xcp_d.workflows.connectivity.init_functional_connectivity_nifti_wf

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

Extract BOLD time series and compute functional connectivity.

Workflow Graph

(Source code)

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/”.

  • 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).

  • boldref (str) – Path to the BOLD reference file associated with the target BOLD run. This comes from the preprocessing derivatives.

  • denoised_bold – clean bold after filtered out nuisscance and filtering

  • template_to_anat_xfm (str) – Path to the MNI-to-T1w transform file. May be “identity”, for testing purposes.

  • anat_to_native_xfm (str) – Path to the T1w-to-native BOLD space transform file. May be “identity”, for testing purposes.

Outputs:

  • 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: “Schaefer117”, “Schaefer217”, “Schaefer317”, “Schaefer417”, “Schaefer517”, “Schaefer617”, “Schaefer717”, “Schaefer817”, “Schaefer917”, “Schaefer1017”, “Glasser”, “Gordon”, and “subcortical” (Tian). Used for indexing timeseries and correlations.

  • 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.