xcp_d.workflows.execsummary module

Workflows for generating the executive summary.

xcp_d.workflows.execsummary.init_brainsprite_figures_wf(output_dir, t1w_available, t2w_available, mem_gb, omp_nthreads, name='init_brainsprite_figures_wf')[source]

Create mosaic and PNG files for executive summary brainsprite.

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/”.

  • t1w_available (bool) – True if a T1w image is available.

  • t2w_available (bool) – True if a T2w image is available.

  • 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 “init_brainsprite_figures_wf”.

Inputs:

  • t1w – Path to T1w image. Optional. Should only be defined if t1w_available is True.

  • t2w – Path to T2w image. Optional. Should only be defined if t2w_available is True.

  • lh_wm_surf

  • rh_wm_surf

  • lh_pial_surf

  • rh_pial_surf

xcp_d.workflows.execsummary.init_execsummary_anatomical_plots_wf(t1w_available, t2w_available, output_dir, name='execsummary_anatomical_plots_wf')[source]

Generate the anatomical figures for an executive summary.

Workflow Graph

(Source code)

Parameters:

  • t1w_available (bool) – Generally True.

  • t2w_available (bool) – Generally False.

  • 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/”.

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

Inputs:

  • t1w

  • t2w

  • template

xcp_d.workflows.execsummary.init_execsummary_functional_plots_wf(preproc_nifti, t1w_available, t2w_available, output_dir, layout, name='execsummary_functional_plots_wf')[source]

Generate the functional figures for an executive summary.

Workflow Graph

(Source code)

Parameters:

  • preproc_nifti (str or None) – BOLD data before post-processing. A NIFTI file, not a CIFTI.

  • t1w_available (bool) – Generally True.

  • t2w_available (bool) – Generally False.

  • 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/”.

  • layout (bids.layout.BIDSLayout) – BIDSLayout indexing the ingested (e.g., fMRIPrep-format) derivatives.

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

Inputs:

  • preproc_nifti – BOLD data before post-processing. A NIFTI file, not a CIFTI. Set from the parameter.

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

  • t1w

  • t2w

xcp_d.workflows.execsummary.init_plot_custom_slices_wf(output_dir, desc, name='plot_custom_slices_wf')[source]

Plot a custom selection of slices with Slicer.

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/”.

  • desc (str) – String to be used as desc entity in output filename.

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

xcp_d.workflows.execsummary.init_plot_overlay_wf(output_dir, desc, name='plot_overlay_wf')[source]

Use the default slices from slicesdir to make a plot.