xcp_d.workflows.bold.connectivity module

Workflows for extracting time series and computing functional connectivity.

xcp_d.workflows.bold.connectivity.init_functional_connectivity_cifti_wf(mem_gb, exact_scans, name='connectivity_wf')[source]

Extract CIFTI time series.

This will parcellate the CIFTI file using the selected atlases and compute functional connectivity between all regions for the selected atlases. It will also parcellate ReHo and ALFF maps if they are provided.

Workflow Graph

(Source code)

Parameters:

  • mem_gb (dict) – Dictionary of memory allocations.

  • exact_scans (list) – List of exact scans to compute correlations for.

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

Inputs:

  • name_source (str) – Path to the file that will be used as the source_file for derivatives. This is generally the preprocessed BOLD file. This file does not need to exist (e.g., in the case of a concatenated version of the filename).

  • denoised_bold – Clean CIFTI after filtering and nuisance regression. The CIFTI file is in the same standard space as the atlases, so no transformations will be applied to the data before parcellation.

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

  • alff

  • reho

  • atlases (list of str) – A list of atlases used for parcellating the BOLD data. The set of atlases to use is defined by the user.

  • atlas_files

  • atlas_labels_files

Outputs:

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

  • correlation_ciftis_exact

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

  • correlations_exact

  • parcellated_reho

  • parcellated_alff

xcp_d.workflows.bold.connectivity.init_functional_connectivity_nifti_wf(mem_gb, name='connectivity_wf')[source]

Extract BOLD time series and compute functional connectivity.

Workflow Graph

(Source code)

Parameters:

  • mem_gb (dict) – Dictionary of memory allocations.

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

Inputs:

  • name_source (str) – Path to the file that will be used as the source_file for derivatives. This is generally the preprocessed BOLD file. This file does not need to exist (e.g., in the case of a concatenated version of the filename).

  • denoised_bold – clean bold after filtered out nuisscance and filtering

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

  • alff

  • reho

  • atlases (list of str) – A list of atlases used for parcellating the BOLD data. The set of atlases to use is defined by the user.

  • atlas_files

  • atlas_labels_files

Outputs:

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

  • correlations_exact (list of list of str) – Exact-scan-wise list of lists of paths to atlas-specific ROI-to-ROI correlation TSV files. These correlations are produced from the timeseries outputs and the temporal_mask input.

  • parcellated_alff

  • parcellated_reho