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, exact_scans, 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)

  • exact_scans (list of int, optional) – If used, this parameter will produce correlation matrices limited to each requested amount of time. If there is more than the required amount of low-motion data, then volumes will be randomly selected to produce denoised outputs with the exact amounts of time requested. If there is less than the required amount of ‘good’ data, then the run will not be post-processed.

  • 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.