xcp_d.workflows.connectivity.init_functional_connectivity_cifti_wf

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

Extract CIFTI time series.

Workflow Graph
../_images/xcp_d-workflows-connectivity-init_functional_connectivity_cifti_wf-1.png

(Source code, png, svg, pdf)

Parameters:

  • output_dir (str) – Path to the output directory for xcp_d derivatives. This should not include the xcp_d folder. For example, “/path/to/dset/derivatives/”.

  • alff_available

  • min_coverage (float) – Coverage threshold to apply to parcels in each atlas. Any parcels with lower coverage than the threshold will be replaced with NaNs. Must be a value between zero and one. Default is 0.5.

  • mem_gb (float) – Memory limit, in gigabytes.

  • omp_nthreads (int) – Maximum number of threads an individual process may use.

  • 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

  • atlas_names (list of str) – A list of atlases used for parcellating the BOLD data. The list of atlas names is generated by xcp_d.utils.atlas.get_atlas_names(). The atlases include: “4S156Parcels”, “4S256Parcels”, “4S356Parcels”, “4S456Parcels”, “4S556Parcels”, “4S656Parcels”, “4S756Parcels”, “4S856Parcels”, “4S956Parcels”, “4S1056Parcels”, “Glasser”, “Gordon”, “Tian”, and “HCP”.

  • 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