xcp_d.workflows.postprocessing.init_denoise_bold_wf

xcp_d.workflows.postprocessing.init_denoise_bold_wf(TR, low_pass, high_pass, bpf_order, bandpass_filter, smoothing, cifti, mem_gb, omp_nthreads, name='denoise_bold_wf')[source]

Denoise BOLD data.

Workflow Graph

(Source code)

Parameters:

  • TR (float) – Repetition time of the BOLD run, in seconds.

  • low_pass (float) – Upper cut-off frequency for the Butterworth bandpass filter, in Hertz. The bandpass filter is applied to the fMRI data after post-processing and denoising. Bandpass filtering will only be performed if bandpass_filter is True. This internal parameter corresponds to the command-line parameter --upper-bpf. If set to <= 0, low-pass filtering will be disabled.

    Default value is 0.08.

  • high_pass (float) – Lower cut-off frequency for the Butterworth bandpass filter, in Hertz. The bandpass filter is applied to the fMRI data after post-processing and denoising. Bandpass filtering will only be performed if bandpass_filter is True. This internal parameter corresponds to the command-line parameter --lower-bpf. If set to <= 0, high-pass filtering will be disabled.

    Default value is 0.01.

  • bpf_order (int) – Number of filter coefficients for Butterworth bandpass filter. Bandpass filtering will only be performed if bandpass_filter is True. This parameter is used in conjunction with lower_bpf/high_pass and upper_bpf/low_pass.

  • bandpass_filter (bool) – If True, a Butterworth bandpass filter will be applied to the fMRI data after interpolation, but before regression. If False, bandpass filtering will not be performed.

  • smoothing (float) – The full width at half maximum (FWHM), in millimeters, of the Gaussian smoothing kernel that will be applied to the post-processed and denoised data. ALFF and ReHo outputs will also be smoothing with this kernel.

  • cifti (bool) – Post-process surface data (CIFTIs) instead of volumetric data (NIFTIs). This parameter is overridden when DCAN- or HCP-format data are provided. Default is False.

  • mem_gb (float) – Memory limit, in gigabytes.

  • omp_nthreads (int) – Maximum number of threads an individual process may use.

  • name (str, optional) – Name of the workflow. This is used for working directories and workflow graphs. Default is “denoise_bold_wf”.

Inputs:

  • preprocessed_bold

  • temporal_mask (str) – Temporal mask; all values above fd_thresh set to 1. This is a TSV file with one column: ‘framewise_displacement’.

  • mask

  • confounds_file

Outputs:

  • uncensored_denoised_bold (str) – Path to the uncensored, denoised BOLD file. This file is the result of denoising the full (uncensored) preprocessed BOLD data using betas estimated using the censored BOLD data and nuisance regressors.

    This output should not be used for analysis. It is primarily used for DCAN QC plots.

  • interpolated_filtered_bold (str) – Path to the censored, denoised, interpolated, and filtered BOLD file. This file is the result of denoising the censored preprocessed BOLD data, followed by cubic spline interpolation and band-pass filtering.

    This output should not be used for analysis. It is primarily for DCAN QC plots.

  • censored_denoised_bold (str) – Path to the censored, denoised, interpolated, filtered, and re-censored BOLD file. This file is the result of denoising the censored preprocessed BOLD data, followed by cubic spline interpolation, band-pass filtering, and re-censoring.

    This output is the primary derivative for analysis.

  • smoothed_denoised_bold (str) – Path to the censored, denoised, interpolated, filtered, re-censored, and smoothed BOLD file. This file is the result of denoising the censored preprocessed BOLD data, followed by cubic spline interpolation, band-pass filtering, re-censoring, and spatial smoothing.