xcp_d.workflows.outputs module

Workflows for collecting and saving xcp_d outputs.

xcp_d.workflows.outputs.init_copy_inputs_to_outputs_wf(name='copy_inputs_to_outputs_wf')[source]

Copy files from the preprocessing derivatives to the output folder, with no modifications.

Workflow Graph

(Source code)

Parameters:

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

Inputs:

  • lh_pial_surf

  • rh_pial_surf

  • lh_wm_surf

  • rh_wm_surf

  • sulcal_depth

  • sulcal_curv

  • cortical_thickness

  • cortical_thickness_corr

  • myelin

  • myelin_smoothed

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

Write out the xcp_d derivatives in BIDS format.

Workflow Graph

(Source code)

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.

  • custom_confounds_file – Only used for Sources metadata.

  • 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_interpolated_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.

  • alff – alff nifti

  • parcellated_alff

  • smoothed_alff – smoothed alff

  • reho

  • parcellated_reho

  • confounds_file

  • confounds_metadata

  • filtered_motion (str) – Framewise displacement timeseries, potentially after bandstop or low-pass filtering. This is a TSV file with one column: ‘framewise_displacement’.

  • 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.