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')

Create mosaic and PNG files for executive summary brainsprite.

Workflow Graph

(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/”.

• 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')

Generate the anatomical figures for an executive summary.

Workflow Graph

(Source code, png, svg, pdf)

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 – T1w image, after warping to standard space.

• t2w – T2w image, after warping to standard space.

• template

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

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 – T1w image in a standard space, taken from the output of init_postprocess_anat_wf.

• t2w – T2w image in a standard space, taken from the output of init_postprocess_anat_wf.

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

Plot a custom selection of slices with Slicer.

This workflow is used to produce subcortical registration plots specifically for infant data.

Workflow Graph

(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/”.

• 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”.

Inputs:

• underlay_file

• overlay_file

• name_source

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

Use the default slices from slicesdir to make a plot.