xcp_d.workflows.bold.outputs module

Workflows for collecting and saving functional outputs.

xcp_d.workflows.bold.outputs.init_postproc_derivatives_wf(name_source, source_metadata, has_multiple_runs, name='postproc_derivatives_wf')[source]

Write out the xcp_d derivatives in BIDS format.

Workflow Graph
../_images/xcp_d-workflows-bold-outputs-1.png

(Source code, png, svg, pdf)

Parameters:

  • name_source (str) – bold or cifti files

  • source_metadata (dict)

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

Inputs:

  • atlas_files

  • timeseries (list of str) – List of paths to atlas-specific time series TSV files. These time series are produced from the censored_denoised_bold outputs.

  • correlations (list of str) – List of paths to atlas-specific ROI-to-ROI correlation TSV files. These correlations are produced from the timeseries outputs.

  • coverage (list of str) – List of paths to atlas-specific coverage TSV files.

  • timeseries_ciftis (list of str) – List of paths to atlas-specific time series CIFTI (ptseries) files. These time series are produced from the censored_denoised_bold outputs.

  • correlation_ciftis (list of str) – List of paths to atlas-specific ROI-to-ROI correlation CIFTI (pconn) files. These correlations are produced from the timeseries_cifti outputs.

  • coverage_ciftis (list of str) – List of paths to atlas-specific coverage CIFTI (pscalar) files.

  • qc_file – LINC-style quality control file

  • denoised_bold

  • smoothed_denoised_bold

  • alff – alff nifti

  • parcellated_alff

  • smoothed_alff – smoothed alff

  • reho

  • parcellated_reho

  • confounds_tsv

  • confounds_metadata

  • motion_file

  • motion_metadata

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

  • temporal_mask_metadata

  • dummy_scans (int or “auto”) – Number of volumes to remove from the beginning of each run. If set to ‘auto’, xcp_d will extract non-steady-state volume indices from the preprocessing derivatives’ confounds file.