xcp_d.workflows.connectivity module

Workflows for extracting time series and computing functional connectivity.

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

Extract CIFTI time series.

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 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

  • parcellated_atlas_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.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

xcp_d.workflows.connectivity.init_load_atlases_wf(name='load_atlases_wf')[source]

Load atlases and warp them to the same space as the BOLD file.

Workflow Graph

(Source code)

Parameters:

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

  • bold_file

Outputs:

  • atlas_files

  • atlas_labels_files

  • parcellated_atlas_files

xcp_d.workflows.connectivity.init_parcellate_surfaces_wf(files_to_parcellate, name='parcellate_surfaces_wf')[source]

Parcellate surface files and write them out to the output directory.

Workflow Graph

(Source code)

Parameters:

  • files_to_parcellate (list of str) – List of surface file types to parcellate (e.g., “sulcal_depth”, “sulcal_curv”, “cortical_thickness”).

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

Inputs:

  • sulcal_depth

  • sulcal_curv

  • cortical_thickness

  • cortical_thickness_corr

  • myelin

  • myelin_smoothed