xcp_d.workflows.anatomical.plotting module

Workflows for generating plots from anatomical data.

xcp_d.workflows.anatomical.plotting.init_brainsprite_figures_wf(t1w_available, t2w_available, apply_transform, name='brainsprite_figures_wf')[source]

Create mosaic and PNG files for executive summary brainsprite.

Workflow Graph
../_images/xcp_d-workflows-anatomical-plotting-1.png

(Source code, png, svg, pdf)

Parameters:

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

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

  • apply_transform (bool) – Whether to apply the transform to the surfaces.

  • 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

  • template_to_anat_xfm

xcp_d.workflows.anatomical.plotting.init_execsummary_anatomical_plots_wf(t1w_available, t2w_available, apply_template_mask=False, name='execsummary_anatomical_plots_wf')[source]

Generate the anatomical figures for an executive summary.

Workflow Graph
../_images/xcp_d-workflows-anatomical-plotting-2.png

(Source code, png, svg, pdf)

Parameters:

  • t1w_available (bool) – Generally True.

  • t2w_available (bool) – Generally False.

  • apply_template_mask (bool) – Whether to apply the template mask to the template image (i.e., a skullstripped template image wasn’t available).

  • 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 – Template image.

  • template_mask – Template mask image.

xcp_d.workflows.anatomical.plotting.init_itk_warp_gifti_surface_wf(name='itk_warp_gifti_surface_wf')[source]

Apply an arbitrary ITK transform to a Gifti file.

Workflow Graph
../_images/xcp_d-workflows-anatomical-plotting-3.png

(Source code, png, svg, pdf)

Parameters:

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

Inputs:

  • native_surf_gii – T1w image, after warping to standard space.

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

Outputs:

warped_surf_gii – Gifti file where the transform in itk_warp_file has been applied to the vertices in native_surf_gii.