xcp_d.workflows.parcellation module

Workflows for parcellating imaging data.

xcp_d.workflows.parcellation.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

xcp_d.workflows.parcellation.init_parcellate_cifti_wf(mem_gb, compute_mask=True, name='parcellate_cifti_wf')[source]

Parcellate a CIFTI file using a set of atlases.

Part of the parcellation includes applying vertex-wise and node-wise masks.

Vertex-wise masks are typically calculated from the full BOLD run, wherein any vertex that has a time series of all zeros or NaNs is excluded. Additionally, if any volumes in a vertex’s time series are NaNs, that vertex will be excluded.

The node-wise mask is determined based on the vertex-wise mask and the workflow’s coverage threshold. Any nodes in the atlas with less than the coverage threshold’s % of vertices retained by the vertex-wise mask will have that node’s time series set to NaNs.

Workflow Graph
../_images/xcp_d-workflows-parcellation-2.png

(Source code, png, svg, pdf)

Parameters:

  • mem_gb (dict) – Dictionary of memory allocations.

  • compute_mask (bool) – Whether to compute a vertex-wise mask for the CIFTI file. When processing full BOLD runs, this should be True. When processing truncated BOLD runs or scalar maps, this should be False, and the vertex-wise mask should be provided via the inputnode.. Default is True.

  • name (str) – Workflow name. Default is “parcellate_cifti_wf”.

Inputs:

  • in_file – CIFTI file to parcellate.

  • atlas_files – List of CIFTI atlas files.

  • atlas_labels_files – List of TSV atlas labels files.

  • vertexwise_coverage – Vertex-wise coverage mask. Only used if compute_mask is False.

  • coverage_cifti – Coverage CIFTI files. One for each atlas. Only used if compute_mask is False.

Outputs:

  • parcellated_cifti – Parcellated CIFTI files. One for each atlas.

  • parcellated_tsv – Parcellated TSV files. One for each atlas.

  • vertexwise_coverage – Vertex-wise coverage mask. Only output if compute_mask is True.

  • coverage_cifti – Coverage CIFTI files. One for each atlas. Only output if compute_mask is True.

  • coverage_tsv – Coverage TSV files. One for each atlas. Only output if compute_mask is True.