xcp_d.workflows.connectivity module

Workflows for extracting time series and computing functional connectivity.

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

Extract CIFTI time series.

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).
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.

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.
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.
correlations (list of str) – List of paths to atlas-specific ROI-to-ROI correlation TSV files. These correlations are produced from the timeseries 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 (list of str) – List of paths to atlas-specific coverage TSV files.
coverage_ciftis (list of str) – List of paths to atlas-specific coverage CIFTI (pscalar) files.

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.