coherence values.

  • timedelay_array (an array) – The pairwise time delays between the ROIs (in seconds).

  • timedelay_csv (a pathlike object or string representing a file) – A csv file containing the pairwise time delay values.

  • timedelay_fig (a pathlike object or string representing a file) – Figure representing coherence values.